From e12c690a272aa30ba4adc1c38cd83870e716d7e0 Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Mon, 26 Oct 2020 17:18:02 -0700 Subject: [PATCH 01/13] upd tests for mult user dbs; db dir env variable --- dammit/tests/test_annotate.py | 91 ++++++++++++++++++++--------------- 1 file changed, 52 insertions(+), 39 deletions(-) diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index 032d6bbc..11a98d3a 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -23,7 +23,7 @@ def compare_gff(fn_a, fn_b): df_a.reset_index(inplace=True, drop=True) df_b = gff3.GFF3Parser(fn_b).read().sort_values(['seqid', 'start', 'end', 'ID', 'Target']) df_b.reset_index(inplace=True, drop=True) - + print('First DF:', df_a, '\n', '=' * 40) print('Second DF:', df_b, '\n', '=' * 40) return df_a.equals(df_b) @@ -76,7 +76,7 @@ def test_annotate_evalue(self, tmpdir, datadir): assert compare_gff(gff3_fn, exp_gff3) assert open(fasta_fn).read() == open(exp_fasta).read() - + @pytest.mark.parametrize('n_threads', (1,4)) def test_annotate_user_database(self, tmpdir, datadir, n_threads): '''--pipeline quick annotate --user-database [PEP.fa] [INPUT.fa] @@ -100,26 +100,33 @@ def test_annotate_user_database(self, tmpdir, datadir, n_threads): assert compare_gff(gff3_fn, exp_gff3) assert open(fasta_fn).read() == open(exp_fasta).read() +## run this on pom20! store the results somewhere and then compare using compare_gff3! + @pytest.mark.parametrize('n_threads', (1,4)) + def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): + '''--pipeline quick annotate --user-database [PEP1.fa] --user-database [PEP2.fa] [INPUT.fa] + ''' -# def test_annotate_multiple_user_databases(self, tmpdir, datadir): -# '''--pipeline quick annotate --user-database [PEP1.fa] --user-database [PEP2.fa] [INPUT.fa] -# ''' -# -# with tmpdir.as_cwd(): -# transcripts = datadir('pom.single.fa') -# pep = datadir('pep.fa') -# pep2 = datadir('odb_subset.fa') -# exp_gff3 = datadir('pom.single.fa.dammit.gff3.udb') -# exp_fasta = datadir('pom.single.fa.dammit.fasta.udb') -# -# args = ['annotate', '--quick', -# transcripts, '--user-databases', pep, pep2, -# '--verbosity', '2'] -# status, out, err = run(args) -# -# outdir = '{0}.dammit'.format(transcripts) -# -# assert status == 0 + with tmpdir.as_cwd(): + transcripts = datadir('pom.20.fa') + pep = datadir('pep.fa') + pep2 = datadir('odb_subset.fa') + exp_gff3 = datadir('pom.20.udbs.dammit.gff3') + exp_fasta = datadir('pom.20.udbs.dammit.fasta') + + args = ['run', '--n-threads', str(n_threads), + '--pipeline', 'quick', 'annotate', + '--user-database', pep, + '--user-database', pep2, + transcripts] + status, out, err = run(*args) + + outdir = 'pom.20.dammit' + gff3_fn = os.path.join(outdir, 'pom.20.dammit.gff3') + fasta_fn = os.path.join(outdir, 'pom.20.dammit.fasta') + + assert status == 0 + assert compare_gff(gff3_fn, exp_gff3) + assert open(fasta_fn).read() == open(exp_fasta).read() def test_annotate_name(self, tmpdir, datadir): '''--pipeline quick annotate --base-name [NAME] [INPUT.fa] @@ -128,9 +135,9 @@ def test_annotate_name(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') - args = ['--pipeline', 'quick', 'annotate', + args = ['run', '--pipeline', 'quick', 'annotate', transcripts, '--base-name', 'Test'] - status, out, err = run(args) + status, out, err = run(*args) assert status == 0 fn = os.path.join('pom.20.dammit', 'pom.20.fasta') @@ -147,31 +154,37 @@ def test_annotate_outdir(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') outdir = 'test_out' - args = ['annotate', '--quick', transcripts, '-o', outdir] - status, out, err = run(args) + args = ['run', 'annotate', '--quick', transcripts, '-o', outdir] + status, out, err = run(*args) assert os.path.isfile(os.path.join(outdir, 'pom.20.fasta')) -def test_annotate_dbdir_fail(self, tmpdir, datadir): - '''Test annotation with a faulty database directory. - ''' - - with tmpdir.as_cwd(): - transcripts = datadir('pom.single.fa') +# FIX: since annotate currently auto installs dbs if they're not found, this will not fail. +# if change this, also remove --pipeline quick, as failure to find db's means nothing will be run +#def test_annotate_dbdir_fail(tmpdir, datadir): +# '''Test annotation with a faulty database directory. +# dammit run --database-dir [DB_DIR] annotate [INPUT.fa] +# ''' +# +# with tmpdir.as_cwd(): +# transcripts = datadir('pom.20.fa') +# +# args = ['run', '--pipeline', 'quick', '--database-dir', '.', 'annotate', transcripts] +# status, out, err = run(*args, fail_ok=True) +# assert 'install databases to continue' in out +# assert status == 2 - args = ['annotate', transcripts, '--database-dir', '.'] - status, out, err = run(args, fail_ok=True) - assert 'install databases to continue' in out - assert status == 2 -def test_annotate_dbdir(self, tmpdir, datadir): +# make sure DAMMIT_DB_DIR is set in your testing env +# (export DAMMIT_DB_DIR=/path/to/databases) +def test_annotate_dbdir(tmpdir, datadir): '''Test that --database-dir works. ''' with tmpdir.as_cwd(): - transcripts = datadir('pom.single.fa') + transcripts = datadir('pom.20.fa') db_dir = os.environ['DAMMIT_DB_DIR'] - args = ['annotate', '--quick', transcripts, '--database-dir', db_dir] - status, out, err = run(args) \ No newline at end of file + args = ['run', '--pipeline', 'quick', '--database-dir', db_dir, 'annotate', transcripts] + status, out, err = run(*args) From ef5473f620758cb16cd4760fcb7eec7375e51907 Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Wed, 13 Jan 2021 16:57:30 -0800 Subject: [PATCH 02/13] working user database tests --- .../tests/test-data/pom.20.udbs.dammit.fasta | 40 ++++++ .../tests/test-data/pom.20.udbs.dammit.gff3 | 122 ++++++++++++++++++ dammit/tests/test_annotate.py | 12 +- 3 files changed, 171 insertions(+), 3 deletions(-) create mode 100644 dammit/tests/test-data/pom.20.udbs.dammit.fasta create mode 100644 dammit/tests/test-data/pom.20.udbs.dammit.gff3 diff --git a/dammit/tests/test-data/pom.20.udbs.dammit.fasta b/dammit/tests/test-data/pom.20.udbs.dammit.fasta new file mode 100644 index 00000000..5ae58780 --- /dev/null +++ b/dammit/tests/test-data/pom.20.udbs.dammit.fasta @@ -0,0 +1,40 @@ +>Transcript_0 len=5662 CDS=0-5661 exon=0-5662 gene=0-5662 mRNA=0-5662 +ATGGTCGTCGCTTCAGAAATTGCTAAAGTCGCTTCAAAAACTGCTAGAGATATCGCCGGATGCTTTACTTGTCAATGTGGAACTCAATTTGATAATGTAGAAAGGATCGTTCAACATTTCAAGGAATGTCGATACAGAGACGAAACTTGTAAAGACGATGATATCGTCGTCTATGAACCCAGCTCTTTCGTTCAGGACGAGAAAAAGGATAAGCCAATCATCGTTGAGGCTGCCAGTGAGGCTACCAGTGAGGAGGCTTGCAATTCTTCCAAGGAGCGTCAACTACCCGCTCTCTCTGCTCTCTCTGCTCTCTCTACTCTCACTACGAGTGCAAATGACGACTTGTGGACTGCACGGCTAATTTGGCAAAGTACAAATGACACCAAATTGGACAACAGCCCATCATCAAATTATACTGACTTGAATCACAAGTTGGCTAATTATGGACTCTCCATTTTGTCTATTCATGCTTTGATGTGCGTAGAATGTGAATGCTTGTTAAACGTGATTCACACTGCGCAACATATGCAAATTGTGCATAAACTAGAGTTAAACGAAGATCTTTTGTGGTTTCAAGAACTAAGGACTTTAAAGTTAAAAAGTCCAACAAATGTTTTACAAACTCATTCTTCTCAAACCCATGTATACCCATACATCAGAGGACTACCAGTACTTTTAAATGGATATGAGTGTGTGCCGTGCACAAAAAACGGAACAGGATTCGTACATGCAATCATGGATACCTTTCGCCATCATGTTCGACGTACTCATGGAAAAGTTATAAAATTGGAAAATTGTATACGTCGAACAGCTTTGCAAACGGTTAAGAACAAGTATGCTCAACGATGTCAGTTCTTCAAAGTCGATTATGTACCTTTGAATGGAGGAGAAGAAGAAGAAGAGGAGGAGGGGGAGGAGAAAGAAGATGCACAAAACATCAAGGAAAGAATGGTGGACTTTTGCTTTTCAAAATTTATGGAGAAGAATCAACAGCGGCGGGAGCAGCAAGACAAAGGTGAAAATAAAAAACGACAAGATGATGTTGACCAAGCAACAGACAACAACACTAACACTATTCTTGAAGATGATGAAAAAGATAACGATGAAGAGGAAGAGGAAGAGATTGTCAATGCACGAGAGAAAAATCTTTTAAATCAACAATTCAATTGGACGGCAATTGTGAAAAAACTTGGAGAAAATTGGGATCAGCTGGTTCGATTCGAATATACGAATGGAATTGTAACTTTGGATACCATTGTAAACCAGTTGATTCGTTATTACTATCGAGGATTCCGTCATCTAAGTGGAATGACCATGGGCATGAGACGAATGTTTACTCAAGGAGGAAGCTATAGTGCACAAGAGCGAGGACTTTGTCGCTTAGAGCAAAAGGATACAGTTGTGAGATATGCTCAAAGTGCAGCACTATACCTAATATTTCTGTTACGTCGTCCATCAGCGGACTCGGGGATAAGAAGACACTTGGAAGCAATGTGTGGAGCAACAGTGGAGAGAAAAGAAGGTGGCAGTAACAGCAGCAGTAACATCAGCAACGTCGCCAACTTTGATAGTGCTGAAGACGACAATGACAATGACAATGACAATGACAGAGACAGTAACAATAACAATAACAATAACAACACCAATACTGACGATGATGATAAGCTGGCATACTTGGAACTGCACGAGGCATTAAAATTGGCTTTTCTGCAACAATACGATTTTTCTAAAAATGTTCAAGACTTGGAAATCATGGAGTTTCTTGCATGCATGTCTTTGCATAAAGATGGTACTTCAAAATATGCCTATGAAATCTCTGCCTGCTTTGCACCCCTAATATACACGTGTCGTCTTGTAGCAGCATGTGAGTTACAACGATTGATCGATGAAAAACAAATCGACTTGTTGTCCATTCCATCGTTTCAAACCGCTGGTTCTATTGCTTATGCTCATGTGTTTTGCTTTATCACGCTTGGTCAAAGAAATTTATATGATGTTCTTTACGAAACCCAAAAAGTCGTTAGGGATATCATTCGAACGGAAGGGTATGCAAATACACTGCAAGGACTAAGCCCAAGTACCGTATTGTTTCAGCCACGAAGTAATTCTATGTACCCGTGCATTGGAGATGCATTCAATAACATGGTGCGATTGGACTTGAGTGAGCTGACAGCTCTGTATGAGGGGATGTTTGCCAAAGTTCAGGACTTGTTAAAAGAGCTATGTTTTGATATGAATGTGGAAAAACTATTACCCATTTCGTTACTAAGGTCAATTGGAGATGACATAAACAATAGTAAATTGGGATATTCATTCTTTAAAGAGTCGATAGAGATACGTTCATCTCATAGTGTGCTGTTACGAACAATACTTAAGAACAGTGAACTTTGTCATCGGTTTTTCCCATCGATGTCTAAGAAGGATCTGACAAAGTTGTTTGGTGGAGTAAGTGATCAGCAAAGAAATGAGTGCGACAACTATAGCAACCACTACAACGACAACTCTAATGATAATGACAATGATGTGTTTCTCAAATTACATTGGTCTAAATCTGCTATTAAAAAGTATGAGACAAAGGCATCTATCTTCAATGAGTTATTGTTTTGTCTAGTGTACATATCTGCTGGACAACCAGCCAGAGCACAAGAGATGGTGTATTGGACTTTGCGGAATGGCAAGTATAAGACTCGCGAATTGTATTTGATGTTTGGAAGGCTGATGATTTACAGCAGATACGATAAGACTCGTAATATGAAGTTTGCTGAAAAGCCAATCCCCAGGTTTCTTTCTGAGCCGCTTTCCATTTTAGCACTTCGGTACTATGTTTTGGTTCGACCATTGGAAGCATTGATGAAGTATGTGACAACCGCTGATAGGTCGAAAGTAGCTGTATACTTGGATTTCATGTTTGTGATTGCTGGCGAACGATTGCAAAGAGATTTACCGTATCGAATTTTTCCAAAGGCCACCTACCAATGCATTCAAAAACCGTTGGGATTTCGAAACTACAGGCACATTGCTCACTATTTTAAAGAAAAAAACATCGAGGAAGAAATGACGAGGGAATCATATTTCGATTTACAGGCTGGACATACACGAAACACAGCGCTCTACATCTATGGGCGCACTATGGACAACTTGCATTATCTGCCGTCGGATTATTTCGCCAACTTTTTTCGTGCAAGCTATAAGTGGCAGGAACTATTACAGATTCGAGATAACCCGACCCATGGACTGTTGGTGGAAACAAAGCACCCATTCATCAAGCGAGTTGATCAATTGGAGGAAGCGCTGAATGAGAAGCTGGCAAGGTTGGTAGGTGAACAAATGGTGGAGGGGGACAAGGAAAAGGACAAGACAAATGAGGAGAAGAACAAGGACGAGGTAAAGGCTGAAATGACACAGCCCGTTGTAAATCAAGACTCTCATGACTTACAAGACCAATTGGCCACTACGCCCACCGCGCCCACCGCATTTCACTACCGCCCAGGACTTCTTCAACCATCTCAAACTTCTGTTCAACATTGTTGTTGGGCATTGTCTCAATATTATGGTCTCGAAGCGAAATTCCGTTCGCTGAAACAATTTCAATCGGTTTATTTTTCTCTTTTAAATCGTATGAATTTGATTACCGTACTCCCAACTGGAGGTGGAAAGTCTTTGTCGTTTTTGATACCGGCGCTCATCGAAAAAAAAAGACAAACCCCAGGAAAGGTGATGAATATGGTCACGCTGGTTCTAGTGCCCATGATGTCGTTACGGCAAGATATGATGCTCAGAGTGAATGAAAAGGGACTGCTTGTTTGTTCGGGGAATTGGACCGCATTCAAAGATGTACGATTGACTTTAGAGACGCAACTTCCCGATTTGTTTATCTTGACATACGAGTCAGCATTAACCAACAGTGGTCTTCGGTTTTTTGAAAGTTTGGCAACACTTGGTCGTTTGGCACGAGTGGTAATTGATGAAGCACATTTGTTACTCACCAGTGGAGCATGGAGAACGGCTTTGTCGAGAGCATCGCGGTTGTCTGGCTTGTATGCACCATTGCACTTGTTGAGTGCCACCTTTCCCAGGCAACTAGAGATGGTTGCCAGACAAACGTTTTGTACAAACTTTTACGTTTTACGAGAAACGTCTACTGCACGGGAAAACATCTTTTACTTTTTGCATCCCTATGATAATACCGAGTTTTTGTTGGACTTGCGAACGTTGATGAAACGAACAAAGGTCTTTGAAGGTGATGGACGTGCTATCATCTTTTGTCGAACCAAAAAGGATGTCGAATACATTCATCGTCGTCTTCACCAGTCGGACTTGTTCGCTCACACCCATGTAACCATTTACACAGGAGATGTAAGCGACGAAGAACGACAAATGAACTTTGACGCGTTTCGAAATGCAAATGGGAAGACACGAATCATGATCGCTACCAAGGCATTCGGACTCGGTATCAACTATATGGGAGTGCGTTTAGTAGTACACTATGGATTACCAGCTTCATCTATGGATTATGTACAGGAGACAGGTCGAGCTGGAAGAGATGGCAAGTATGCGATTGCAGCATTGTTTTACGAGAAATATGATTCTACATGGTCGAGCTACGTAGAGGATTCGATGAAAAACTTTCTTAATGATAATACGATGTGTGTTCGATCGTTTCTCGCAAGTGAAATGGATGGCGAATGTGTATGTTGTGCATCGTTTGCTAACTGTGTTTACTGCTCAAGATGCTCAGATTCGTTACTTGGTGAAGAATCAACTGTGTCTACGATGTATGGAGTGAAACCGACATTGCCAGAAACACCGAAACCAGCCATTGCAACACATTCGCGTTATAATGCATCGTTTTCGTCTTCCCCCCCACCACAGCCAGGGAATAGCAGTGGTATGAGTGCTATGAACACTAACACTACTAGTACTACGCCAGTGTCTTTGTCGGAATTATCGGAAATCACTTTGTTCCCTTCGTCTGTATCGCCAACATGGAAGAAAAGCTTTGGCAATGCTAATACGAATCTAAAGTATGGTTTGGAAGACATGTCGCTCAGCCATCGTCGTGGTCATAAACGCACATACGATGAACATTTGAACAATGTACAACAGGGCGTCAACCATGACATGAATCGTGTTCATGGTAGTGTTGGAGGTATGAGTGGTATTGTTGGTATTGGTATTGGTATTGGTGATGGTGATGGTGATGGTGATGTTGATTCTCGTACCATTCATTTCGCCGAGTATAAAAGTCGTGTGCAAGCCGTCAAAAAACAATGGGTAGACTCAACTGACATTTCAGCACAACTCGAGCGATTCTTTCGAGTGTATAAAGATGAATGTCTAAGTTGCACTCTTGGTAACCCAGACACAGAAATTCGTGCTCATACCGGGAAAGCATGCCCCGTACGCTTATCTACTTGTTATAAATGTGGCAAGGCCGACCACAACTTGCGAGAATGTAAACTACGTATTCGATTTCAAGGACTTTGTTTATTTTGTGGTTTGACAAAGTTTGAACATGCCGACAGTGATATGGCTTACACTTCTGACTGTAGGTCATGGGCTAGAAAGGCAAACTTGATATCGTTAGTTTACTATGCTTGGAACAATGTACAATACCGAAGGACTATTGCAGATAAATTCTTACAAGGTGATGTACGTGATC +>Transcript_1 len=1211 CDS=374-1211 exon=0-1211 five_prime_UTR=0-374 gene=0-1211 mRNA=0-1211 +CAGATTCACGTTCGTTTGCTCACGGTTTTTGTTTAAGCTAATGGCAAAAATCAAATACTCATTACAAATACTGACAGATCGATAAATGATAGAAGAAATCCAAAAAATGTTAATCGGATGGTATTAAATATACAAGATTATTGGTTTTGTTTCAATTATTAAATTCAAATTCAATTTACAACTAATTAATTTGATAAAATACATCTGTTATTTTTGATTGGATTATTTGGATTATTTCATGAAATTCCTATAATTTCAAGCTGTTTTCTGCAGCATTGATCGTCCATTTCCCGGTCAAAAAACAGTATTTCATCTGCTCTTCTCCCAAACTCCACACCATATCTACAACAGGATTGATTGCTTTAATTTCAAACATGTCCCCTTTAATAGTTGGGACTTTAATAATTATCCTATTGTCAGGACTCGCAACTGCTTTTTATGTTACGTGGCAAGGCAGACTCATTTGTGCTGGTGTAGGGCTCATACTTGAACAGGCTTATGAGGGTGGTCAGATGTTTAACACATTGATGGCACATTGCTTTGAAACGTACAATGGTGTTGAGAAAAGTGGAACGCAGTGTGTGGCCGATTGGCTTAAAGTAGGGCTTTTGGCTGTCACATTTGGGGCTGGAGGACCTAGATTGGTTAACACATTAGGTGGTACTTTTCTCACTTCTCCTACTGCAAAACGGAGCAATCTATATTGTGATGATTTTACTGGTGCTGATTACTTTAGCTGTGAACTTGAAACATTAAGGCCTTACACATTGATGAGAAAGAGCCTGCCGTATGGTAATATACACGATGTATGGATTAACACAACCGACACTCATCAGATGATAGGTGTACATATGACATTGAATGGAACAGATATGATTCATTATTATAATAAAACTTATGTAATTAATTATTCTGGTCTCAAACTAAATAGCTCTGCTATTAATAAAAGGTCTTACTTTTATCCTCAGGATTCCTTTCTTGTGAGTCATGCCGAATGGCAAGATGGTAATGGTATATGGACGGATACGGATTATTTCGCAGCTATGGCGGATTGTGACTTCTTGGGTCAAAATCTTGGTTTCTGGCTTGCAAGTTCCTATCCAAACGCATATAAGTGGGAAACACAACTGTGGCGCACCGTAGGAATAAACCTAAACGGTAATATAATATACCCGGGGCAACTCATTATGCAGACATTTAACGGTAGCTAA +>Transcript_2 len=372 CDS=0-372 exon=0-372 gene=0-372 mRNA=0-372 +ATGTCCCCTTTAATAGTTGGGACTTTAATAATTATCCTATTGTCAGGACTCGCAACTGCTTTTTATGTTACGTGGCAAGGCAGACTCATTTGTGCTGGTGTAGGGCTCATACTTGAACAGGCTTATGAGGGTGGTCAGATGTTTAACACATTGATGGCACATTGCTTTGAAACGTACAATGGTGTTGAGAAAAGTGGAACGCAGTGTGTGGCCGATTGGCTTAAAGTAGGGCTTTTGGCTGTCACATTTGGGGCTGGAGGACCTAGATTGGTTAACACATTAGGTGGTTCTTCGCCTACTACAAAACGGGTAATCTATATTGTGATGATTTTACTGGTGCTGATTACTTTAGCTGTGAACTTGAAACATTAA +>Transcript_3 len=891 CDS=0-474 exon=0-891 gene=0-891 mRNA=0-891 three_prime_UTR=474-891 +AGCAAGGGATTTGGACTCGGTATCAACTATATGGGAGTGCGTTTAGTAGTACACTATAGATTACCAGCTTCATCTATGGATTATGTACAGGAGACAGGTCGAGCTGGAAGAGATGGCAAGTATGCGATTGCAGCATTGTTTTACGAGAAATATGATTCTACATGGTCGAGCTACGTGGAGGATTCGATGAAAAACTTTCTTAATGATAATACGATGTGTGTTCGATCGTTTCTCGCAAGTGAAATGGATGGCGAATGTGTATGTTATTCGTTACTTGGTGAAGAATCAACTGTGTCTACGATGTATGGAGTGAAACCGACATTGCCAGAAACACCGAAACCAGCCATTGCAACACATTCGCGTTATAATGCATCGTTTTCGTCTTCCCCCCCACCACAGCCAGGGAGTAGCAGTGGTATGAGTGCTATGAACACTAACACTACTAGTACTACGCCAGTGTCTGGTAAAACTTAACTACACATTACGCTGAGAGGTAAAATACTCTGACAACATTCGTTCGATTGTATAAAACAAAATCCAGCCGAAACGATTGTTGTCAGTAATCAAGATTACGATCTAAATTGAGTACCAAGACAAAACGAAATGGTTAAAAAGTTAAAGTCGTTTTTGTATGGACACAATTTCTATAAAATAGACATGAGTAAAATCTCGCTATTTGTTTGTTATTGTGGAATAATGAAGAGTCATGGGAGATGAATGTTGTAAACGATGGCATAGAATTGGTAACGAAAAGTGAAATCGTTGGGATCAACTATTTCAGTATTTTGTTTAAAGAAAATGTTGAACTCGACAAGTAATGAGAGGTGGTGCTTTCGTTAAATAATGAGTGGTGGTTACGGTTATACAGGATATGATATGTGTATGGTGAGA +>Transcript_4 len=1615 CDS=206-1073 exon=0-1615 five_prime_UTR=0-206 gene=0-1615 mRNA=0-1615 three_prime_UTR=1073-1615 +TAATGCTTTTCCTAAATAAATGAGACACCTCAGAACGTAAAACATTCACCATTTTGGTTTTTTTTTTAATTTTCTCGTTTATGGCTTAAAATATTTTAGTATATTTTCTTTTTTATTTTCCATAAACCACTCTTTTTAATTTTACTTTGGGGAAAAATACTAGTGAATCAGAAGTCATCAAATTACAGTGCTGTCGTTCTATTCCAATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACTTGATTTGTGTAAGCCTGAAAAGGTAAACAAACAATCTCAACGATCTCGACAATCCCGACAATCCCTCTTTACCAACACCATTAAGCCTCAAAAAGACAAGATGAATATTAAAACAAATAAAATAAAAGAGTTTTTAAATGACCTTTTTACTGAATTTTCTAAATTCCACAATAGCTATTATCCTAATGGAAGAATTTCTACTCAGGACAAATCTCGATGGGTCTTGCTTATTATTTGGTCTATTATCACTATTTTAACAATAGACAAGAAATTTAAAATAAAAGAGTCATATTTAGAATGGATAGGTGAAAATCAGTCCCACAGTGAAATTTGGGGGCCTATTGTTATTTATGTTGGCTTATTCATACTCTTATTGTCTGCTTTTAACTACTGCTCCAAGCTTATTATAAAAGCTCTACCGTTAATCAGTATGGTTATAGCATGGGTCGGTGTGGTTATAGCAGCGTTCAGTGTGATTATCACTGCAACAATAGCAGGAGTTATAGCAGCGTTCAGTGTGATTATCACTGCAACAATAGCAGGAGTTATAGCAGCTATGGTTGGAATCTTATATTTCGGCCATTGGCTGGTCTACAAGATTTTAATTTTGGCTTTCGGCTTTAAAATTGTGACATCAGGAGACGTCTGTGTTTCTAACACTCTTCCTACACATAACGGAGAAACAGCATTACATTCAGATGCAACAGTTGGTTCTGATATTGAACAAATAGAACTACAAAATATGCCTACTCCTGTGAAAAAATAATTTTCTTTATCGTTTTCATGATCATATAGAATATAACTATTCTTAACAATGTTCGAATTGACTGTCCTGTCCAAATCATGCACATAAGGTGCGTTCGTTATGAATTTCAATTATGGAACCAACCAGAATCACCTCACAGGTGTTTCATTAACCAAAATTTATTAATTGGTTTTAATTAAGATATTATCACATAATGTTACTAATGTTTTTATCTCTCGTTTTATGCTTAATCAAATACTATGAATGTCATTTACTGCGTTTACAAAATGAATTCTTAATGATACATCATGAATGACTCGTTTCTAAGGTTATGTGTCTGGAAACTTGAAAAATGCAATGTAGTATATGCAAACTGATAAGTCGCTTATTTATTAATTTAATAAATTTCTGAATTGCAAGTTAAATTCTGGTAGCAAAGAATTAAATTATTCAGAGTCTTTCTAAAATCACTGTTTTTATATTGACATCCTCACTAGATTAGCTTTTCAACAATATACTGCTGCTACAAAAAAATAATATTCCTTTTTTCCGCTCGTGCAAAC +>Transcript_5 len=466 CDS=76-466 exon=0-466 five_prime_UTR=0-76 gene=0-466 mRNA=0-466 +GGGTTGCTTTTCATTATGAAATGGCAATTTAGATGATGTGCCAATATGTTCAGTATCTCTCTTTGCGTTGACTACTATGAGTATTGAATTCGATGACAGTTCAAGACATAATATGAACATGACTCAGCTGATGCAATTAGGTGCGTTTGATAGACGCTCAGGCGACGATTTCATGGTCCAAGACTTCAAAAACGGTATACGTGATTGTTCAGGAATACCAGTTAATAATCGAAATTTAGCATTTAAGGCTTATGATGCTGTTAAACAGAAGTGCGATAGTTCCATAAAAGTTTTTAACATACAGGATATAACTATAAAAGGAGCAACATGGCAGCACCATAACTGCCAAAGTACAGGCAAATGGTATTCCCAGCTTTACGATTATCAAAATACTTTTATAGGAAAGCAAGAATACAATATTTTATTCGATTGTTACTCATACTTGAAATACAATTTGAATGGTTAA +>Transcript_6 len=411 CDS=0-411 exon=0-411 gene=0-411 mRNA=0-411 +ATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGGGGGGTAATGTTATACAAACCTTTGGTAGTAAAAGCGTGTCTTACTGAGATCTAG +>Transcript_7 len=862 CDS=0-843 exon=0-862 gene=0-862 mRNA=0-862 three_prime_UTR=843-862 +ATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACTTGATTTGTGTAAGCCTGAAAAGGTAAACAAACAATCTCAACGATCTCGACAATCCCGACAATCCCTCTTTACCAACACCATTAAGCCTCAAAAAGACAAGATGAATATTAAAACAAATAAAATAAAAGAGTTTTTAAATGACCTTTTTACTGAATTTTCTAAATTCCACAATAGCTATTATCCTGATGGAAGGATTTCTACCCGCAGTAATTTTCGTTGGCCCTTGCTTATTATTTGGTCTATTATCATTGTATTCGCAGTAGACAAAAAGTTCGAAGTCCAAAAGTTTCTTTCAATTTGGATAAATGAAAATCGGTTCTACAGTGAAATTTGGGTGCCTATTGCTATTTACGTTTGTTTGCTTGTTTTAATGTTACTTAGTTTAATTTTCTTTGCAGAGTTTGCGGTACTTGCTTTACGGGTGACCGGTGTGATTATAGCAGTCTTGGGTGCAGTCTTGGGTATGATTATAGCAGTCTTGGGAATGATTATAGCAGCCTTGGGAATGATTATAGCAGCCCTGGGTGCAACTATAACTGGCCTTTTGTATTTTGGTCATTGGGCTCTTTACAAACTTGTAATATTGTCTTTAGGCTTTAAAATTGTGACACCAGGAGACGTCTGTGTTTCTAACACTCTTCCTACACATAACGGAGAAACAGCATTACATTCAGAAACAACAGTTGGTTCTGATATTGAACAAATAGAACTACAAAATATGCCTACTCCTGTGAAAAAATAATTTTCTTTATCGTTTTCAT +>Transcript_8 len=1306 CDS=2-953 exon=0-1306 gene=0-1306 mRNA=0-1306 three_prime_UTR=953-1306 +GATCATTTGCATATTCTGGTAACTCGGAATCGGTATGGACGGGCGAAAATATTACAAGTATATGGAAAACTATTTTGATTAATGAAACGGGTTCTTACTGCGTAGCTGCGAGACCAATGACAATGGATGGAGCTGAATTTAATTTAGACCTTATGGGGTATTCGGTTTCAGAAGATCAAATTAATAATGACGAAATTGGCATTTGGAACTATATTTCTGTAGCTGAAATGGGAGGAGTACTATTATTTTTGAGCTATTGGATATGGACTTGTTTACATTTCAGCAAGATTATATTTCCTGCTCAAAAGGTAATCTGCCTTTATATTTTTCTTTTTGCGTTAAATCAGACTCTACAAGAATGCATTGAGGAGTATGTTTTTTCTTCCGAATGTATAAAATACAGACAATTTTATTCGGTGTATGAAATAATTGATTTTCTTCGGACAAATTTTTATCGATTATTTGTGATTTACTGTGCATTGGGTTTCGGCATAACTAGAACTGTTCCTAAATATCTTATGATAAAAGGAATTAGTATTGTCATTGCTTTATGTTCTGTATACTGGATTTCTTTATATAAAGACGTATATGTAGTATCAGAGATTTTTGACATGATCCAGTATGAGGTATCTCCTGCAATTTGGGTGTATTCTATTTGTCATTTATTGAAACAATGCACGTCTGTAACAACTTACGAAAATGCTTCAAAAGCCAGATTTTTCAGAAGAATGCTAAATGCATTTATCTTTATATTCTGTGCATCTCCAATGTTGCATTACCTGTCGAATATTATATTTGGAAACTTTGATTACAGACTGTCGGTGATCATTGGTGATCTTTTCACTTTTATGGAGAAAATTGCTTTTCCATGTTACATAATGTTTCCCACCCATAATGAAGCACTTGCCTACAATCGAAATGTAGCTGAAGAGGCTCAAGAGAAAATGATTTGACAAAAACCATGGTTTACTTGATTCACCTTTAAAGGGGTTACCGGGATTATTTTATTTATTATTTGTTTATCAATGGATTAATATCCAGTTATTTTAATCTCACTTTTTTACACAGAAATTGTGTAGTAAGTTCATTCTTATTTAATATACCACCTATTTATTTTTTACAAATGAATATTTTTTTACTGGAACGTTTTAAATACACATAACCTTTGAGTCGATGTGAAATAATGTTTTGTTCAAACTTAAAAGTTGCGAATCTGACATATAGACAAAAAAAAAAAAAAAGAAAAAACTGGTTACCTTCATAAACATATTTTGCTAATTTATTGAATTTAATTATTTTCAACTTG +>Transcript_9 len=747 CDS=158-560 exon=0-747 five_prime_UTR=0-158 gene=0-747 mRNA=0-747 three_prime_UTR=560-747 +GTGAGGCTTAGTCTTGGTATAAATAGAGGGACTCTGTCAAAACAAATATTTTGAACTAGACTCGAATTCTTCATAATTCTATTCACTTGAGTGTTTATTTTTTTTAACAATGCCATTACATTTACGAGATATGTGGATATCCACTGACGATTATAAGGATGTTTTACTTACGTGTCCTGTGTGTTCAAAGAAGACTGGTACGAGAAATAAACAAGTTGAGTAGTTTCGAAAGCAATTGGCTCTTTCTTTTGTTTTTAGTCCGAGTATGTCGTCAGTTGAAAACCGTAACGGTTCTCATTGTGCCTGTTCTTCCGGTTTATACGAATAAGGTACTTCGTTGTTCTCAGTGTGACTGGCACGAACCAGCAAACTTGGATTCGATTTATCAAAGGAGTAGTCATGATGATGATCTTCCTACCATTAAGGGTTCTGATGCTAGTACTCAACAGTATGAAAGAAAAACTTATATTACCGATGCTAGTCCCGAATCTCAGAATCTGTTTTTAAGCAAAAGTAAAGAGGAGGGAGTTATCTTCTTATGCATACAAGTAAGCTTTTAACCTTGATTCTATTTATTCACTTTTACCATTTACTACTTTCGCAAATTCCTGTTTTTTGTTGGGGATATGAAGGGGAATATAAGGGTAAAGTAGATGAAATGGATGTATTTGAAAGTTGATTTGGATTCGATTTATTACTTTGAATCCCCGTTTATTATTATACGTTTATGTCGTTTTAAAGAAAACC +>Transcript_10 len=979 CDS=196-637 exon=0-979 five_prime_UTR=0-196 gene=0-979 mRNA=0-979 three_prime_UTR=637-979 +AATAATAAACAAAATACGAGTCGCTAATTTTTGAAACTAATCGCTTCCAACAACTGTTTCATTATAACTTCACCATTTTAATATTGTCCCCAAACAGCATGATTTAATTCTCTTTCACTAATTTCATACCACACAGGACACGTAAGTAAAACATCCTTATAATCGTCAGTGGATATCCACATATCTCGTAAATGTAATGGCATTGTTAAAAAAAATAAACACTCAAGTGAATAGAATTATGAAGAATTCGAGTCTAGTTCAAAATATTTGTTTTGACAGAGTCCCTCTATTTATACCAAGACTAAGCCTCACAGTGAAATATTGTCTAGCAGTAAAATTGCTGATTTATTTATTATATTGTTGGTACATTTACTCGGAAGTACCATCGGCTTCATCTAAATTCCGATCCTTTACATTTGGATGCGTCGTAGTATATCATAACAAATTTTTTCCTCGTTTCATTAGAACTCACTCCATTAACTCCATTAGAACGTTTTCTAAATTTCAAGTCATTATACTTTTCTCTATTGAGAAAGTCACTAGGTCAGAAAGCAAGAATCATTCTTACTCGAAAACCGATATTAGTGATCTGCACCAGGGCTATAATAATCCACCATCAAGATTCATATCACGATAACAATTCCATAGTATCTTGCTATATACGTGTAATGAGTATTCGATACTGGCTTGATTGCTATTTCTCCCTTGCTTGTAATCGTAAAATTGACTTGAAGATCTAAACCTTCTAATGCAATCATTGGAATTCTGCCTAACCTGATCAAATATGGCTTGATCACCGTTATGTTAAACCAGGAAGCTATGCCAATCAGTACGATTGTAACTTACAAAAAAATATAGCACAACGACATACAACATTATGGTACAATAAAGAGGACTTGATATATTAAGAACGAGGTTCAGTTTGTGCTCCGTTTATATTATTGTATTTCTATATATGACATTACTTGATGCAATCGCT +>Transcript_11 len=438 CDS=0-438 exon=0-438 gene=0-438 mRNA=0-438 +ATGAATCTTGTACAACTGGGGAAATTACATGAGAATGTATTAGATGCCGGTTGTGAACCAAATAGAAATGCTAGATATTTAGCCAGTCTTGGATATAAAGTCGTGGGTATTGATATTTCCGAAAGGGCTATTTCTAAAGCAATCGATAAAACATCTAGTGAAAAAAGTAATGTCAACTTTAATCAACGCGATTTTTCAAGATTAAATGAATTCAAGGGGCATTTCGACACTGTGATTGACATTGGTTGTTTTCATTCAATTCTAAATAGTGATCATGAGCCACACACAGCTTCGTTAAGTCATATATGTCACTCTGATAGCTCCGTTTTCCTAAGAGCGTTTAGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCTTTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAA +>Transcript_12 len=681 CDS=0-519 exon=0-681 gene=0-681 mRNA=0-681 three_prime_UTR=519-681 +AGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGTGAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACCGGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGATTCAATGAAACTATTATAAACCT +>Transcript_13 len=615 CDS=0-615 exon=0-615 gene=0-615 mRNA=0-615 +ATGATTTTCAAAAACTTAATATCTCTCTTTTTCATTGGGCTCGCTACCGCCATACGCTTCAACCTCACTGATCTTGAGTGTAGTAGACTACGCGGTCCGCATTGTGGTACGTATCTACTGAAAGTAGTAGGAACGAATGCTACATACGTTGGTGAAAAATCATTTATAGGTCTTGATGCTTTGACTGAAAGTAAAGGTGAATTTTTTCAGCGTATGTTGGAACAAGAACCTCGACTTATTCCACGTTTGTTTACGATAGCTGAAAACGACACGGCCAACTTTACTCCCTTGACATTTACAACGTATTTGAAAACATGCAATCCTCAAAGTATTGAAAATGCAATGATCCCTTTTGTGAATACTGTTACCAGTGAAATTTCTTTTGATGCATGGGCGTATACAGCACAAAATTCAAGTCGGATAACGGGTCTTAGCAACCAACTGATGAATTCTACTCTATATAATGTTCAAGTAGCAACATGTACTCCCGGATTCTCTGCGTTATTGTTAGATAGTCCTACAATCAATGTTTTTAATAACGAGGAAGGCATGCCAAGTTGGTGTCAGCCCATTGAACTTATACCAGTTTGTCCTTTGGATGAGGGATTCAACTGA +>Transcript_14 len=607 CDS=0-585 exon=0-607 gene=0-607 mRNA=0-607 three_prime_UTR=585-607 +TACAATGAGTTATTTATGGTAAGAGATACTCGTAATGTGGACCTGGAGCGGGGACTTGAATTGTGTAAGCCTGAAAAGGTAAACAAACAAAATCTCTTTACCAACATCATCAAGCCTCAAAAAGATAAAATAAACATTAAGACAGATAAAATAAAGTTCTTTTTAAATAACCTTTTTACTGAATTTTCTAAATTTCATGATAGTTGTTATCCTGATGGTAGGATTTCTACCCGCAGTAAACTTCGTTGGCCCTTGCTTATTATTTGGTGTATTTTGATTGTTTTCGCAATAGACAAGAACTTTGAAGTCAAAGATTTTCTTTCAATTTGGATAAATGAAAGTTTTATAAATGAAAATCGGTTTTACAGTGAAATTTGGGGGCCTATTGCTATTTACATTTGTTTGTTTGTTTTATTGTTGCTTGGTTTAATTTACTGCTCCAAGATTGTTGTAAAAGCTATACCATTGATCAGTATAGTTATAGCAGCGGTCGTAGTAATTATCGCGGTGGCTATGGTTAAAATTTTATACATCTGCCATTGGCTTCTACAAAATTTTAATTTTGGCTTTCGGCATAAAAGTTAAGCCATTGGGAGACACTCTTCCT +>Transcript_15 len=1251 CDS=0-1251 exon=0-1251 gene=0-1251 mRNA=0-1251 +ATGAACTTCTTTCTTTATTTTCGTACCATCTTTCTCATTCAACTATATTTTTTTAACTACTCCACATTTGGTTGTTCGGCAAGCTCAACTAGTGTACAAAGTGACACAACAAACCAAGTATCTGTTTCATGTCCAAAGTATACCACTATTTACACATCAGGAACGTCTCCAGACACAAAAACAATATATCCTGAATCCACCTCGACTAAATCCATCACAACAAGCACGCAATCGCACAGCTCTCCCGTTATCGTTGTGTCCACAGTAGGAACTGTTACGGAAACAACTATTTCTGGTTCCACTGAATATACCACAACGATTCCCGCAGAGGGCATTACATCTGGAACTGTCGAAATAGTAGAACCAACTGCAGGAACAGTTACTGAGACTATAACAAGTGGTACTTTACCATTTACTACTACGCTAGCACAAGCTAGTGGTACTGTTTCAGGAACTGTCGAGATAGTAAGTCCTAAAAATAATCCTACCACCGTATATAGTGGTACGGTCGCTACTACGGAGACGTTTAGCTCATCCACAGTTGTTGTTATTCCAACAGCTATATGTGATGGCGTTCGTGGTTTAGAGTATGCTGTTTATGATTATACAATTTCATCATCAATGAACGAATTCTGTTATCCTAAAAACGGTCAAACTGATGTCTTTGCTTTTAATGAGCCCGCTTACTTTGGTTCCTCAGACTTGGATCAGTCATCTCCATTGTTTACCGGTGTGTTTAGTTCTACAGATGACATACCTGAGTGGGCATCGTCTTGGTATCTCCCACCGTATCCACCACAGGCTTCAGATATGGCTTCGACCTACTGTGCCTGTAAAGTAATTGTTTACCAGTTCTTTCTACGAATCCCAGAAACTGATACCTACACCCTAGTCGTTAACAATGTAGATGATGTTTTCTTTGGTTGGTTTGGTGATAAAGCTATTTCTGGTTGGTCCAATAATAACTTTGATGCGTATTCTTATTGGCATGAGTCGCCTAATATGGGTTTAGGAACTGTGGGCATGGGAAATTTCACTGTAGGCAATTATCCTGAAGGCTACTTTTTGCCCGTTAGATTTGTTGTAGCAAATGGAGCATATATCGGTGGATTTGATTTTTACTTTACTTCTGATTCAACGGGTCCACTTGCTACTACCTCTTATTCTTACACGAAAACATGCACTCAACAATTCTTACCATTTGGTCAAGGTAATGGCGGTGTAAACGGGCCAACGGAAAAATTGTCGTAA +>Transcript_16 len=825 CDS=60-771 exon=0-825 five_prime_UTR=0-60 gene=0-825 mRNA=0-825 three_prime_UTR=771-825 +TATACTAGTTACCAAACTATTTAAAAAGCTTATATTTTGCAAACATTATTTTTTGCTACTATGCGTGAACCCAAGAATGCCAAAGTGCTAAGCAGACTTGAAAATGTTCTGGTGACTCAATTAGATGTAAATAACTTTTCTTCGATTAAAAAATCTGTGGAAAAAGCAATTTCGCATTTTGGTAGAATCGACGTGTTACTAAATAACGCTGGCTATTCCGTCTATTCTCCACTTGAAAGTACTACCGAAGAACAAATTCATAACATTTTCAATACAAATGTGTTTGGCGCTTTGGAGGTTATCAAAGCAATAACTCCTATCTTCCGCTCACAACATAATGGAATGATTATAAACGTATCATCGATCGGAGGAAAGATGACATTCCCACTTGGATGTTTGTATTATGGTACCAAGTATGCAATCGAAGGTATTTCTGAAGCTCTGACTTGGGAAATGCAAAGCATTGGTGTAAAAGTCAAGATTATAGAACCTGGTTTTACAGCAACTGAATTTAGGGTTGAAGAGGGTGCAGGTAAACATTATGCTGAGTACGACAATCTGAAACAAAAGTTGTACGAAGACTTGCTACCTAAATTGAAAACAGCTACACCACCGCAAAAAATCGCAGAAGTGATATTGCAAGCGGCAACGGATGAAAGTGATGAGCTACGATACCCTACTGGAGATTATGTTGTTGAATGGATGGCATTGAGAAGCAAAGTTGATGATGCTACATTTTTAGCAACACACCGAAAACAAATGGGTCTTTAAACGATTTCGTTCTACCAATTGAATATTCCTCTTTTACTGTTTTTTGTACCAAAC +>Transcript_17 len=2461 CDS=239-2261 exon=0-2461 five_prime_UTR=0-239 gene=0-2461 mRNA=0-2461 three_prime_UTR=2261-2461 +GCCTAACGTTTGCGAATTTTGCAGCAAGCATTGTTTCGTATTTAAGATCACTTTTGTAGACAGATCTTGAGATAACGCGACAAATTTTGGGGCTTTTAAAGTTCGGAATTCTTTCTTCCGGATCAGAGATGTGTAGTGCGCCAGAGTAATATATGATTTAATATTCTTCCGTGTAGTACACTTTTCCATGCGAACTTCAATTTTTACAGCTTTTGTTTGAACTTTTTTTATTTTCTGCAATGTATGTCAACTATATTGGACTCTTTGCTTTCGTTCAAATTTCGTTGACGTTAGCTTATCCTCCCGGTCGTGTGGAGATTTCTGAAATATATGATTTTGAAGAATCTAGTTCGTATAAAGGACAAGATATTGATACATCCGTACTTTACACTTTGTCTAAAAGGAAACCTGCGCTCGTAAAACGAAGTACCGACGCTTCGTATGCCCCTTTCAATGTGACCTGTTCAAACGACAATCTGTTGAGGCCGGCTTCTGAAGGTTTAAATGAGGGCGAACAGAGCTATATCAACAAACGTATTTCTAAGGTTAACAGTGAACTCCGATCATTTATTTCTAAGACAGGTTTGAATGTTGACTTGGATAAGGTGGTTAACAGCTCGGATGGTCCACGTTTAGGAATTGCATTCTCAGGTGGTGGGTTACGGGCGATGGTTAATGGAGGTGGTGCATTCAATGCTTTTGACTCAAGATTCGAGAGTGACTCTCCACTTTCTGGTCTGCTGCAATCCGCGATGTATATCAGCGGTCTTTCTGGTGGTTCATGGCTTGTTGGATCAGTGGCTATTAATAATTTTACGAATATAACATACTTACGTGATAATGTCTGGAATTTGGAACATAGCGTTTTTGCTCCTCATGGGGATAATGTCATTGAAAATTTGAATTATTATAATGACTTGCGCAAAGAAATTGATCAAAAGAAACATGCGGGCTTTGACTGTTCTTTGACGGATTTATGGGGACGTGCTTTGTCCCGTAAACTTGTTGATGCTGAAAGGGGAGGACCAGGCATTACATATTCCAGTATGAGAAATCAAAGCTGGTTTCAAAATGCTGATTATCCTTATCCCATCATCGTTGCGGATAGCCGATTAGAAGAAGAAACGGCCATCCCTGCCAATACCAGTATCTTTGAGTTCACGGCGTATGAATTTGGTACATGGGACAATGGAATTAAAGCATTCATTCCAATGGAATATGTGGGAACTCACTTGTTGGATGGGGTTCCACCCGATAAGTCTTGCATTCATAACTATGATAATGCAGGTTTTGTTATGGGCACTTCAGCTACTTTATTCAACTCTTTTCTTCTTGACTGGAATGAAAATGTCAAAAAGAATGATACCTATTACGATATTCTTCATGCGATTCTTGAAGATCTTTCTAAGCATCAAGATGATATTGCTCCTTATCCCAATCCTTACCAAAATTATACTACTTCCAATACCTCTGTAGTGAATGCGTTCGAACCGTATGATACTATTGATCTAGTTGATGGTGGTGAGGATAGGGAAAACATTCCCCTTTGGCCTTTGTTACACCCACAACGATTTGTGGACGTTGTATTTGCGATTGATTCGACTTATAATGATCCTTATGGTTGGCCCCTTGGATCTTCCATTGTTGCTACATATGAGAGAGTTGTAACCTTTAATGCGAACAAGAGTGTTGATGTGCGTGGATTTCCATATATTCCGGACGAAAACACTATTATCTCTTTGGGACTAAACACTCGTCCTACGTTTTTTGGATGTGACGGTAAAAATACTACAGCAGGAAATCATGATGTAGACAATAATACCCCACCTCTCCTTGTATACTTTCCAAATTACCCTTGGACTTATTATTCCAATATATCGACATTTACTATGAGCATGGACGACAAGATGGCTAATGGAATTCTTGAGAATGCATTTATGTCGACTACGCAAAACAATAATGAATCTTTTGCAGTTTGCTTAGCATGCGCTATAATTCAACGCTCTTTGGAACGCAAGAAATTGAGTACTCCTACCCAGTGCTCTTCTTGTTTCCAAGAATACTGTTGGGACGGAACTCTTGCAACTAGTACGGCTTCTGTATATGATCCTACCGTAATGTCTGCTGCGACAACATCTCGTGCACCGTCAGGCACAACCTCGGGTACAGCCTCTAGTACAACATCTTCATCTGTAGCATCAGCCACTCCCACTCATAAACATTGGTGGGACTCGATTTTCGAAGCGAAAGAAAATCCGTAAAAAGATTCCATTGATGTTGTTTCAATGGATTCTCAGGCATGTGAGAAATTTAGAATAGATAGATTTACCTTTATTGTACTTGGTTACGAATTCGTTATGAAAGAGAACTAAGGATTTTCCTCATTCGTGAGACTGCTCAGTTAAACCCTTTACGTTTGATGGAGCTATGTAAACGGGTAAATGAATAATTTGTTATCTCT +>Transcript_18 len=2836 CDS=946-2578 exon=0-2836 five_prime_UTR=0-946 gene=0-2836 mRNA=0-2836 three_prime_UTR=2578-2836 +ACGGTTTATTGTTTAAAGGCTAGAAGTAATGAAAATCGTCTTTTATAAAAGTCTAAATAGTATGAAATTTGATATTAAGTAAGCGAGTGGCCTTAAACGCTCTATATTCTGGATCTGCAACTCATGGGGTGAGACTCGGTTGTGTCTATGTAACTAACCTTGCCACCACATTGTGCATGAAAGCAAATGATTCATTTAAACGTAAAGTGTTTCTCGTTTTATTTGACATGAAAGGAGCTCTTGAATTCTTCCTAAGTTGTTCATGAGGAGAAATTGTCCACTGAAAAAGAACAAGTTCAAACATTCGCTCATGACTTTTCTCCTGCCCGTAATCGAAATACCAAATTCCTTCTGTGTTCGGTAGTCAATACCTTGGCCGTTATCTCATCAATTAACAAGTTTCCCCCACCAATGTGATTATAGGCCTGGCAATTCCTTTGACAGAACGTGTCAACTGGATATTTGTGTAATTTCGTCGTTCTCGTTAATCCCATACAGTTTTTCATTGCTAATTTAACTCTACATATGGTTGAATTACAAGAGTGCTTGTTTTATGCTCACTACTTCCTTTTTTAAGTAGTATAAAAGATTGACTTCTGTTACACTAGTAATCAAATCCTATAGAAAGAATTTTCAATATTTTTGATTTATTGCCACTTATGTCATATTGAGATAAAATGCCTTAATCCAATCAGGTCTTTTTAGCTAAGTTATAATCAAAGCTTTTTGCTGCCGAGGTATTAATAGCTTACAAGTGAGTACACAACACCCTTTCAATCAATTTAATGGTGCTAAATTTATATAAACATACGATGTATAACAATCGCACAATATTTACAATTCACTATCCTGCTAAAATTGTATAAAAAAAAATAATATAACAGCCCACCTCAAATGTGCTTAATCAGTCTCAGTGAATTTAAAATTGAATAGTTACTTAAAAGGCATGTTTTTTAAGTTGATAAGCGTTAAAACCCAAGTAACAAGCTTTGTTACTCCAATCAAAAAGATAACTAAGGTACCCCGGTCCTCAAGTATAAACCACAGGCATGCACGCATCAGTCCGTGGCTAACTGTATCTTTTGCCACATTTTATGTCGAATACTCTAAAAAAAATATTATAGGAATTTATTACAAGAAAACATTCTCTTGTGGATATTGCCTAATTACTATGGGCTGGAGACAACTTGATATAGACAAAGTCCATTTAGCTTTAATAGTGGCCGGGGGATTTATAACATTTTTCTGCTATTTTTCAGAAGTTTTTCGAAAAAAATTACTAGTTGGAGAAGCTGTTCTTGGAAGTATCACTGGATTAATATTTGGGCCTCATGCTGCTAAACTCGTAGACCCTTTTTCCTGGGGTGACCATGGAGATTACTTGACAGTAGAGATTTGTAGAATCGTACTTGATGTGCGTGTGTTTGCTTCTGCAATAGAACTCCCCGGTGCATATTTTCAACATAATTTTCGAAGCATCATTGTAATGCTATTACCAGTTATGGCTTACGGGTGGTTAGTTACAGCTGGATTTGCATATGCATTGTTTCCACAAATTAACTTTTTAGGATCTTTGCTGATCGCAGGATGTATAACTTCTACTGATCCTGTTCTATCAGCATTGATTGTAGGAGAAGGTCCATTAGCTAAAAAGACTCCTGAACGGATTCGGTCTTTATTGATCGCTGAGTCTGGATGTAATGATGGAATGGCGGTTCCTTTTTTCTATTTTGCTATCAAACTTCTTACTGTTAAGCCATCGAGGAATGCAGGGAGGGATTGGGTGCTGCTTGTTGTGTTGTATGAATGTGCATTTGGTATATTTTTTGGGTGTGTAATAGGGTATCTTTTATCGTTCATTTTAAAGCACGCTCAGAAATACCGTTTAATTGATGCTATTAGTTATTATTCCCTTCCGCTAGCGATACCTTTATTATGTTCTGGGATAGGAACTATTATTGGAGTTGATGACCTGTTGATGTCCTTTTTTGCTGGAATATTATTTAACTGGAATGATTTATTTTCCAAAAATATATCTGCTTGTTCTGTACCTGCTTTTATTGATCAGACTTTTAGTTTACTATTTTTTACCTATTATGGTACAATCATTCCCTGGAATAATTTTAATTGGTCTGTTGAAGGCTTGCCTGTTTGGCGTTTAATTGTCTTTAGCATATTGACTCTAGTTTGTCGTCGATTACCGGTTGTATTTTCGGTGAAGCCTTTAGTTCCGGACATTAAGACATGGAAAGAAGCCCTTTTCGTTGGACATTTCGGACCAATAGGGGTTTGCGCAGTTTATATGGCATTTCTTGCAAAATTACTGTTGTCCCCGGATGAAATTGAAAAGAGTATTTATGAATCAACTACAGTATTTTCAACACTTAATGAAATAATTTGGCCGATCATTTCGTTTGTTATCTTATCCTCAATCATTGTTCATGGTTTCAGTATCCATGTATTAGTGATTTGGGGAAAGTTAAAAAGTCTGTATTTAAATCGAAAAGTCACCAAGTCCGATTCCGATTTGGAGTTACAAGTAATAGGGGTTGATAAGTCACAGGAAGATTACGTTTAGGAAAGCTCTTTTAATGTCAATTCGGATTTCCAAATTATTTTCAAATGTATTGTGAATCGCTGTCTCTGGTCAAAAAGATTACTGCACTCATATTTTGAAATTCCTTCTATAGTTGATATATACTATAAGATAAGTGATTCTCAGAATCACAAGGCTAACCACCAACAGGGATGGAGTGTATATTTTTGTTGTACATATATATTATCTACAATAGAGTAATTTTCGGCTTCTATAATTCATTTATTTTCTTACTACTCT +>Transcript_19 len=1250 CDS=215-1151 exon=0-1250 five_prime_UTR=0-215 gene=0-1250 mRNA=0-1250 three_prime_UTR=1151-1250 +GGCTTTAAGTCTTTTTGAAAGAATTTTCTTTTTGTTTTGTTTTATTAACCTAAGTCGATTTAAAATACTTTTTCTCTCTTTATTTTAAGAAATTACTATAGTCTCGAAGCCTTTATCGAGGCTATCGCTCCGTATATATAGAATTGTGATAGACACTCCGGAATAGTTGCATTTTCCTTCTAATCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGCTATTAACACAGTCTTACTTTTGTATAATGTCTATGTTGGGGACGCTAGCTCGTCTAGGACTTACTGCATTAAACACATACCCAGGTGCACCGTTTTCTGGACTTTTATGGGTTCAATTTGTTGGATGCGTTATTATGGGATTTTGTCAGACAGAGTCTGTTTTCTTTCCTCGACCCAAACATAATGCTACTTTTTTGCTAGCCATTACTACAGGTTTTTGTGGATCTCTTACAACGTTTTCTTCTTGGATGTTGCAAATGTTTACAGGGATGGCTAACTTGGATCCATTTGAACGTAGGGGCCGAGGCTATTCATTTTTAAGTGTGGTTTCCGATTTTATGGTAACTATGTGCATTGCGATGTCCAGCTTAATATGGGGGAAGCAGATTGGAAAAACGACGGGACAGTGGAGAATTGGCAAAGTTGCATTTGCCTGGCCTATCCCGGCGCACACGCATATCGTAGTGCGGGTATTACTTTTGTTACTCTCGATTTGTTTTTTTGTTGGTGCAGCATTTTATACGGCATATACAACCAATGTGACACATCGTGGCATAGGTTTTAGTCTAATATTCTCTCCTTTTGCTGCCTTGACACGTTTGTATCTTGCGCGATTCCTTAATTCACCTCAATATTTTATTCCCTATGGAACTCTTTGTGCCAATGTCTTTGCTACACTTTTGCTTTCTATCATGTACATGATACCACAAATCACACACTGCACTCCTGTGTCTAGAAGTGTGATGTATGGAATCCAAAACGGATTTTGTGCTGTACTCTCTACCCTTTCAACATTCTCCAACGAACTCCACACAATGCCTATAAAACGAGCATATATTTATTGTATAATTTCAGTTGCTATTTCCTTTTCAATATGTGTCATTGTCGATGGAGCTACTGCATGGGGTCATGGTTATACTGAAAAGTATTAGACTTACTATTAAATTAGAGATTTTTTTTTTAAAGTTTTTGTATATAATTAAAGTATTCATTCTTTATCTTTAATATTATTTATTTTTTTTTGTTTATAA diff --git a/dammit/tests/test-data/pom.20.udbs.dammit.gff3 b/dammit/tests/test-data/pom.20.udbs.dammit.gff3 new file mode 100644 index 00000000..b9051960 --- /dev/null +++ b/dammit/tests/test-data/pom.20.udbs.dammit.gff3 @@ -0,0 +1,122 @@ +##gff-version 3.2.1 +Transcript_0 shmlast.LAST conditional_reciprocal_best_LAST 1 1887 0.000000e+00 + . ID=homology:94a770b951c0d15c4b3d0d2b57d07c3851565147;Name=SPAC212.11|tlh1|I|RecQ type DNA helicase;Target=SPAC212.11|tlh1|I|RecQ type DNA helicase 1 1887 +;database=pep.fa +Transcript_0 transdecoder CDS 1 5661 . + 0 ID=cds.Transcript_0.p1;Parent=Transcript_0.p1 +Transcript_0 transdecoder exon 1 5662 . + . ID=Transcript_0.p1.exon1;Parent=Transcript_0.p1 +Transcript_0 transdecoder gene 1 5662 . + . ID=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3A3prime_partial%20len%3A1888%20%28%2B%29%2Cscore%3D464.77%2CHelicase_C%7CPF00271.27%7C3.2e-18%2CHelicase_C%7CPF00271.27%7C1.1e%2B04%2CDEAD%7CPF00270.25%7C2.1e-10 +Transcript_0 transdecoder mRNA 1 5662 . + . ID=Transcript_0.p1;Parent=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3A3prime_partial%20len%3A1888%20%28%2B%29%2Cscore%3D464.77%2CHelicase_C%7CPF00271.27%7C3.2e-18%2CHelicase_C%7CPF00271.27%7C1.1e%2B04%2CDEAD%7CPF00270.25%7C2.1e-10 +Transcript_10 shmlast.LAST conditional_reciprocal_best_LAST 66 211 3.300000e-103 + . ID=homology:5bddc141f52e14a4e285ddcb7c87aea1cbd54ce4;Name=SPAC977.02|SPAC977.02|I|S. pombe specific 5Tm protein family;Target=SPAC977.02|SPAC977.02|I|S. pombe specific 5Tm protein family 1 146 +;database=pep.fa +Transcript_10 transdecoder CDS 197 637 . + 0 ID=cds.Transcript_10.p1;Parent=Transcript_10.p1 +Transcript_10 transdecoder exon 1 979 . + . ID=Transcript_10.p1.exon1;Parent=Transcript_10.p1 +Transcript_10 transdecoder five_prime_UTR 1 196 . + . ID=Transcript_10.p1.utr5p1;Parent=Transcript_10.p1 +Transcript_10 transdecoder gene 1 979 . + . ID=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A147%20%28%2B%29%2Cscore%3D82.86%2CPombe_5TM%7CPF09437.6%7C1.3e-10%2CPombe_5TM%7CPF09437.6%7C5.1e-26 +Transcript_10 transdecoder mRNA 1 979 . + . ID=Transcript_10.p1;Parent=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A147%20%28%2B%29%2Cscore%3D82.86%2CPombe_5TM%7CPF09437.6%7C1.3e-10%2CPombe_5TM%7CPF09437.6%7C5.1e-26 +Transcript_10 transdecoder three_prime_UTR 638 979 . + . ID=Transcript_10.p1.utr3p1;Parent=Transcript_10.p1 +Transcript_11 shmlast.LAST conditional_reciprocal_best_LAST 1 145 4.300000e-109 + . ID=homology:a69c6cd647c5cc147e84d4553dbeab70cff38442;Name=SPAC977.03|SPAC977.03|I|methyltransferase (predicted);Target=SPAC977.03|SPAC977.03|I|methyltransferase (predicted) 1 145 +;database=pep.fa +Transcript_11 transdecoder CDS 1 438 . + 0 ID=cds.Transcript_11.p1;Parent=Transcript_11.p1 +Transcript_11 transdecoder exon 1 438 . + . ID=Transcript_11.p1.exon1;Parent=Transcript_11.p1 +Transcript_11 transdecoder gene 1 438 . + . ID=GENE.Transcript_11~~Transcript_11.p1;Name=ORF%20type%3Acomplete%20len%3A146%20%28%2B%29%2Cscore%3D85.63%2CMethyltransf_23%7CPF13489.2%7C1.4e-11%2CMethyltransf_31%7CPF13847.2%7C6.1e-10%2CMethyltransf_11%7CPF08241.8%7C7.9e-10%2CMethyltransf_12%7CPF08242.8%7C1.8e-09%2CMethyltransf_18%7CPF12847.3%7C5.4e-09%2CMethyltransf_25%7CPF13649.2%7C8.6e-09%2CTPMT%7CPF05724.7%7C7.5e-06 +Transcript_11 transdecoder mRNA 1 438 . + . ID=Transcript_11.p1;Parent=GENE.Transcript_11~~Transcript_11.p1;Name=ORF%20type%3Acomplete%20len%3A146%20%28%2B%29%2Cscore%3D85.63%2CMethyltransf_23%7CPF13489.2%7C1.4e-11%2CMethyltransf_31%7CPF13847.2%7C6.1e-10%2CMethyltransf_11%7CPF08241.8%7C7.9e-10%2CMethyltransf_12%7CPF08242.8%7C1.8e-09%2CMethyltransf_18%7CPF12847.3%7C5.4e-09%2CMethyltransf_25%7CPF13649.2%7C8.6e-09%2CTPMT%7CPF05724.7%7C7.5e-06 +Transcript_12 shmlast.LAST conditional_reciprocal_best_LAST 18 172 1.200000e-116 + . ID=homology:c435df18cff450cb65b1c8a55bc27e28a97c9f50;Name=SPAC977.04|SPAC977.04|I|truncated C terminal region of membrane transporter;Target=SPAC977.04|SPAC977.04|I|truncated C terminal region of membrane transporter 1 155 +;database=pep.fa +Transcript_12 transdecoder CDS 1 519 . + 0 ID=cds.Transcript_12.p1;Parent=Transcript_12.p1 +Transcript_12 transdecoder exon 1 681 . + . ID=Transcript_12.p1.exon1;Parent=Transcript_12.p1 +Transcript_12 transdecoder gene 1 681 . + . ID=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A173%20%28%2B%29%2Cscore%3D104.11 +Transcript_12 transdecoder mRNA 1 681 . + . ID=Transcript_12.p1;Parent=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A173%20%28%2B%29%2Cscore%3D104.11 +Transcript_12 transdecoder three_prime_UTR 520 681 . + . ID=Transcript_12.p1.utr3p1;Parent=Transcript_12.p1 +Transcript_13 shmlast.LAST conditional_reciprocal_best_LAST 1 204 2.700000e-155 + . ID=homology:3c4185a4986c931924c0b92956b14295ccf302f1;Name=SPAC977.05c|SPAC977.05c|I|conserved fungal family;Target=SPAC977.05c|SPAC977.05c|I|conserved fungal family 1 204 +;database=pep.fa +Transcript_13 transdecoder CDS 1 615 . + 0 ID=cds.Transcript_13.p1;Parent=Transcript_13.p1 +Transcript_13 transdecoder exon 1 615 . + . ID=Transcript_13.p1.exon1;Parent=Transcript_13.p1 +Transcript_13 transdecoder gene 1 615 . + . ID=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A205%20%28%2B%29%2Cscore%3D126.49%2CVel1p%7CPF10339.5%7C6.7e-107 +Transcript_13 transdecoder mRNA 1 615 . + . ID=Transcript_13.p1;Parent=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A205%20%28%2B%29%2Cscore%3D126.49%2CVel1p%7CPF10339.5%7C6.7e-107 +Transcript_14 shmlast.LAST conditional_reciprocal_best_LAST 6 194 2.900000e-143 + . ID=homology:bbbbb2217ab55d406588836a15266f0f6ec3bcd4;Name=SPAC977.06|SPAC977.06|I|S. pombe specific DUF999 family protein 3;Target=SPAC977.06|SPAC977.06|I|S. pombe specific DUF999 family protein 3 1 189 +;database=pep.fa +Transcript_14 transdecoder CDS 1 585 . + 0 ID=cds.Transcript_14.p1;Parent=Transcript_14.p1 +Transcript_14 transdecoder exon 1 607 . + . ID=Transcript_14.p1.exon1;Parent=Transcript_14.p1 +Transcript_14 transdecoder gene 1 607 . + . ID=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3A5prime_partial%20len%3A195%20%28%2B%29%2Cscore%3D142.29%2CDUF999%7CPF06198.7%7C6e-78%2CDUF999%7CPF06198.7%7C1.1e%2B04 +Transcript_14 transdecoder mRNA 1 607 . + . ID=Transcript_14.p1;Parent=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3A5prime_partial%20len%3A195%20%28%2B%29%2Cscore%3D142.29%2CDUF999%7CPF06198.7%7C6e-78%2CDUF999%7CPF06198.7%7C1.1e%2B04 +Transcript_14 transdecoder three_prime_UTR 586 607 . + . ID=Transcript_14.p1.utr3p1;Parent=Transcript_14.p1 +Transcript_15 shmlast.LAST conditional_reciprocal_best_LAST 1 416 1.976263e-323 + . ID=homology:3f9fd792943afae5b71c19f6a6348e97e0f632b2;Name=SPAC977.07c|pfl6|I|cell surface glycoprotein, adhesion molecule (predicted);Target=SPAC977.07c|pfl6|I|cell surface glycoprotein, adhesion molecule (predicted) 1 416 +;database=pep.fa +Transcript_15 transdecoder CDS 1 1251 . + 0 ID=cds.Transcript_15.p1;Parent=Transcript_15.p1 +Transcript_15 transdecoder exon 1 1251 . + . ID=Transcript_15.p1.exon1;Parent=Transcript_15.p1 +Transcript_15 transdecoder gene 1 1251 . + . ID=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3Acomplete%20len%3A417%20%28%2B%29%2Cscore%3D268.06%2CPA14_2%7CPF10528.5%7C4.7e%2B03%2CPA14_2%7CPF10528.5%7C6e%2B03%2CPA14_2%7CPF10528.5%7C1.2e-49 +Transcript_15 transdecoder mRNA 1 1251 . + . ID=Transcript_15.p1;Parent=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3Acomplete%20len%3A417%20%28%2B%29%2Cscore%3D268.06%2CPA14_2%7CPF10528.5%7C4.7e%2B03%2CPA14_2%7CPF10528.5%7C6e%2B03%2CPA14_2%7CPF10528.5%7C1.2e-49 +Transcript_16 shmlast.LAST conditional_reciprocal_best_LAST 21 256 6.300000e-174 + . ID=homology:669a1dd29f2b40aa7db12d129b95ccef21219987;Name=SPAC977.08|SPAC977.08|I|short chain dehydrogenase (predicted);Target=SPAC977.08|SPAC977.08|I|short chain dehydrogenase (predicted) 1 236 +;database=pep.fa +Transcript_16 transdecoder CDS 61 771 . + 0 ID=cds.Transcript_16.p1;Parent=Transcript_16.p1 +Transcript_16 transdecoder exon 1 825 . + . ID=Transcript_16.p1.exon1;Parent=Transcript_16.p1 +Transcript_16 transdecoder five_prime_UTR 1 60 . + . ID=Transcript_16.p1.utr5p1;Parent=Transcript_16.p1 +Transcript_16 transdecoder gene 1 825 . + . ID=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A237%20%28%2B%29%2Cscore%3D135.27%2Cadh_short%7CPF00106.21%7C9.1e-36%2Cadh_short_C2%7CPF13561.2%7C2e-12 +Transcript_16 transdecoder mRNA 1 825 . + . ID=Transcript_16.p1;Parent=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A237%20%28%2B%29%2Cscore%3D135.27%2Cadh_short%7CPF00106.21%7C9.1e-36%2Cadh_short_C2%7CPF13561.2%7C2e-12 +Transcript_16 transdecoder three_prime_UTR 772 825 . + . ID=Transcript_16.p1.utr3p1;Parent=Transcript_16.p1 +Transcript_17 shmlast.LAST conditional_reciprocal_best_LAST 80 752 0.000000e+00 + . ID=homology:02b94f4c02b2a78881d6e3cdddea00d4f99be7db;Name=SPAC977.09c|SPAC977.09c|I|phospholipase (predicted);Target=SPAC977.09c|SPAC977.09c|I|phospholipase (predicted) 1 673 +;database=pep.fa +Transcript_17 transdecoder CDS 240 2261 . + 0 ID=cds.Transcript_17.p1;Parent=Transcript_17.p1 +Transcript_17 transdecoder exon 1 2461 . + . ID=Transcript_17.p1.exon1;Parent=Transcript_17.p1 +Transcript_17 transdecoder five_prime_UTR 1 239 . + . ID=Transcript_17.p1.utr5p1;Parent=Transcript_17.p1 +Transcript_17 transdecoder gene 1 2461 . + . ID=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A674%20%28%2B%29%2Cscore%3D453.37%2CPLA2_B%7CPF01735.14%7C7.1e-204 +Transcript_17 transdecoder mRNA 1 2461 . + . ID=Transcript_17.p1;Parent=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A674%20%28%2B%29%2Cscore%3D453.37%2CPLA2_B%7CPF01735.14%7C7.1e-204 +Transcript_17 transdecoder three_prime_UTR 2262 2461 . + . ID=Transcript_17.p1.utr3p1;Parent=Transcript_17.p1 +Transcript_18 shmlast.LAST conditional_reciprocal_best_LAST 391 858 0.000000e+00 + . ID=homology:e135e2e2099cb1a8d9495f2345471292a4e72722;Name=SPAC977.10|sod2|I|plasma membrane sodium ion/proton antiporter Sod2;Target=SPAC977.10|sod2|I|plasma membrane sodium ion/proton antiporter Sod2 1 468 +;database=pep.fa +Transcript_18 transdecoder CDS 947 2578 . + 0 ID=cds.Transcript_18.p1;Parent=Transcript_18.p1 +Transcript_18 transdecoder exon 1 2836 . + . ID=Transcript_18.p1.exon1;Parent=Transcript_18.p1 +Transcript_18 transdecoder five_prime_UTR 1 946 . + . ID=Transcript_18.p1.utr5p1;Parent=Transcript_18.p1 +Transcript_18 transdecoder gene 1 2836 . + . ID=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A544%20%28%2B%29%2Cscore%3D299.04%2CNa_H_Exchanger%7CPF00999.17%7C2.6e-76 +Transcript_18 transdecoder mRNA 1 2836 . + . ID=Transcript_18.p1;Parent=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A544%20%28%2B%29%2Cscore%3D299.04%2CNa_H_Exchanger%7CPF00999.17%7C2.6e-76 +Transcript_18 transdecoder three_prime_UTR 2579 2836 . + . ID=Transcript_18.p1.utr3p1;Parent=Transcript_18.p1 +Transcript_19 shmlast.LAST conditional_reciprocal_best_LAST 72 382 5.700000e-237 + . ID=homology:c7170753b69543028628218cfc2957aaca46be84;Name=SPAC977.11|SPAC977.11|I|CRCB domain protein;Target=SPAC977.11|SPAC977.11|I|CRCB domain protein 1 311 +;database=pep.fa +Transcript_19 transdecoder CDS 216 1151 . + 0 ID=cds.Transcript_19.p1;Parent=Transcript_19.p1 +Transcript_19 transdecoder exon 1 1250 . + . ID=Transcript_19.p1.exon1;Parent=Transcript_19.p1 +Transcript_19 transdecoder five_prime_UTR 1 215 . + . ID=Transcript_19.p1.utr5p1;Parent=Transcript_19.p1 +Transcript_19 transdecoder gene 1 1250 . + . ID=GENE.Transcript_19~~Transcript_19.p1;Name=ORF%20type%3Acomplete%20len%3A312%20%28%2B%29%2Cscore%3D203.47%2CCRCB%7CPF02537.11%7C2e-15%2CCRCB%7CPF02537.11%7C5e%2B03%2CCRCB%7CPF02537.11%7C9.1e-15 +Transcript_19 transdecoder mRNA 1 1250 . + . ID=Transcript_19.p1;Parent=GENE.Transcript_19~~Transcript_19.p1;Name=ORF%20type%3Acomplete%20len%3A312%20%28%2B%29%2Cscore%3D203.47%2CCRCB%7CPF02537.11%7C2e-15%2CCRCB%7CPF02537.11%7C5e%2B03%2CCRCB%7CPF02537.11%7C9.1e-15 +Transcript_19 transdecoder three_prime_UTR 1152 1250 . + . ID=Transcript_19.p1.utr3p1;Parent=Transcript_19.p1 +Transcript_1 shmlast.LAST conditional_reciprocal_best_LAST 125 402 3.000000e-216 + . ID=homology:89e3c799b148e94ed8dca8df7bfd9b8c4b2de625;Name=SPAC212.08c|SPAC212.08c|I|S. pombe specific GPI anchored protein family 1;Target=SPAC212.08c|SPAC212.08c|I|S. pombe specific GPI anchored protein family 1 1 278 +;database=pep.fa +Transcript_1 transdecoder CDS 375 1211 . + 0 ID=cds.Transcript_1.p1;Parent=Transcript_1.p1 +Transcript_1 transdecoder exon 1 1211 . + . ID=Transcript_1.p1.exon1;Parent=Transcript_1.p1 +Transcript_1 transdecoder five_prime_UTR 1 374 . + . ID=Transcript_1.p1.utr5p1;Parent=Transcript_1.p1 +Transcript_1 transdecoder gene 1 1211 . + . ID=GENE.Transcript_1~~Transcript_1.p1;Name=ORF%20type%3Acomplete%20len%3A279%20%28%2B%29%2Cscore%3D220.14 +Transcript_1 transdecoder mRNA 1 1211 . + . ID=Transcript_1.p1;Parent=GENE.Transcript_1~~Transcript_1.p1;Name=ORF%20type%3Acomplete%20len%3A279%20%28%2B%29%2Cscore%3D220.14 +Transcript_2 shmlast.LAST conditional_reciprocal_best_LAST 1 123 7.000000e-90 + . ID=homology:962be10307d04a237970c81641eb8f829cd0955e;Name=SPAC212.12|SPAC212.12|I|S. pombe specific GPI anchored protein family 1;Target=SPAC212.12|SPAC212.12|I|S. pombe specific GPI anchored protein family 1 1 123 +;database=pep.fa +Transcript_2 transdecoder CDS 1 372 . + 0 ID=cds.Transcript_2.p1;Parent=Transcript_2.p1 +Transcript_2 transdecoder exon 1 372 . + . ID=Transcript_2.p1.exon1;Parent=Transcript_2.p1 +Transcript_2 transdecoder gene 1 372 . + . ID=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A124%20%28%2B%29%2Cscore%3D125.11 +Transcript_2 transdecoder mRNA 1 372 . + . ID=Transcript_2.p1;Parent=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A124%20%28%2B%29%2Cscore%3D125.11 +Transcript_3 shmlast.LAST conditional_reciprocal_best_LAST 11 157 4.900000e-106 + . ID=homology:90a3fa8c08141359b39bce4833db5842fde36a7d;Name=SPAC212.06c|SPAC212.06c|I|DNA helicase in rearranged telomeric region, truncated;Target=SPAC212.06c|SPAC212.06c|I|DNA helicase in rearranged telomeric region, truncated 1 147 +;database=pep.fa +Transcript_3 transdecoder CDS 1 474 . + 0 ID=cds.Transcript_3.p1;Parent=Transcript_3.p1 +Transcript_3 transdecoder exon 1 891 . + . ID=Transcript_3.p1.exon1;Parent=Transcript_3.p1 +Transcript_3 transdecoder gene 1 891 . + . ID=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3A5prime_partial%20len%3A158%20%28%2B%29%2Cscore%3D108.17%2CHelicase_C%7CPF00271.27%7C1e-05 +Transcript_3 transdecoder mRNA 1 891 . + . ID=Transcript_3.p1;Parent=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3A5prime_partial%20len%3A158%20%28%2B%29%2Cscore%3D108.17%2CHelicase_C%7CPF00271.27%7C1e-05 +Transcript_3 transdecoder three_prime_UTR 475 891 . + . ID=Transcript_3.p1.utr3p1;Parent=Transcript_3.p1 +Transcript_4 shmlast.LAST conditional_reciprocal_best_LAST 69 356 8.700000e-207 + . ID=homology:245ebc80e8bb87a88ca8462b3ede0ac3ea3d7978;Name=SPAC212.04c|SPAC212.04c|I|S. pombe specific DUF999 family protein 1;Target=SPAC212.04c|SPAC212.04c|I|S. pombe specific DUF999 family protein 1 1 288 +;database=pep.fa +Transcript_4 transdecoder CDS 207 1073 . + 0 ID=cds.Transcript_4.p1;Parent=Transcript_4.p1 +Transcript_4 transdecoder exon 1 1615 . + . ID=Transcript_4.p1.exon1;Parent=Transcript_4.p1 +Transcript_4 transdecoder five_prime_UTR 1 206 . + . ID=Transcript_4.p1.utr5p1;Parent=Transcript_4.p1 +Transcript_4 transdecoder gene 1 1615 . + . ID=GENE.Transcript_4~~Transcript_4.p1;Name=ORF%20type%3Acomplete%20len%3A289%20%28%2B%29%2Cscore%3D286.81%2CDUF999%7CPF06198.7%7C2.6e-88 +Transcript_4 transdecoder mRNA 1 1615 . + . ID=Transcript_4.p1;Parent=GENE.Transcript_4~~Transcript_4.p1;Name=ORF%20type%3Acomplete%20len%3A289%20%28%2B%29%2Cscore%3D286.81%2CDUF999%7CPF06198.7%7C2.6e-88 +Transcript_4 transdecoder three_prime_UTR 1074 1615 . + . ID=Transcript_4.p1.utr3p1;Parent=Transcript_4.p1 +Transcript_5 shmlast.LAST conditional_reciprocal_best_LAST 26 154 1.200000e-100 + . ID=homology:02257bb29738d9df3cd8a6b10606b67a92664d3b;Name=SPAC212.03|SPAC212.03|I|hypothetical protein;Target=SPAC212.03|SPAC212.03|I|hypothetical protein 1 129 +;database=pep.fa +Transcript_5 transdecoder CDS 77 466 . + 0 ID=cds.Transcript_5.p1;Parent=Transcript_5.p1 +Transcript_5 transdecoder exon 1 466 . + . ID=Transcript_5.p1.exon1;Parent=Transcript_5.p1 +Transcript_5 transdecoder five_prime_UTR 1 76 . + . ID=Transcript_5.p1.utr5p1;Parent=Transcript_5.p1 +Transcript_5 transdecoder gene 1 466 . + . ID=GENE.Transcript_5~~Transcript_5.p1;Name=ORF%20type%3Acomplete%20len%3A130%20%28%2B%29%2Cscore%3D68.44 +Transcript_5 transdecoder mRNA 1 466 . + . ID=Transcript_5.p1;Parent=GENE.Transcript_5~~Transcript_5.p1;Name=ORF%20type%3Acomplete%20len%3A130%20%28%2B%29%2Cscore%3D68.44 +Transcript_6 shmlast.LAST conditional_reciprocal_best_LAST 1 136 9.400000e-103 + . ID=homology:aa2030cc9fa44f795e7308c594832186506cc04f;Name=SPAC212.02|SPAC212.02|I|Schizosaccharomyces pombe specific protein;Target=SPAC212.02|SPAC212.02|I|Schizosaccharomyces pombe specific protein 1 136 +;database=pep.fa +Transcript_6 transdecoder CDS 1 411 . + 0 ID=cds.Transcript_6.p1;Parent=Transcript_6.p1 +Transcript_6 transdecoder exon 1 411 . + . ID=Transcript_6.p1.exon1;Parent=Transcript_6.p1 +Transcript_6 transdecoder gene 1 411 . + . ID=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A137%20%28%2B%29%2Cscore%3D91.01 +Transcript_6 transdecoder mRNA 1 411 . + . ID=Transcript_6.p1;Parent=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A137%20%28%2B%29%2Cscore%3D91.01 +Transcript_7 shmlast.LAST conditional_reciprocal_best_LAST 1 280 8.400000e-209 + . ID=homology:c6aff8c4d38d12fb8cbc360f91d42eb384e58ebd;Name=SPAC212.01c|SPAC212.01c|I|S. pombe specific DUF999 family protein 2;Target=SPAC212.01c|SPAC212.01c|I|S. pombe specific DUF999 family protein 2 1 280 +;database=pep.fa +Transcript_7 transdecoder CDS 1 843 . + 0 ID=cds.Transcript_7.p1;Parent=Transcript_7.p1 +Transcript_7 transdecoder exon 1 862 . + . ID=Transcript_7.p1.exon1;Parent=Transcript_7.p1 +Transcript_7 transdecoder gene 1 862 . + . ID=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A281%20%28%2B%29%2Cscore%3D279.01%2CDUF999%7CPF06198.7%7C1.9e-91 +Transcript_7 transdecoder mRNA 1 862 . + . ID=Transcript_7.p1;Parent=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A281%20%28%2B%29%2Cscore%3D279.01%2CDUF999%7CPF06198.7%7C1.9e-91 +Transcript_7 transdecoder three_prime_UTR 844 862 . + . ID=Transcript_7.p1.utr3p1;Parent=Transcript_7.p1 +Transcript_8 shmlast.LAST conditional_reciprocal_best_LAST 1 316 8.700000e-241 + . ID=homology:4b1595941d7f979b3c480239a7fb19274ab1fcda;Name=SPAC977.01|SPAC977.01|I|S. pombe specific 5Tm protein family;Target=SPAC977.01|SPAC977.01|I|S. pombe specific 5Tm protein family 1 316 +;database=pep.fa +Transcript_8 transdecoder CDS 3 953 . + 0 ID=cds.Transcript_8.p1;Parent=Transcript_8.p1 +Transcript_8 transdecoder exon 1 1306 . + . ID=Transcript_8.p1.exon1;Parent=Transcript_8.p1 +Transcript_8 transdecoder gene 1 1306 . + . ID=GENE.Transcript_8~~Transcript_8.p1;Name=ORF%20type%3A5prime_partial%20len%3A317%20%28%2B%29%2Cscore%3D163.63%2CPombe_5TM%7CPF09437.6%7C1.6e-155%2CLung_7-TM_R%7CPF06814.9%7C1.3e-05 +Transcript_8 transdecoder mRNA 1 1306 . + . ID=Transcript_8.p1;Parent=GENE.Transcript_8~~Transcript_8.p1;Name=ORF%20type%3A5prime_partial%20len%3A317%20%28%2B%29%2Cscore%3D163.63%2CPombe_5TM%7CPF09437.6%7C1.6e-155%2CLung_7-TM_R%7CPF06814.9%7C1.3e-05 +Transcript_8 transdecoder three_prime_UTR 954 1306 . + . ID=Transcript_8.p1.utr3p1;Parent=Transcript_8.p1 +Transcript_9 shmlast.LAST conditional_reciprocal_best_LAST 53 185 4.400000e-95 + . ID=homology:e26c123afd68729a1a3c67041d92510505a2fd93;Name=SPAC977.18|SPAC977.18|I|conserved fungal protein;Target=SPAC977.18|SPAC977.18|I|conserved fungal protein 1 133 +;database=pep.fa +Transcript_9 transdecoder CDS 159 560 . + 0 ID=cds.Transcript_9.p1;Parent=Transcript_9.p1 +Transcript_9 transdecoder exon 1 747 . + . ID=Transcript_9.p1.exon1;Parent=Transcript_9.p1 +Transcript_9 transdecoder five_prime_UTR 1 158 . + . ID=Transcript_9.p1.utr5p1;Parent=Transcript_9.p1 +Transcript_9 transdecoder gene 1 747 . + . ID=GENE.Transcript_9~~Transcript_9.p1;Name=ORF%20type%3Acomplete%20len%3A134%20%28%2B%29%2Cscore%3D88.84 +Transcript_9 transdecoder mRNA 1 747 . + . ID=Transcript_9.p1;Parent=GENE.Transcript_9~~Transcript_9.p1;Name=ORF%20type%3Acomplete%20len%3A134%20%28%2B%29%2Cscore%3D88.84 +Transcript_9 transdecoder three_prime_UTR 561 747 . + . ID=Transcript_9.p1.utr3p1;Parent=Transcript_9.p1 diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index fb078d88..16821c98 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -99,7 +99,6 @@ def test_annotate_user_database(self, tmpdir, datadir, n_threads): assert compare_gff(gff3_fn, exp_gff3) assert open(fasta_fn).read() == open(exp_fasta).read() - ## run this on pom20! store the results somewhere and then compare using compare_gff3! @pytest.mark.parametrize('n_threads', (1,4)) def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): '''--pipeline quick annotate --user-database [PEP1.fa] --user-database [PEP2.fa] [INPUT.fa] @@ -145,7 +144,6 @@ def test_annotate_basename(self, tmpdir, datadir): contents = open(fn).read() assert 'Test_0' in contents -""" def test_annotate_outdir(self, tmpdir, datadir): ''' Test output directory option @@ -188,5 +186,13 @@ def test_annotate_dbdir(tmpdir, datadir): database_dir = os.environ['DAMMIT_DB_DIR'] args = ['run', '--database-dir', database_dir, '--pipeline', 'quick', 'annotate', transcripts] status, out, err = run(*args) + + outdir = 'pom.20.dammit' + gff3_fn = os.path.join(outdir, 'pom.20.dammit.gff3') + fasta_fn = os.path.join(outdir, 'pom.20.dammit.fasta') + assert status == 0 -""" + assert compare_gff(gff3_fn, exp_gff3) + assert open(fasta_fn).read() == open(exp_fasta).read() + + From 1bdf76c5f39180d885163a6310f5a8816e15bd1b Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Fri, 22 Jan 2021 15:46:00 -0800 Subject: [PATCH 03/13] upd dbdir tests; add tmpdir test --- dammit/tests/test_annotate.py | 45 +++++++++++++++++++++++++++-------- 1 file changed, 35 insertions(+), 10 deletions(-) diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index 16821c98..7dbce8a7 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -127,7 +127,7 @@ def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): assert open(fasta_fn).read() == open(exp_fasta).read() def test_annotate_basename(self, tmpdir, datadir): - '''--pipeline quick annotate --base-name [NAME] [INPUT.fa] + '''Test annotate --base_name ''' with tmpdir.as_cwd(): @@ -153,14 +153,14 @@ def test_annotate_outdir(self, tmpdir, datadir): transcripts = datadir('pom.20.fa') outdir = 'test_out' - args = ['run', 'annotate', '--quick', transcripts, '-o', outdir] + args = ['run', '--pipeline', 'quick', 'annotate', + transcripts, '--output-dir', outdir] status, out, err = run(*args) assert os.path.isfile(os.path.join(outdir, 'pom.20.fasta')) - -# make sure DAMMIT_DB_DIR is set in your testing env -# (export DAMMIT_DB_DIR=/path/to/databases) - def test_annotate_dbdir_fail(tmpdir, datadir): + # make sure DAMMIT_DB_DIR is set in your testing env + # (export DAMMIT_DB_DIR=/path/to/databases) + def test_annotate_dbdir_fail(self, tmpdir, datadir): '''Test annotation with a faulty database directory. dammit run --database-dir [DB_DIR] annotate [INPUT.fa] ''' @@ -168,22 +168,24 @@ def test_annotate_dbdir_fail(tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') - args = ['run', '--database-dir', '.', 'annotate', transcripts] + args = ['run', '--pipeline', 'quick', '--database-dir', '.', 'annotate', transcripts] status, out, err = run(*args, fail_ok=True) print(status, out, err) - assert 'you probably need to install the dammit databases' in err - #assert 'install databases to continue' in out + assert 'you probably need to install the dammit databases' in err assert status == 1 - def test_annotate_dbdir(tmpdir, datadir): + def test_annotate_dbdir(self, tmpdir, datadir): '''Test that --database-dir works. ''' with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') database_dir = os.environ['DAMMIT_DB_DIR'] + exp_gff3 = datadir('pom.20.udb.dammit.gff3') + exp_fasta = datadir('pom.20.udb.dammit.fasta') + args = ['run', '--database-dir', database_dir, '--pipeline', 'quick', 'annotate', transcripts] status, out, err = run(*args) @@ -196,3 +198,26 @@ def test_annotate_dbdir(tmpdir, datadir): assert open(fasta_fn).read() == open(exp_fasta).read() + def test_temp_dir(self, tmpdir, datadir): + '''Test that --temp-dir works. + ''' + + with tmpdir.as_cwd(): + transcripts = datadir('pom.20.fa') + exp_gff3 = datadir('pom.20.udb.dammit.gff3') + exp_fasta = datadir('pom.20.udb.dammit.fasta') + database_dir = os.environ['DAMMIT_DB_DIR'] + dammit_temp_dir = "." + args = ['run', '--temp-dir', dammit_temp_dir, '--pipeline', 'quick', 'annotate', transcripts] + status, out, err = run(*args) + + outdir = 'pom.20.dammit' + gff3_fn = os.path.join(outdir, 'pom.20.dammit.gff3') + fasta_fn = os.path.join(outdir, 'pom.20.dammit.fasta') + + assert status == 0 + # assert "" in dammit_temp_dir + # assert compare_gff(gff3_fn, exp_gff3) + # assert open(fasta_fn).read() == open(exp_fasta).read() + + From aa04c958c8b4c81cc94ba592dd042ae3b37d784f Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Mon, 25 Jan 2021 10:34:19 -0800 Subject: [PATCH 04/13] save in-progress changes --- dammit/tests/test_annotate.py | 75 +++++++++++++++++++++++++++++++---- 1 file changed, 67 insertions(+), 8 deletions(-) diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index 38bebf31..1e84bf03 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -202,20 +202,79 @@ def test_temp_dir(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') - exp_gff3 = datadir('pom.20.udb.dammit.gff3') - exp_fasta = datadir('pom.20.udb.dammit.fasta') - database_dir = os.environ['DAMMIT_DB_DIR'] dammit_temp_dir = "." args = ['run', '--temp-dir', dammit_temp_dir, '--pipeline', 'quick', 'annotate', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' - gff3_fn = os.path.join(outdir, 'pom.20.dammit.gff3') - fasta_fn = os.path.join(outdir, 'pom.20.dammit.fasta') assert status == 0 - # assert "" in dammit_temp_dir - # assert compare_gff(gff3_fn, exp_gff3) - # assert open(fasta_fn).read() == open(exp_fasta).read() + tempd_contents = os.listdir(dammit_temp_dir) + assert "pom.20.fa" in tempd_contents + assert "pom.20.dammit" in tempd_contents + + + def test_busco_group(self, tmpdir, datadir): + '''Test that --busco-group works. + ''' + + with tmpdir.as_cwd(): + transcripts = datadir('pom.20.fa') + dammit_temp_dir = "." + args = ['run', '--busco-group', 'bacteria_odb10', '--pipeline', 'quick', 'annotate', transcripts] + status, out, err = run(*args) + outdir = 'pom.20.dammit' + + assert status == 0 + assert os.path.isfile(os.path.join(outdir, "pom.20.busco/bacteria_odb10_outputs/run_bacteria_odb10/short_summary.txt")) + + def test_max_threads_per_task(self, tmpdir, datadir): + '''Test that --max_threads_per_task works. + ''' + + with tmpdir.as_cwd(): + transcripts = datadir('pom.20.fa') + args = ['run', '--max-threads-per-task', 1, '--pipeline', 'quick', 'annotate', transcripts] + status, out, err = run(*args) + outdir = 'pom.20.dammit' + + print(status, out, err) + + assert status == 0 + assert "Threads (per-task): 1" in out + +## do we not enable this anymore? + #def test_config_file(self, tmpdir, datadir): + # '''Test that --config-file works. + # ''' +# + # with tmpdir.as_cwd(): + # transcripts = datadir('pom.20.fa') + # conf = datadir('test-conf.yml') + # args = ['run', '--config-file', conf, 'annotate', transcripts] + # status, out, err = run(*args) + # outdir = 'pom.20.dammit' +# +# print(status, out, err) +# +# assert status == 0 + + + def test_busco_config_file(self, tmpdir, datadir): + '''Test that --busco-config-file works. + ''' + + with tmpdir.as_cwd(): + transcripts = datadir('pom.20.fa') + conf = datadir('test-busco-conf.ini') + args = ['run', '--busco-config-file', conf, 'annotate', transcripts] + status, out, err = run(*args) + outdir = 'pom.20.dammit' + + print(status, out, err) + assert status == 0 + + + From 734087ca321debfe429285d8db01dd0fee21f6ef Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Fri, 29 Jan 2021 17:52:58 -0800 Subject: [PATCH 05/13] upd tests; mult user db testdata --- .../tests/test-data/pom.20.udbs.dammit.fasta | 28 ++++---- .../tests/test-data/pom.20.udbs.dammit.gff3 | 31 ++++++++ dammit/tests/test_annotate.py | 70 ++++++++----------- 3 files changed, 73 insertions(+), 56 deletions(-) diff --git a/dammit/tests/test-data/pom.20.udbs.dammit.fasta b/dammit/tests/test-data/pom.20.udbs.dammit.fasta index 5ae58780..b74860ac 100644 --- a/dammit/tests/test-data/pom.20.udbs.dammit.fasta +++ b/dammit/tests/test-data/pom.20.udbs.dammit.fasta @@ -1,40 +1,40 @@ ->Transcript_0 len=5662 CDS=0-5661 exon=0-5662 gene=0-5662 mRNA=0-5662 +>Transcript_0 len=5662 CDS=0-5661 exon=0-5662 gene=0-5662 mRNA=0-5662 hmm_matches=DEAD:3603-4089,Helicase_C:4206-4548,Helicase_C:5217-5274 ATGGTCGTCGCTTCAGAAATTGCTAAAGTCGCTTCAAAAACTGCTAGAGATATCGCCGGATGCTTTACTTGTCAATGTGGAACTCAATTTGATAATGTAGAAAGGATCGTTCAACATTTCAAGGAATGTCGATACAGAGACGAAACTTGTAAAGACGATGATATCGTCGTCTATGAACCCAGCTCTTTCGTTCAGGACGAGAAAAAGGATAAGCCAATCATCGTTGAGGCTGCCAGTGAGGCTACCAGTGAGGAGGCTTGCAATTCTTCCAAGGAGCGTCAACTACCCGCTCTCTCTGCTCTCTCTGCTCTCTCTACTCTCACTACGAGTGCAAATGACGACTTGTGGACTGCACGGCTAATTTGGCAAAGTACAAATGACACCAAATTGGACAACAGCCCATCATCAAATTATACTGACTTGAATCACAAGTTGGCTAATTATGGACTCTCCATTTTGTCTATTCATGCTTTGATGTGCGTAGAATGTGAATGCTTGTTAAACGTGATTCACACTGCGCAACATATGCAAATTGTGCATAAACTAGAGTTAAACGAAGATCTTTTGTGGTTTCAAGAACTAAGGACTTTAAAGTTAAAAAGTCCAACAAATGTTTTACAAACTCATTCTTCTCAAACCCATGTATACCCATACATCAGAGGACTACCAGTACTTTTAAATGGATATGAGTGTGTGCCGTGCACAAAAAACGGAACAGGATTCGTACATGCAATCATGGATACCTTTCGCCATCATGTTCGACGTACTCATGGAAAAGTTATAAAATTGGAAAATTGTATACGTCGAACAGCTTTGCAAACGGTTAAGAACAAGTATGCTCAACGATGTCAGTTCTTCAAAGTCGATTATGTACCTTTGAATGGAGGAGAAGAAGAAGAAGAGGAGGAGGGGGAGGAGAAAGAAGATGCACAAAACATCAAGGAAAGAATGGTGGACTTTTGCTTTTCAAAATTTATGGAGAAGAATCAACAGCGGCGGGAGCAGCAAGACAAAGGTGAAAATAAAAAACGACAAGATGATGTTGACCAAGCAACAGACAACAACACTAACACTATTCTTGAAGATGATGAAAAAGATAACGATGAAGAGGAAGAGGAAGAGATTGTCAATGCACGAGAGAAAAATCTTTTAAATCAACAATTCAATTGGACGGCAATTGTGAAAAAACTTGGAGAAAATTGGGATCAGCTGGTTCGATTCGAATATACGAATGGAATTGTAACTTTGGATACCATTGTAAACCAGTTGATTCGTTATTACTATCGAGGATTCCGTCATCTAAGTGGAATGACCATGGGCATGAGACGAATGTTTACTCAAGGAGGAAGCTATAGTGCACAAGAGCGAGGACTTTGTCGCTTAGAGCAAAAGGATACAGTTGTGAGATATGCTCAAAGTGCAGCACTATACCTAATATTTCTGTTACGTCGTCCATCAGCGGACTCGGGGATAAGAAGACACTTGGAAGCAATGTGTGGAGCAACAGTGGAGAGAAAAGAAGGTGGCAGTAACAGCAGCAGTAACATCAGCAACGTCGCCAACTTTGATAGTGCTGAAGACGACAATGACAATGACAATGACAATGACAGAGACAGTAACAATAACAATAACAATAACAACACCAATACTGACGATGATGATAAGCTGGCATACTTGGAACTGCACGAGGCATTAAAATTGGCTTTTCTGCAACAATACGATTTTTCTAAAAATGTTCAAGACTTGGAAATCATGGAGTTTCTTGCATGCATGTCTTTGCATAAAGATGGTACTTCAAAATATGCCTATGAAATCTCTGCCTGCTTTGCACCCCTAATATACACGTGTCGTCTTGTAGCAGCATGTGAGTTACAACGATTGATCGATGAAAAACAAATCGACTTGTTGTCCATTCCATCGTTTCAAACCGCTGGTTCTATTGCTTATGCTCATGTGTTTTGCTTTATCACGCTTGGTCAAAGAAATTTATATGATGTTCTTTACGAAACCCAAAAAGTCGTTAGGGATATCATTCGAACGGAAGGGTATGCAAATACACTGCAAGGACTAAGCCCAAGTACCGTATTGTTTCAGCCACGAAGTAATTCTATGTACCCGTGCATTGGAGATGCATTCAATAACATGGTGCGATTGGACTTGAGTGAGCTGACAGCTCTGTATGAGGGGATGTTTGCCAAAGTTCAGGACTTGTTAAAAGAGCTATGTTTTGATATGAATGTGGAAAAACTATTACCCATTTCGTTACTAAGGTCAATTGGAGATGACATAAACAATAGTAAATTGGGATATTCATTCTTTAAAGAGTCGATAGAGATACGTTCATCTCATAGTGTGCTGTTACGAACAATACTTAAGAACAGTGAACTTTGTCATCGGTTTTTCCCATCGATGTCTAAGAAGGATCTGACAAAGTTGTTTGGTGGAGTAAGTGATCAGCAAAGAAATGAGTGCGACAACTATAGCAACCACTACAACGACAACTCTAATGATAATGACAATGATGTGTTTCTCAAATTACATTGGTCTAAATCTGCTATTAAAAAGTATGAGACAAAGGCATCTATCTTCAATGAGTTATTGTTTTGTCTAGTGTACATATCTGCTGGACAACCAGCCAGAGCACAAGAGATGGTGTATTGGACTTTGCGGAATGGCAAGTATAAGACTCGCGAATTGTATTTGATGTTTGGAAGGCTGATGATTTACAGCAGATACGATAAGACTCGTAATATGAAGTTTGCTGAAAAGCCAATCCCCAGGTTTCTTTCTGAGCCGCTTTCCATTTTAGCACTTCGGTACTATGTTTTGGTTCGACCATTGGAAGCATTGATGAAGTATGTGACAACCGCTGATAGGTCGAAAGTAGCTGTATACTTGGATTTCATGTTTGTGATTGCTGGCGAACGATTGCAAAGAGATTTACCGTATCGAATTTTTCCAAAGGCCACCTACCAATGCATTCAAAAACCGTTGGGATTTCGAAACTACAGGCACATTGCTCACTATTTTAAAGAAAAAAACATCGAGGAAGAAATGACGAGGGAATCATATTTCGATTTACAGGCTGGACATACACGAAACACAGCGCTCTACATCTATGGGCGCACTATGGACAACTTGCATTATCTGCCGTCGGATTATTTCGCCAACTTTTTTCGTGCAAGCTATAAGTGGCAGGAACTATTACAGATTCGAGATAACCCGACCCATGGACTGTTGGTGGAAACAAAGCACCCATTCATCAAGCGAGTTGATCAATTGGAGGAAGCGCTGAATGAGAAGCTGGCAAGGTTGGTAGGTGAACAAATGGTGGAGGGGGACAAGGAAAAGGACAAGACAAATGAGGAGAAGAACAAGGACGAGGTAAAGGCTGAAATGACACAGCCCGTTGTAAATCAAGACTCTCATGACTTACAAGACCAATTGGCCACTACGCCCACCGCGCCCACCGCATTTCACTACCGCCCAGGACTTCTTCAACCATCTCAAACTTCTGTTCAACATTGTTGTTGGGCATTGTCTCAATATTATGGTCTCGAAGCGAAATTCCGTTCGCTGAAACAATTTCAATCGGTTTATTTTTCTCTTTTAAATCGTATGAATTTGATTACCGTACTCCCAACTGGAGGTGGAAAGTCTTTGTCGTTTTTGATACCGGCGCTCATCGAAAAAAAAAGACAAACCCCAGGAAAGGTGATGAATATGGTCACGCTGGTTCTAGTGCCCATGATGTCGTTACGGCAAGATATGATGCTCAGAGTGAATGAAAAGGGACTGCTTGTTTGTTCGGGGAATTGGACCGCATTCAAAGATGTACGATTGACTTTAGAGACGCAACTTCCCGATTTGTTTATCTTGACATACGAGTCAGCATTAACCAACAGTGGTCTTCGGTTTTTTGAAAGTTTGGCAACACTTGGTCGTTTGGCACGAGTGGTAATTGATGAAGCACATTTGTTACTCACCAGTGGAGCATGGAGAACGGCTTTGTCGAGAGCATCGCGGTTGTCTGGCTTGTATGCACCATTGCACTTGTTGAGTGCCACCTTTCCCAGGCAACTAGAGATGGTTGCCAGACAAACGTTTTGTACAAACTTTTACGTTTTACGAGAAACGTCTACTGCACGGGAAAACATCTTTTACTTTTTGCATCCCTATGATAATACCGAGTTTTTGTTGGACTTGCGAACGTTGATGAAACGAACAAAGGTCTTTGAAGGTGATGGACGTGCTATCATCTTTTGTCGAACCAAAAAGGATGTCGAATACATTCATCGTCGTCTTCACCAGTCGGACTTGTTCGCTCACACCCATGTAACCATTTACACAGGAGATGTAAGCGACGAAGAACGACAAATGAACTTTGACGCGTTTCGAAATGCAAATGGGAAGACACGAATCATGATCGCTACCAAGGCATTCGGACTCGGTATCAACTATATGGGAGTGCGTTTAGTAGTACACTATGGATTACCAGCTTCATCTATGGATTATGTACAGGAGACAGGTCGAGCTGGAAGAGATGGCAAGTATGCGATTGCAGCATTGTTTTACGAGAAATATGATTCTACATGGTCGAGCTACGTAGAGGATTCGATGAAAAACTTTCTTAATGATAATACGATGTGTGTTCGATCGTTTCTCGCAAGTGAAATGGATGGCGAATGTGTATGTTGTGCATCGTTTGCTAACTGTGTTTACTGCTCAAGATGCTCAGATTCGTTACTTGGTGAAGAATCAACTGTGTCTACGATGTATGGAGTGAAACCGACATTGCCAGAAACACCGAAACCAGCCATTGCAACACATTCGCGTTATAATGCATCGTTTTCGTCTTCCCCCCCACCACAGCCAGGGAATAGCAGTGGTATGAGTGCTATGAACACTAACACTACTAGTACTACGCCAGTGTCTTTGTCGGAATTATCGGAAATCACTTTGTTCCCTTCGTCTGTATCGCCAACATGGAAGAAAAGCTTTGGCAATGCTAATACGAATCTAAAGTATGGTTTGGAAGACATGTCGCTCAGCCATCGTCGTGGTCATAAACGCACATACGATGAACATTTGAACAATGTACAACAGGGCGTCAACCATGACATGAATCGTGTTCATGGTAGTGTTGGAGGTATGAGTGGTATTGTTGGTATTGGTATTGGTATTGGTGATGGTGATGGTGATGGTGATGTTGATTCTCGTACCATTCATTTCGCCGAGTATAAAAGTCGTGTGCAAGCCGTCAAAAAACAATGGGTAGACTCAACTGACATTTCAGCACAACTCGAGCGATTCTTTCGAGTGTATAAAGATGAATGTCTAAGTTGCACTCTTGGTAACCCAGACACAGAAATTCGTGCTCATACCGGGAAAGCATGCCCCGTACGCTTATCTACTTGTTATAAATGTGGCAAGGCCGACCACAACTTGCGAGAATGTAAACTACGTATTCGATTTCAAGGACTTTGTTTATTTTGTGGTTTGACAAAGTTTGAACATGCCGACAGTGATATGGCTTACACTTCTGACTGTAGGTCATGGGCTAGAAAGGCAAACTTGATATCGTTAGTTTACTATGCTTGGAACAATGTACAATACCGAAGGACTATTGCAGATAAATTCTTACAAGGTGATGTACGTGATC >Transcript_1 len=1211 CDS=374-1211 exon=0-1211 five_prime_UTR=0-374 gene=0-1211 mRNA=0-1211 CAGATTCACGTTCGTTTGCTCACGGTTTTTGTTTAAGCTAATGGCAAAAATCAAATACTCATTACAAATACTGACAGATCGATAAATGATAGAAGAAATCCAAAAAATGTTAATCGGATGGTATTAAATATACAAGATTATTGGTTTTGTTTCAATTATTAAATTCAAATTCAATTTACAACTAATTAATTTGATAAAATACATCTGTTATTTTTGATTGGATTATTTGGATTATTTCATGAAATTCCTATAATTTCAAGCTGTTTTCTGCAGCATTGATCGTCCATTTCCCGGTCAAAAAACAGTATTTCATCTGCTCTTCTCCCAAACTCCACACCATATCTACAACAGGATTGATTGCTTTAATTTCAAACATGTCCCCTTTAATAGTTGGGACTTTAATAATTATCCTATTGTCAGGACTCGCAACTGCTTTTTATGTTACGTGGCAAGGCAGACTCATTTGTGCTGGTGTAGGGCTCATACTTGAACAGGCTTATGAGGGTGGTCAGATGTTTAACACATTGATGGCACATTGCTTTGAAACGTACAATGGTGTTGAGAAAAGTGGAACGCAGTGTGTGGCCGATTGGCTTAAAGTAGGGCTTTTGGCTGTCACATTTGGGGCTGGAGGACCTAGATTGGTTAACACATTAGGTGGTACTTTTCTCACTTCTCCTACTGCAAAACGGAGCAATCTATATTGTGATGATTTTACTGGTGCTGATTACTTTAGCTGTGAACTTGAAACATTAAGGCCTTACACATTGATGAGAAAGAGCCTGCCGTATGGTAATATACACGATGTATGGATTAACACAACCGACACTCATCAGATGATAGGTGTACATATGACATTGAATGGAACAGATATGATTCATTATTATAATAAAACTTATGTAATTAATTATTCTGGTCTCAAACTAAATAGCTCTGCTATTAATAAAAGGTCTTACTTTTATCCTCAGGATTCCTTTCTTGTGAGTCATGCCGAATGGCAAGATGGTAATGGTATATGGACGGATACGGATTATTTCGCAGCTATGGCGGATTGTGACTTCTTGGGTCAAAATCTTGGTTTCTGGCTTGCAAGTTCCTATCCAAACGCATATAAGTGGGAAACACAACTGTGGCGCACCGTAGGAATAAACCTAAACGGTAATATAATATACCCGGGGCAACTCATTATGCAGACATTTAACGGTAGCTAA >Transcript_2 len=372 CDS=0-372 exon=0-372 gene=0-372 mRNA=0-372 ATGTCCCCTTTAATAGTTGGGACTTTAATAATTATCCTATTGTCAGGACTCGCAACTGCTTTTTATGTTACGTGGCAAGGCAGACTCATTTGTGCTGGTGTAGGGCTCATACTTGAACAGGCTTATGAGGGTGGTCAGATGTTTAACACATTGATGGCACATTGCTTTGAAACGTACAATGGTGTTGAGAAAAGTGGAACGCAGTGTGTGGCCGATTGGCTTAAAGTAGGGCTTTTGGCTGTCACATTTGGGGCTGGAGGACCTAGATTGGTTAACACATTAGGTGGTTCTTCGCCTACTACAAAACGGGTAATCTATATTGTGATGATTTTACTGGTGCTGATTACTTTAGCTGTGAACTTGAAACATTAA ->Transcript_3 len=891 CDS=0-474 exon=0-891 gene=0-891 mRNA=0-891 three_prime_UTR=474-891 +>Transcript_3 len=891 CDS=0-474 exon=0-891 gene=0-891 mRNA=0-891 hmm_matches=Helicase_C:9-117 three_prime_UTR=474-891 AGCAAGGGATTTGGACTCGGTATCAACTATATGGGAGTGCGTTTAGTAGTACACTATAGATTACCAGCTTCATCTATGGATTATGTACAGGAGACAGGTCGAGCTGGAAGAGATGGCAAGTATGCGATTGCAGCATTGTTTTACGAGAAATATGATTCTACATGGTCGAGCTACGTGGAGGATTCGATGAAAAACTTTCTTAATGATAATACGATGTGTGTTCGATCGTTTCTCGCAAGTGAAATGGATGGCGAATGTGTATGTTATTCGTTACTTGGTGAAGAATCAACTGTGTCTACGATGTATGGAGTGAAACCGACATTGCCAGAAACACCGAAACCAGCCATTGCAACACATTCGCGTTATAATGCATCGTTTTCGTCTTCCCCCCCACCACAGCCAGGGAGTAGCAGTGGTATGAGTGCTATGAACACTAACACTACTAGTACTACGCCAGTGTCTGGTAAAACTTAACTACACATTACGCTGAGAGGTAAAATACTCTGACAACATTCGTTCGATTGTATAAAACAAAATCCAGCCGAAACGATTGTTGTCAGTAATCAAGATTACGATCTAAATTGAGTACCAAGACAAAACGAAATGGTTAAAAAGTTAAAGTCGTTTTTGTATGGACACAATTTCTATAAAATAGACATGAGTAAAATCTCGCTATTTGTTTGTTATTGTGGAATAATGAAGAGTCATGGGAGATGAATGTTGTAAACGATGGCATAGAATTGGTAACGAAAAGTGAAATCGTTGGGATCAACTATTTCAGTATTTTGTTTAAAGAAAATGTTGAACTCGACAAGTAATGAGAGGTGGTGCTTTCGTTAAATAATGAGTGGTGGTTACGGTTATACAGGATATGATATGTGTATGGTGAGA ->Transcript_4 len=1615 CDS=206-1073 exon=0-1615 five_prime_UTR=0-206 gene=0-1615 mRNA=0-1615 three_prime_UTR=1073-1615 +>Transcript_4 len=1615 CDS=206-1073 exon=0-1615 five_prime_UTR=0-206 gene=0-1615 mRNA=0-1615 hmm_matches=DUF999:266-695 three_prime_UTR=1073-1615 TAATGCTTTTCCTAAATAAATGAGACACCTCAGAACGTAAAACATTCACCATTTTGGTTTTTTTTTTAATTTTCTCGTTTATGGCTTAAAATATTTTAGTATATTTTCTTTTTTATTTTCCATAAACCACTCTTTTTAATTTTACTTTGGGGAAAAATACTAGTGAATCAGAAGTCATCAAATTACAGTGCTGTCGTTCTATTCCAATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACTTGATTTGTGTAAGCCTGAAAAGGTAAACAAACAATCTCAACGATCTCGACAATCCCGACAATCCCTCTTTACCAACACCATTAAGCCTCAAAAAGACAAGATGAATATTAAAACAAATAAAATAAAAGAGTTTTTAAATGACCTTTTTACTGAATTTTCTAAATTCCACAATAGCTATTATCCTAATGGAAGAATTTCTACTCAGGACAAATCTCGATGGGTCTTGCTTATTATTTGGTCTATTATCACTATTTTAACAATAGACAAGAAATTTAAAATAAAAGAGTCATATTTAGAATGGATAGGTGAAAATCAGTCCCACAGTGAAATTTGGGGGCCTATTGTTATTTATGTTGGCTTATTCATACTCTTATTGTCTGCTTTTAACTACTGCTCCAAGCTTATTATAAAAGCTCTACCGTTAATCAGTATGGTTATAGCATGGGTCGGTGTGGTTATAGCAGCGTTCAGTGTGATTATCACTGCAACAATAGCAGGAGTTATAGCAGCGTTCAGTGTGATTATCACTGCAACAATAGCAGGAGTTATAGCAGCTATGGTTGGAATCTTATATTTCGGCCATTGGCTGGTCTACAAGATTTTAATTTTGGCTTTCGGCTTTAAAATTGTGACATCAGGAGACGTCTGTGTTTCTAACACTCTTCCTACACATAACGGAGAAACAGCATTACATTCAGATGCAACAGTTGGTTCTGATATTGAACAAATAGAACTACAAAATATGCCTACTCCTGTGAAAAAATAATTTTCTTTATCGTTTTCATGATCATATAGAATATAACTATTCTTAACAATGTTCGAATTGACTGTCCTGTCCAAATCATGCACATAAGGTGCGTTCGTTATGAATTTCAATTATGGAACCAACCAGAATCACCTCACAGGTGTTTCATTAACCAAAATTTATTAATTGGTTTTAATTAAGATATTATCACATAATGTTACTAATGTTTTTATCTCTCGTTTTATGCTTAATCAAATACTATGAATGTCATTTACTGCGTTTACAAAATGAATTCTTAATGATACATCATGAATGACTCGTTTCTAAGGTTATGTGTCTGGAAACTTGAAAAATGCAATGTAGTATATGCAAACTGATAAGTCGCTTATTTATTAATTTAATAAATTTCTGAATTGCAAGTTAAATTCTGGTAGCAAAGAATTAAATTATTCAGAGTCTTTCTAAAATCACTGTTTTTATATTGACATCCTCACTAGATTAGCTTTTCAACAATATACTGCTGCTACAAAAAAATAATATTCCTTTTTTCCGCTCGTGCAAAC >Transcript_5 len=466 CDS=76-466 exon=0-466 five_prime_UTR=0-76 gene=0-466 mRNA=0-466 GGGTTGCTTTTCATTATGAAATGGCAATTTAGATGATGTGCCAATATGTTCAGTATCTCTCTTTGCGTTGACTACTATGAGTATTGAATTCGATGACAGTTCAAGACATAATATGAACATGACTCAGCTGATGCAATTAGGTGCGTTTGATAGACGCTCAGGCGACGATTTCATGGTCCAAGACTTCAAAAACGGTATACGTGATTGTTCAGGAATACCAGTTAATAATCGAAATTTAGCATTTAAGGCTTATGATGCTGTTAAACAGAAGTGCGATAGTTCCATAAAAGTTTTTAACATACAGGATATAACTATAAAAGGAGCAACATGGCAGCACCATAACTGCCAAAGTACAGGCAAATGGTATTCCCAGCTTTACGATTATCAAAATACTTTTATAGGAAAGCAAGAATACAATATTTTATTCGATTGTTACTCATACTTGAAATACAATTTGAATGGTTAA >Transcript_6 len=411 CDS=0-411 exon=0-411 gene=0-411 mRNA=0-411 ATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGGGGGGTAATGTTATACAAACCTTTGGTAGTAAAAGCGTGTCTTACTGAGATCTAG ->Transcript_7 len=862 CDS=0-843 exon=0-862 gene=0-862 mRNA=0-862 three_prime_UTR=843-862 +>Transcript_7 len=862 CDS=0-843 exon=0-862 gene=0-862 mRNA=0-862 hmm_matches=DUF999:60-489 three_prime_UTR=843-862 ATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACTTGATTTGTGTAAGCCTGAAAAGGTAAACAAACAATCTCAACGATCTCGACAATCCCGACAATCCCTCTTTACCAACACCATTAAGCCTCAAAAAGACAAGATGAATATTAAAACAAATAAAATAAAAGAGTTTTTAAATGACCTTTTTACTGAATTTTCTAAATTCCACAATAGCTATTATCCTGATGGAAGGATTTCTACCCGCAGTAATTTTCGTTGGCCCTTGCTTATTATTTGGTCTATTATCATTGTATTCGCAGTAGACAAAAAGTTCGAAGTCCAAAAGTTTCTTTCAATTTGGATAAATGAAAATCGGTTCTACAGTGAAATTTGGGTGCCTATTGCTATTTACGTTTGTTTGCTTGTTTTAATGTTACTTAGTTTAATTTTCTTTGCAGAGTTTGCGGTACTTGCTTTACGGGTGACCGGTGTGATTATAGCAGTCTTGGGTGCAGTCTTGGGTATGATTATAGCAGTCTTGGGAATGATTATAGCAGCCTTGGGAATGATTATAGCAGCCCTGGGTGCAACTATAACTGGCCTTTTGTATTTTGGTCATTGGGCTCTTTACAAACTTGTAATATTGTCTTTAGGCTTTAAAATTGTGACACCAGGAGACGTCTGTGTTTCTAACACTCTTCCTACACATAACGGAGAAACAGCATTACATTCAGAAACAACAGTTGGTTCTGATATTGAACAAATAGAACTACAAAATATGCCTACTCCTGTGAAAAAATAATTTTCTTTATCGTTTTCAT ->Transcript_8 len=1306 CDS=2-953 exon=0-1306 gene=0-1306 mRNA=0-1306 three_prime_UTR=953-1306 +>Transcript_8 len=1306 CDS=2-953 exon=0-1306 gene=0-1306 mRNA=0-1306 hmm_matches=Lung_7-TM_R:242-812,Pombe_5TM:2-728 three_prime_UTR=953-1306 GATCATTTGCATATTCTGGTAACTCGGAATCGGTATGGACGGGCGAAAATATTACAAGTATATGGAAAACTATTTTGATTAATGAAACGGGTTCTTACTGCGTAGCTGCGAGACCAATGACAATGGATGGAGCTGAATTTAATTTAGACCTTATGGGGTATTCGGTTTCAGAAGATCAAATTAATAATGACGAAATTGGCATTTGGAACTATATTTCTGTAGCTGAAATGGGAGGAGTACTATTATTTTTGAGCTATTGGATATGGACTTGTTTACATTTCAGCAAGATTATATTTCCTGCTCAAAAGGTAATCTGCCTTTATATTTTTCTTTTTGCGTTAAATCAGACTCTACAAGAATGCATTGAGGAGTATGTTTTTTCTTCCGAATGTATAAAATACAGACAATTTTATTCGGTGTATGAAATAATTGATTTTCTTCGGACAAATTTTTATCGATTATTTGTGATTTACTGTGCATTGGGTTTCGGCATAACTAGAACTGTTCCTAAATATCTTATGATAAAAGGAATTAGTATTGTCATTGCTTTATGTTCTGTATACTGGATTTCTTTATATAAAGACGTATATGTAGTATCAGAGATTTTTGACATGATCCAGTATGAGGTATCTCCTGCAATTTGGGTGTATTCTATTTGTCATTTATTGAAACAATGCACGTCTGTAACAACTTACGAAAATGCTTCAAAAGCCAGATTTTTCAGAAGAATGCTAAATGCATTTATCTTTATATTCTGTGCATCTCCAATGTTGCATTACCTGTCGAATATTATATTTGGAAACTTTGATTACAGACTGTCGGTGATCATTGGTGATCTTTTCACTTTTATGGAGAAAATTGCTTTTCCATGTTACATAATGTTTCCCACCCATAATGAAGCACTTGCCTACAATCGAAATGTAGCTGAAGAGGCTCAAGAGAAAATGATTTGACAAAAACCATGGTTTACTTGATTCACCTTTAAAGGGGTTACCGGGATTATTTTATTTATTATTTGTTTATCAATGGATTAATATCCAGTTATTTTAATCTCACTTTTTTACACAGAAATTGTGTAGTAAGTTCATTCTTATTTAATATACCACCTATTTATTTTTTACAAATGAATATTTTTTTACTGGAACGTTTTAAATACACATAACCTTTGAGTCGATGTGAAATAATGTTTTGTTCAAACTTAAAAGTTGCGAATCTGACATATAGACAAAAAAAAAAAAAAAGAAAAAACTGGTTACCTTCATAAACATATTTTGCTAATTTATTGAATTTAATTATTTTCAACTTG >Transcript_9 len=747 CDS=158-560 exon=0-747 five_prime_UTR=0-158 gene=0-747 mRNA=0-747 three_prime_UTR=560-747 GTGAGGCTTAGTCTTGGTATAAATAGAGGGACTCTGTCAAAACAAATATTTTGAACTAGACTCGAATTCTTCATAATTCTATTCACTTGAGTGTTTATTTTTTTTAACAATGCCATTACATTTACGAGATATGTGGATATCCACTGACGATTATAAGGATGTTTTACTTACGTGTCCTGTGTGTTCAAAGAAGACTGGTACGAGAAATAAACAAGTTGAGTAGTTTCGAAAGCAATTGGCTCTTTCTTTTGTTTTTAGTCCGAGTATGTCGTCAGTTGAAAACCGTAACGGTTCTCATTGTGCCTGTTCTTCCGGTTTATACGAATAAGGTACTTCGTTGTTCTCAGTGTGACTGGCACGAACCAGCAAACTTGGATTCGATTTATCAAAGGAGTAGTCATGATGATGATCTTCCTACCATTAAGGGTTCTGATGCTAGTACTCAACAGTATGAAAGAAAAACTTATATTACCGATGCTAGTCCCGAATCTCAGAATCTGTTTTTAAGCAAAAGTAAAGAGGAGGGAGTTATCTTCTTATGCATACAAGTAAGCTTTTAACCTTGATTCTATTTATTCACTTTTACCATTTACTACTTTCGCAAATTCCTGTTTTTTGTTGGGGATATGAAGGGGAATATAAGGGTAAAGTAGATGAAATGGATGTATTTGAAAGTTGATTTGGATTCGATTTATTACTTTGAATCCCCGTTTATTATTATACGTTTATGTCGTTTTAAAGAAAACC ->Transcript_10 len=979 CDS=196-637 exon=0-979 five_prime_UTR=0-196 gene=0-979 mRNA=0-979 three_prime_UTR=637-979 +>Transcript_10 len=979 CDS=196-637 exon=0-979 five_prime_UTR=0-196 gene=0-979 mRNA=0-979 hmm_matches=Pombe_5TM:199-340,Pombe_5TM:355-598 three_prime_UTR=637-979 AATAATAAACAAAATACGAGTCGCTAATTTTTGAAACTAATCGCTTCCAACAACTGTTTCATTATAACTTCACCATTTTAATATTGTCCCCAAACAGCATGATTTAATTCTCTTTCACTAATTTCATACCACACAGGACACGTAAGTAAAACATCCTTATAATCGTCAGTGGATATCCACATATCTCGTAAATGTAATGGCATTGTTAAAAAAAATAAACACTCAAGTGAATAGAATTATGAAGAATTCGAGTCTAGTTCAAAATATTTGTTTTGACAGAGTCCCTCTATTTATACCAAGACTAAGCCTCACAGTGAAATATTGTCTAGCAGTAAAATTGCTGATTTATTTATTATATTGTTGGTACATTTACTCGGAAGTACCATCGGCTTCATCTAAATTCCGATCCTTTACATTTGGATGCGTCGTAGTATATCATAACAAATTTTTTCCTCGTTTCATTAGAACTCACTCCATTAACTCCATTAGAACGTTTTCTAAATTTCAAGTCATTATACTTTTCTCTATTGAGAAAGTCACTAGGTCAGAAAGCAAGAATCATTCTTACTCGAAAACCGATATTAGTGATCTGCACCAGGGCTATAATAATCCACCATCAAGATTCATATCACGATAACAATTCCATAGTATCTTGCTATATACGTGTAATGAGTATTCGATACTGGCTTGATTGCTATTTCTCCCTTGCTTGTAATCGTAAAATTGACTTGAAGATCTAAACCTTCTAATGCAATCATTGGAATTCTGCCTAACCTGATCAAATATGGCTTGATCACCGTTATGTTAAACCAGGAAGCTATGCCAATCAGTACGATTGTAACTTACAAAAAAATATAGCACAACGACATACAACATTATGGTACAATAAAGAGGACTTGATATATTAAGAACGAGGTTCAGTTTGTGCTCCGTTTATATTATTGTATTTCTATATATGACATTACTTGATGCAATCGCT ->Transcript_11 len=438 CDS=0-438 exon=0-438 gene=0-438 mRNA=0-438 +>Transcript_11 len=438 CDS=0-438 exon=0-438 gene=0-438 mRNA=0-438 hmm_matches=Methyltransf_23:21-342,TPMT:27-252,Methyltransf_31:30-258,Methyltransf_18:30-276,Methyltransf_25:36-267,Methyltransf_12:39-279,Methyltransf_11:39-279 ATGAATCTTGTACAACTGGGGAAATTACATGAGAATGTATTAGATGCCGGTTGTGAACCAAATAGAAATGCTAGATATTTAGCCAGTCTTGGATATAAAGTCGTGGGTATTGATATTTCCGAAAGGGCTATTTCTAAAGCAATCGATAAAACATCTAGTGAAAAAAGTAATGTCAACTTTAATCAACGCGATTTTTCAAGATTAAATGAATTCAAGGGGCATTTCGACACTGTGATTGACATTGGTTGTTTTCATTCAATTCTAAATAGTGATCATGAGCCACACACAGCTTCGTTAAGTCATATATGTCACTCTGATAGCTCCGTTTTCCTAAGAGCGTTTAGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCTTTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAA >Transcript_12 len=681 CDS=0-519 exon=0-681 gene=0-681 mRNA=0-681 three_prime_UTR=519-681 AGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGTGAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACCGGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGATTCAATGAAACTATTATAAACCT ->Transcript_13 len=615 CDS=0-615 exon=0-615 gene=0-615 mRNA=0-615 +>Transcript_13 len=615 CDS=0-615 exon=0-615 gene=0-615 mRNA=0-615 hmm_matches=Vel1p:30-612 ATGATTTTCAAAAACTTAATATCTCTCTTTTTCATTGGGCTCGCTACCGCCATACGCTTCAACCTCACTGATCTTGAGTGTAGTAGACTACGCGGTCCGCATTGTGGTACGTATCTACTGAAAGTAGTAGGAACGAATGCTACATACGTTGGTGAAAAATCATTTATAGGTCTTGATGCTTTGACTGAAAGTAAAGGTGAATTTTTTCAGCGTATGTTGGAACAAGAACCTCGACTTATTCCACGTTTGTTTACGATAGCTGAAAACGACACGGCCAACTTTACTCCCTTGACATTTACAACGTATTTGAAAACATGCAATCCTCAAAGTATTGAAAATGCAATGATCCCTTTTGTGAATACTGTTACCAGTGAAATTTCTTTTGATGCATGGGCGTATACAGCACAAAATTCAAGTCGGATAACGGGTCTTAGCAACCAACTGATGAATTCTACTCTATATAATGTTCAAGTAGCAACATGTACTCCCGGATTCTCTGCGTTATTGTTAGATAGTCCTACAATCAATGTTTTTAATAACGAGGAAGGCATGCCAAGTTGGTGTCAGCCCATTGAACTTATACCAGTTTGTCCTTTGGATGAGGGATTCAACTGA ->Transcript_14 len=607 CDS=0-585 exon=0-607 gene=0-607 mRNA=0-607 three_prime_UTR=585-607 +>Transcript_14 len=607 CDS=0-585 exon=0-607 gene=0-607 mRNA=0-607 hmm_matches=DUF999:15-432,DUF999:480-510 three_prime_UTR=585-607 TACAATGAGTTATTTATGGTAAGAGATACTCGTAATGTGGACCTGGAGCGGGGACTTGAATTGTGTAAGCCTGAAAAGGTAAACAAACAAAATCTCTTTACCAACATCATCAAGCCTCAAAAAGATAAAATAAACATTAAGACAGATAAAATAAAGTTCTTTTTAAATAACCTTTTTACTGAATTTTCTAAATTTCATGATAGTTGTTATCCTGATGGTAGGATTTCTACCCGCAGTAAACTTCGTTGGCCCTTGCTTATTATTTGGTGTATTTTGATTGTTTTCGCAATAGACAAGAACTTTGAAGTCAAAGATTTTCTTTCAATTTGGATAAATGAAAGTTTTATAAATGAAAATCGGTTTTACAGTGAAATTTGGGGGCCTATTGCTATTTACATTTGTTTGTTTGTTTTATTGTTGCTTGGTTTAATTTACTGCTCCAAGATTGTTGTAAAAGCTATACCATTGATCAGTATAGTTATAGCAGCGGTCGTAGTAATTATCGCGGTGGCTATGGTTAAAATTTTATACATCTGCCATTGGCTTCTACAAAATTTTAATTTTGGCTTTCGGCATAAAAGTTAAGCCATTGGGAGACACTCTTCCT ->Transcript_15 len=1251 CDS=0-1251 exon=0-1251 gene=0-1251 mRNA=0-1251 +>Transcript_15 len=1251 CDS=0-1251 exon=0-1251 gene=0-1251 mRNA=0-1251 hmm_matches=PA14_2:177-180,PA14_2:384-477,PA14_2:831-1182 ATGAACTTCTTTCTTTATTTTCGTACCATCTTTCTCATTCAACTATATTTTTTTAACTACTCCACATTTGGTTGTTCGGCAAGCTCAACTAGTGTACAAAGTGACACAACAAACCAAGTATCTGTTTCATGTCCAAAGTATACCACTATTTACACATCAGGAACGTCTCCAGACACAAAAACAATATATCCTGAATCCACCTCGACTAAATCCATCACAACAAGCACGCAATCGCACAGCTCTCCCGTTATCGTTGTGTCCACAGTAGGAACTGTTACGGAAACAACTATTTCTGGTTCCACTGAATATACCACAACGATTCCCGCAGAGGGCATTACATCTGGAACTGTCGAAATAGTAGAACCAACTGCAGGAACAGTTACTGAGACTATAACAAGTGGTACTTTACCATTTACTACTACGCTAGCACAAGCTAGTGGTACTGTTTCAGGAACTGTCGAGATAGTAAGTCCTAAAAATAATCCTACCACCGTATATAGTGGTACGGTCGCTACTACGGAGACGTTTAGCTCATCCACAGTTGTTGTTATTCCAACAGCTATATGTGATGGCGTTCGTGGTTTAGAGTATGCTGTTTATGATTATACAATTTCATCATCAATGAACGAATTCTGTTATCCTAAAAACGGTCAAACTGATGTCTTTGCTTTTAATGAGCCCGCTTACTTTGGTTCCTCAGACTTGGATCAGTCATCTCCATTGTTTACCGGTGTGTTTAGTTCTACAGATGACATACCTGAGTGGGCATCGTCTTGGTATCTCCCACCGTATCCACCACAGGCTTCAGATATGGCTTCGACCTACTGTGCCTGTAAAGTAATTGTTTACCAGTTCTTTCTACGAATCCCAGAAACTGATACCTACACCCTAGTCGTTAACAATGTAGATGATGTTTTCTTTGGTTGGTTTGGTGATAAAGCTATTTCTGGTTGGTCCAATAATAACTTTGATGCGTATTCTTATTGGCATGAGTCGCCTAATATGGGTTTAGGAACTGTGGGCATGGGAAATTTCACTGTAGGCAATTATCCTGAAGGCTACTTTTTGCCCGTTAGATTTGTTGTAGCAAATGGAGCATATATCGGTGGATTTGATTTTTACTTTACTTCTGATTCAACGGGTCCACTTGCTACTACCTCTTATTCTTACACGAAAACATGCACTCAACAATTCTTACCATTTGGTCAAGGTAATGGCGGTGTAAACGGGCCAACGGAAAAATTGTCGTAA ->Transcript_16 len=825 CDS=60-771 exon=0-825 five_prime_UTR=0-60 gene=0-825 mRNA=0-825 three_prime_UTR=771-825 +>Transcript_16 len=825 CDS=60-771 exon=0-825 five_prime_UTR=0-60 gene=0-825 mRNA=0-825 hmm_matches=adh_short_C2:105-510,adh_short:75-528 three_prime_UTR=771-825 TATACTAGTTACCAAACTATTTAAAAAGCTTATATTTTGCAAACATTATTTTTTGCTACTATGCGTGAACCCAAGAATGCCAAAGTGCTAAGCAGACTTGAAAATGTTCTGGTGACTCAATTAGATGTAAATAACTTTTCTTCGATTAAAAAATCTGTGGAAAAAGCAATTTCGCATTTTGGTAGAATCGACGTGTTACTAAATAACGCTGGCTATTCCGTCTATTCTCCACTTGAAAGTACTACCGAAGAACAAATTCATAACATTTTCAATACAAATGTGTTTGGCGCTTTGGAGGTTATCAAAGCAATAACTCCTATCTTCCGCTCACAACATAATGGAATGATTATAAACGTATCATCGATCGGAGGAAAGATGACATTCCCACTTGGATGTTTGTATTATGGTACCAAGTATGCAATCGAAGGTATTTCTGAAGCTCTGACTTGGGAAATGCAAAGCATTGGTGTAAAAGTCAAGATTATAGAACCTGGTTTTACAGCAACTGAATTTAGGGTTGAAGAGGGTGCAGGTAAACATTATGCTGAGTACGACAATCTGAAACAAAAGTTGTACGAAGACTTGCTACCTAAATTGAAAACAGCTACACCACCGCAAAAAATCGCAGAAGTGATATTGCAAGCGGCAACGGATGAAAGTGATGAGCTACGATACCCTACTGGAGATTATGTTGTTGAATGGATGGCATTGAGAAGCAAAGTTGATGATGCTACATTTTTAGCAACACACCGAAAACAAATGGGTCTTTAAACGATTTCGTTCTACCAATTGAATATTCCTCTTTTACTGTTTTTTGTACCAAAC ->Transcript_17 len=2461 CDS=239-2261 exon=0-2461 five_prime_UTR=0-239 gene=0-2461 mRNA=0-2461 three_prime_UTR=2261-2461 +>Transcript_17 len=2461 CDS=239-2261 exon=0-2461 five_prime_UTR=0-239 gene=0-2461 mRNA=0-2461 hmm_matches=PLA2_B:632-2081 three_prime_UTR=2261-2461 GCCTAACGTTTGCGAATTTTGCAGCAAGCATTGTTTCGTATTTAAGATCACTTTTGTAGACAGATCTTGAGATAACGCGACAAATTTTGGGGCTTTTAAAGTTCGGAATTCTTTCTTCCGGATCAGAGATGTGTAGTGCGCCAGAGTAATATATGATTTAATATTCTTCCGTGTAGTACACTTTTCCATGCGAACTTCAATTTTTACAGCTTTTGTTTGAACTTTTTTTATTTTCTGCAATGTATGTCAACTATATTGGACTCTTTGCTTTCGTTCAAATTTCGTTGACGTTAGCTTATCCTCCCGGTCGTGTGGAGATTTCTGAAATATATGATTTTGAAGAATCTAGTTCGTATAAAGGACAAGATATTGATACATCCGTACTTTACACTTTGTCTAAAAGGAAACCTGCGCTCGTAAAACGAAGTACCGACGCTTCGTATGCCCCTTTCAATGTGACCTGTTCAAACGACAATCTGTTGAGGCCGGCTTCTGAAGGTTTAAATGAGGGCGAACAGAGCTATATCAACAAACGTATTTCTAAGGTTAACAGTGAACTCCGATCATTTATTTCTAAGACAGGTTTGAATGTTGACTTGGATAAGGTGGTTAACAGCTCGGATGGTCCACGTTTAGGAATTGCATTCTCAGGTGGTGGGTTACGGGCGATGGTTAATGGAGGTGGTGCATTCAATGCTTTTGACTCAAGATTCGAGAGTGACTCTCCACTTTCTGGTCTGCTGCAATCCGCGATGTATATCAGCGGTCTTTCTGGTGGTTCATGGCTTGTTGGATCAGTGGCTATTAATAATTTTACGAATATAACATACTTACGTGATAATGTCTGGAATTTGGAACATAGCGTTTTTGCTCCTCATGGGGATAATGTCATTGAAAATTTGAATTATTATAATGACTTGCGCAAAGAAATTGATCAAAAGAAACATGCGGGCTTTGACTGTTCTTTGACGGATTTATGGGGACGTGCTTTGTCCCGTAAACTTGTTGATGCTGAAAGGGGAGGACCAGGCATTACATATTCCAGTATGAGAAATCAAAGCTGGTTTCAAAATGCTGATTATCCTTATCCCATCATCGTTGCGGATAGCCGATTAGAAGAAGAAACGGCCATCCCTGCCAATACCAGTATCTTTGAGTTCACGGCGTATGAATTTGGTACATGGGACAATGGAATTAAAGCATTCATTCCAATGGAATATGTGGGAACTCACTTGTTGGATGGGGTTCCACCCGATAAGTCTTGCATTCATAACTATGATAATGCAGGTTTTGTTATGGGCACTTCAGCTACTTTATTCAACTCTTTTCTTCTTGACTGGAATGAAAATGTCAAAAAGAATGATACCTATTACGATATTCTTCATGCGATTCTTGAAGATCTTTCTAAGCATCAAGATGATATTGCTCCTTATCCCAATCCTTACCAAAATTATACTACTTCCAATACCTCTGTAGTGAATGCGTTCGAACCGTATGATACTATTGATCTAGTTGATGGTGGTGAGGATAGGGAAAACATTCCCCTTTGGCCTTTGTTACACCCACAACGATTTGTGGACGTTGTATTTGCGATTGATTCGACTTATAATGATCCTTATGGTTGGCCCCTTGGATCTTCCATTGTTGCTACATATGAGAGAGTTGTAACCTTTAATGCGAACAAGAGTGTTGATGTGCGTGGATTTCCATATATTCCGGACGAAAACACTATTATCTCTTTGGGACTAAACACTCGTCCTACGTTTTTTGGATGTGACGGTAAAAATACTACAGCAGGAAATCATGATGTAGACAATAATACCCCACCTCTCCTTGTATACTTTCCAAATTACCCTTGGACTTATTATTCCAATATATCGACATTTACTATGAGCATGGACGACAAGATGGCTAATGGAATTCTTGAGAATGCATTTATGTCGACTACGCAAAACAATAATGAATCTTTTGCAGTTTGCTTAGCATGCGCTATAATTCAACGCTCTTTGGAACGCAAGAAATTGAGTACTCCTACCCAGTGCTCTTCTTGTTTCCAAGAATACTGTTGGGACGGAACTCTTGCAACTAGTACGGCTTCTGTATATGATCCTACCGTAATGTCTGCTGCGACAACATCTCGTGCACCGTCAGGCACAACCTCGGGTACAGCCTCTAGTACAACATCTTCATCTGTAGCATCAGCCACTCCCACTCATAAACATTGGTGGGACTCGATTTTCGAAGCGAAAGAAAATCCGTAAAAAGATTCCATTGATGTTGTTTCAATGGATTCTCAGGCATGTGAGAAATTTAGAATAGATAGATTTACCTTTATTGTACTTGGTTACGAATTCGTTATGAAAGAGAACTAAGGATTTTCCTCATTCGTGAGACTGCTCAGTTAAACCCTTTACGTTTGATGGAGCTATGTAAACGGGTAAATGAATAATTTGTTATCTCT ->Transcript_18 len=2836 CDS=946-2578 exon=0-2836 five_prime_UTR=0-946 gene=0-2836 mRNA=0-2836 three_prime_UTR=2578-2836 +>Transcript_18 len=2836 CDS=946-2578 exon=0-2836 five_prime_UTR=0-946 gene=0-2836 mRNA=0-2836 hmm_matches=Na_H_Exchanger:1216-2473 three_prime_UTR=2578-2836 ACGGTTTATTGTTTAAAGGCTAGAAGTAATGAAAATCGTCTTTTATAAAAGTCTAAATAGTATGAAATTTGATATTAAGTAAGCGAGTGGCCTTAAACGCTCTATATTCTGGATCTGCAACTCATGGGGTGAGACTCGGTTGTGTCTATGTAACTAACCTTGCCACCACATTGTGCATGAAAGCAAATGATTCATTTAAACGTAAAGTGTTTCTCGTTTTATTTGACATGAAAGGAGCTCTTGAATTCTTCCTAAGTTGTTCATGAGGAGAAATTGTCCACTGAAAAAGAACAAGTTCAAACATTCGCTCATGACTTTTCTCCTGCCCGTAATCGAAATACCAAATTCCTTCTGTGTTCGGTAGTCAATACCTTGGCCGTTATCTCATCAATTAACAAGTTTCCCCCACCAATGTGATTATAGGCCTGGCAATTCCTTTGACAGAACGTGTCAACTGGATATTTGTGTAATTTCGTCGTTCTCGTTAATCCCATACAGTTTTTCATTGCTAATTTAACTCTACATATGGTTGAATTACAAGAGTGCTTGTTTTATGCTCACTACTTCCTTTTTTAAGTAGTATAAAAGATTGACTTCTGTTACACTAGTAATCAAATCCTATAGAAAGAATTTTCAATATTTTTGATTTATTGCCACTTATGTCATATTGAGATAAAATGCCTTAATCCAATCAGGTCTTTTTAGCTAAGTTATAATCAAAGCTTTTTGCTGCCGAGGTATTAATAGCTTACAAGTGAGTACACAACACCCTTTCAATCAATTTAATGGTGCTAAATTTATATAAACATACGATGTATAACAATCGCACAATATTTACAATTCACTATCCTGCTAAAATTGTATAAAAAAAAATAATATAACAGCCCACCTCAAATGTGCTTAATCAGTCTCAGTGAATTTAAAATTGAATAGTTACTTAAAAGGCATGTTTTTTAAGTTGATAAGCGTTAAAACCCAAGTAACAAGCTTTGTTACTCCAATCAAAAAGATAACTAAGGTACCCCGGTCCTCAAGTATAAACCACAGGCATGCACGCATCAGTCCGTGGCTAACTGTATCTTTTGCCACATTTTATGTCGAATACTCTAAAAAAAATATTATAGGAATTTATTACAAGAAAACATTCTCTTGTGGATATTGCCTAATTACTATGGGCTGGAGACAACTTGATATAGACAAAGTCCATTTAGCTTTAATAGTGGCCGGGGGATTTATAACATTTTTCTGCTATTTTTCAGAAGTTTTTCGAAAAAAATTACTAGTTGGAGAAGCTGTTCTTGGAAGTATCACTGGATTAATATTTGGGCCTCATGCTGCTAAACTCGTAGACCCTTTTTCCTGGGGTGACCATGGAGATTACTTGACAGTAGAGATTTGTAGAATCGTACTTGATGTGCGTGTGTTTGCTTCTGCAATAGAACTCCCCGGTGCATATTTTCAACATAATTTTCGAAGCATCATTGTAATGCTATTACCAGTTATGGCTTACGGGTGGTTAGTTACAGCTGGATTTGCATATGCATTGTTTCCACAAATTAACTTTTTAGGATCTTTGCTGATCGCAGGATGTATAACTTCTACTGATCCTGTTCTATCAGCATTGATTGTAGGAGAAGGTCCATTAGCTAAAAAGACTCCTGAACGGATTCGGTCTTTATTGATCGCTGAGTCTGGATGTAATGATGGAATGGCGGTTCCTTTTTTCTATTTTGCTATCAAACTTCTTACTGTTAAGCCATCGAGGAATGCAGGGAGGGATTGGGTGCTGCTTGTTGTGTTGTATGAATGTGCATTTGGTATATTTTTTGGGTGTGTAATAGGGTATCTTTTATCGTTCATTTTAAAGCACGCTCAGAAATACCGTTTAATTGATGCTATTAGTTATTATTCCCTTCCGCTAGCGATACCTTTATTATGTTCTGGGATAGGAACTATTATTGGAGTTGATGACCTGTTGATGTCCTTTTTTGCTGGAATATTATTTAACTGGAATGATTTATTTTCCAAAAATATATCTGCTTGTTCTGTACCTGCTTTTATTGATCAGACTTTTAGTTTACTATTTTTTACCTATTATGGTACAATCATTCCCTGGAATAATTTTAATTGGTCTGTTGAAGGCTTGCCTGTTTGGCGTTTAATTGTCTTTAGCATATTGACTCTAGTTTGTCGTCGATTACCGGTTGTATTTTCGGTGAAGCCTTTAGTTCCGGACATTAAGACATGGAAAGAAGCCCTTTTCGTTGGACATTTCGGACCAATAGGGGTTTGCGCAGTTTATATGGCATTTCTTGCAAAATTACTGTTGTCCCCGGATGAAATTGAAAAGAGTATTTATGAATCAACTACAGTATTTTCAACACTTAATGAAATAATTTGGCCGATCATTTCGTTTGTTATCTTATCCTCAATCATTGTTCATGGTTTCAGTATCCATGTATTAGTGATTTGGGGAAAGTTAAAAAGTCTGTATTTAAATCGAAAAGTCACCAAGTCCGATTCCGATTTGGAGTTACAAGTAATAGGGGTTGATAAGTCACAGGAAGATTACGTTTAGGAAAGCTCTTTTAATGTCAATTCGGATTTCCAAATTATTTTCAAATGTATTGTGAATCGCTGTCTCTGGTCAAAAAGATTACTGCACTCATATTTTGAAATTCCTTCTATAGTTGATATATACTATAAGATAAGTGATTCTCAGAATCACAAGGCTAACCACCAACAGGGATGGAGTGTATATTTTTGTTGTACATATATATTATCTACAATAGAGTAATTTTCGGCTTCTATAATTCATTTATTTTCTTACTACTCT ->Transcript_19 len=1250 CDS=215-1151 exon=0-1250 five_prime_UTR=0-215 gene=0-1250 mRNA=0-1250 three_prime_UTR=1151-1250 +>Transcript_19 len=1250 CDS=215-1151 exon=0-1250 five_prime_UTR=0-215 gene=0-1250 mRNA=0-1250 hmm_matches=CRCB:236-566,CRCB:710-755,CRCB:782-1103 three_prime_UTR=1151-1250 GGCTTTAAGTCTTTTTGAAAGAATTTTCTTTTTGTTTTGTTTTATTAACCTAAGTCGATTTAAAATACTTTTTCTCTCTTTATTTTAAGAAATTACTATAGTCTCGAAGCCTTTATCGAGGCTATCGCTCCGTATATATAGAATTGTGATAGACACTCCGGAATAGTTGCATTTTCCTTCTAATCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGCTATTAACACAGTCTTACTTTTGTATAATGTCTATGTTGGGGACGCTAGCTCGTCTAGGACTTACTGCATTAAACACATACCCAGGTGCACCGTTTTCTGGACTTTTATGGGTTCAATTTGTTGGATGCGTTATTATGGGATTTTGTCAGACAGAGTCTGTTTTCTTTCCTCGACCCAAACATAATGCTACTTTTTTGCTAGCCATTACTACAGGTTTTTGTGGATCTCTTACAACGTTTTCTTCTTGGATGTTGCAAATGTTTACAGGGATGGCTAACTTGGATCCATTTGAACGTAGGGGCCGAGGCTATTCATTTTTAAGTGTGGTTTCCGATTTTATGGTAACTATGTGCATTGCGATGTCCAGCTTAATATGGGGGAAGCAGATTGGAAAAACGACGGGACAGTGGAGAATTGGCAAAGTTGCATTTGCCTGGCCTATCCCGGCGCACACGCATATCGTAGTGCGGGTATTACTTTTGTTACTCTCGATTTGTTTTTTTGTTGGTGCAGCATTTTATACGGCATATACAACCAATGTGACACATCGTGGCATAGGTTTTAGTCTAATATTCTCTCCTTTTGCTGCCTTGACACGTTTGTATCTTGCGCGATTCCTTAATTCACCTCAATATTTTATTCCCTATGGAACTCTTTGTGCCAATGTCTTTGCTACACTTTTGCTTTCTATCATGTACATGATACCACAAATCACACACTGCACTCCTGTGTCTAGAAGTGTGATGTATGGAATCCAAAACGGATTTTGTGCTGTACTCTCTACCCTTTCAACATTCTCCAACGAACTCCACACAATGCCTATAAAACGAGCATATATTTATTGTATAATTTCAGTTGCTATTTCCTTTTCAATATGTGTCATTGTCGATGGAGCTACTGCATGGGGTCATGGTTATACTGAAAAGTATTAGACTTACTATTAAATTAGAGATTTTTTTTTTAAAGTTTTTGTATATAATTAAAGTATTCATTCTTTATCTTTAATATTATTTATTTTTTTTTGTTTATAA diff --git a/dammit/tests/test-data/pom.20.udbs.dammit.gff3 b/dammit/tests/test-data/pom.20.udbs.dammit.gff3 index b9051960..74dcf108 100644 --- a/dammit/tests/test-data/pom.20.udbs.dammit.gff3 +++ b/dammit/tests/test-data/pom.20.udbs.dammit.gff3 @@ -1,9 +1,15 @@ ##gff-version 3.2.1 +Transcript_0 BUSCO BUSCO_ortholog 1 5662 8.400000e+01 . . ID=busco:c175e99ae828326adaedd0e8e20181c562f2cc2a;Name=367596at33208a;length=154;status=Fragmented +Transcript_0 HMMER protein_hmm_match 3604 4089 2.100000e-10 . . ID=homology:84650fc4aa4df19d561278cef53cd46b3c22f7a4;Name=DEAD;Target=DEAD 10 174 +;accuracy=0.75;env_coords=3580 4092;Dbxref="Pfam-A:PF00270.25";Note=DEAD/DEAH box helicase +Transcript_0 HMMER protein_hmm_match 4207 4548 3.200000e-18 . . ID=homology:ee81caa0c6870a9a9014dd352cc1c65031b1a930;Name=Helicase_C;Target=Helicase_C 8 105 +;accuracy=0.87;env_coords=4186 4548;Dbxref="Pfam-A:PF00271.27";Note=Helicase conserved C-terminal domain +Transcript_0 HMMER protein_hmm_match 5218 5274 1.100000e+04 . . ID=homology:f97b334d076a68dd960fa2da62071da10c0973b1;Name=Helicase_C;Target=Helicase_C 16 34 +;accuracy=0.78;env_coords=5203 5307;Dbxref="Pfam-A:PF00271.27";Note=Helicase conserved C-terminal domain Transcript_0 shmlast.LAST conditional_reciprocal_best_LAST 1 1887 0.000000e+00 + . ID=homology:94a770b951c0d15c4b3d0d2b57d07c3851565147;Name=SPAC212.11|tlh1|I|RecQ type DNA helicase;Target=SPAC212.11|tlh1|I|RecQ type DNA helicase 1 1887 +;database=pep.fa Transcript_0 transdecoder CDS 1 5661 . + 0 ID=cds.Transcript_0.p1;Parent=Transcript_0.p1 Transcript_0 transdecoder exon 1 5662 . + . ID=Transcript_0.p1.exon1;Parent=Transcript_0.p1 Transcript_0 transdecoder gene 1 5662 . + . ID=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3A3prime_partial%20len%3A1888%20%28%2B%29%2Cscore%3D464.77%2CHelicase_C%7CPF00271.27%7C3.2e-18%2CHelicase_C%7CPF00271.27%7C1.1e%2B04%2CDEAD%7CPF00270.25%7C2.1e-10 Transcript_0 transdecoder mRNA 1 5662 . + . ID=Transcript_0.p1;Parent=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3A3prime_partial%20len%3A1888%20%28%2B%29%2Cscore%3D464.77%2CHelicase_C%7CPF00271.27%7C3.2e-18%2CHelicase_C%7CPF00271.27%7C1.1e%2B04%2CDEAD%7CPF00270.25%7C2.1e-10 +Transcript_10 HMMER protein_hmm_match 200 340 1.300000e-10 . . ID=homology:360d91ea72c98f8edd46f422390080235e870699;Name=Pombe_5TM;Target=Pombe_5TM 1 52 +;accuracy=0.95;env_coords=200 352;Dbxref="Pfam-A:PF09437.6";Note=Pombe specific 5TM protein +Transcript_10 HMMER protein_hmm_match 356 598 5.100000e-26 . . ID=homology:79cc2e997715c97105ac3dff1b1fd643258a1218;Name=Pombe_5TM;Target=Pombe_5TM 118 220 +;accuracy=0.93;env_coords=341 634;Dbxref="Pfam-A:PF09437.6";Note=Pombe specific 5TM protein Transcript_10 shmlast.LAST conditional_reciprocal_best_LAST 66 211 3.300000e-103 + . ID=homology:5bddc141f52e14a4e285ddcb7c87aea1cbd54ce4;Name=SPAC977.02|SPAC977.02|I|S. pombe specific 5Tm protein family;Target=SPAC977.02|SPAC977.02|I|S. pombe specific 5Tm protein family 1 146 +;database=pep.fa Transcript_10 transdecoder CDS 197 637 . + 0 ID=cds.Transcript_10.p1;Parent=Transcript_10.p1 Transcript_10 transdecoder exon 1 979 . + . ID=Transcript_10.p1.exon1;Parent=Transcript_10.p1 @@ -11,6 +17,13 @@ Transcript_10 transdecoder five_prime_UTR 1 196 . + . ID=Transcript_10.p1.utr5p1 Transcript_10 transdecoder gene 1 979 . + . ID=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A147%20%28%2B%29%2Cscore%3D82.86%2CPombe_5TM%7CPF09437.6%7C1.3e-10%2CPombe_5TM%7CPF09437.6%7C5.1e-26 Transcript_10 transdecoder mRNA 1 979 . + . ID=Transcript_10.p1;Parent=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A147%20%28%2B%29%2Cscore%3D82.86%2CPombe_5TM%7CPF09437.6%7C1.3e-10%2CPombe_5TM%7CPF09437.6%7C5.1e-26 Transcript_10 transdecoder three_prime_UTR 638 979 . + . ID=Transcript_10.p1.utr3p1;Parent=Transcript_10.p1 +Transcript_11 HMMER protein_hmm_match 22 342 1.400000e-11 . . ID=homology:720816922e5720ad3a3b08c8ec4dcec41f989599;Name=Methyltransf_23;Target=Methyltransf_23 21 120 +;accuracy=0.79;env_coords=1 420;Dbxref="Pfam-A:PF13489.2";Note=Methyltransferase domain +Transcript_11 HMMER protein_hmm_match 28 252 7.500000e-06 . . ID=homology:fef38a04a9928995794ff4003df57fb2dc428ba4;Name=TPMT;Target=TPMT 38 126 +;accuracy=0.66;env_coords=7 360;Dbxref="Pfam-A:PF05724.7";Note=Thiopurine S-methyltransferase (TPMT) +Transcript_11 HMMER protein_hmm_match 31 258 6.100000e-10 . . ID=homology:efdb8560b80a01eed3e13b9b49d21ffc75e6459a;Name=Methyltransf_31;Target=Methyltransf_31 5 85 +;accuracy=0.84;env_coords=22 387;Dbxref="Pfam-A:PF13847.2";Note=Methyltransferase domain +Transcript_11 HMMER protein_hmm_match 31 276 5.400000e-09 . . ID=homology:b83291ea939d431142fac383446959f9dc24253b;Name=Methyltransf_18;Target=Methyltransf_18 3 87 +;accuracy=0.8;env_coords=28 345;Dbxref="Pfam-A:PF12847.3";Note=Methyltransferase domain +Transcript_11 HMMER protein_hmm_match 37 267 8.600000e-09 . . ID=homology:15a224e5b577b0264be925afd2a9fa31e69e462e;Name=Methyltransf_25;Target=Methyltransf_25 1 82 +;accuracy=0.88;env_coords=37 354;Dbxref="Pfam-A:PF13649.2";Note=Methyltransferase domain +Transcript_11 HMMER protein_hmm_match 40 279 1.800000e-09 . . ID=homology:78d115e66b6c61c97055fab1b8a6265814cea958;Name=Methyltransf_12;Target=Methyltransf_12 1 80 +;accuracy=0.74;env_coords=40 315;Dbxref="Pfam-A:PF08242.8";Note=Methyltransferase domain +Transcript_11 HMMER protein_hmm_match 40 279 7.900000e-10 . . ID=homology:e61b3cf4766a563d73c1f0590712ce9a66d146d5;Name=Methyltransf_11;Target=Methyltransf_11 1 77 +;accuracy=0.85;env_coords=40 333;Dbxref="Pfam-A:PF08241.8";Note=Methyltransferase domain Transcript_11 shmlast.LAST conditional_reciprocal_best_LAST 1 145 4.300000e-109 + . ID=homology:a69c6cd647c5cc147e84d4553dbeab70cff38442;Name=SPAC977.03|SPAC977.03|I|methyltransferase (predicted);Target=SPAC977.03|SPAC977.03|I|methyltransferase (predicted) 1 145 +;database=pep.fa Transcript_11 transdecoder CDS 1 438 . + 0 ID=cds.Transcript_11.p1;Parent=Transcript_11.p1 Transcript_11 transdecoder exon 1 438 . + . ID=Transcript_11.p1.exon1;Parent=Transcript_11.p1 @@ -22,22 +35,30 @@ Transcript_12 transdecoder exon 1 681 . + . ID=Transcript_12.p1.exon1;Parent=Tra Transcript_12 transdecoder gene 1 681 . + . ID=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A173%20%28%2B%29%2Cscore%3D104.11 Transcript_12 transdecoder mRNA 1 681 . + . ID=Transcript_12.p1;Parent=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A173%20%28%2B%29%2Cscore%3D104.11 Transcript_12 transdecoder three_prime_UTR 520 681 . + . ID=Transcript_12.p1.utr3p1;Parent=Transcript_12.p1 +Transcript_13 HMMER protein_hmm_match 31 612 6.700000e-107 . . ID=homology:25e04c02da322c661bcb7e475a4f11af32c0eebf;Name=Vel1p;Target=Vel1p 8 201 +;accuracy=0.97;env_coords=7 612;Dbxref="Pfam-A:PF10339.5";Note=Yeast-specific zinc responsive Transcript_13 shmlast.LAST conditional_reciprocal_best_LAST 1 204 2.700000e-155 + . ID=homology:3c4185a4986c931924c0b92956b14295ccf302f1;Name=SPAC977.05c|SPAC977.05c|I|conserved fungal family;Target=SPAC977.05c|SPAC977.05c|I|conserved fungal family 1 204 +;database=pep.fa Transcript_13 transdecoder CDS 1 615 . + 0 ID=cds.Transcript_13.p1;Parent=Transcript_13.p1 Transcript_13 transdecoder exon 1 615 . + . ID=Transcript_13.p1.exon1;Parent=Transcript_13.p1 Transcript_13 transdecoder gene 1 615 . + . ID=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A205%20%28%2B%29%2Cscore%3D126.49%2CVel1p%7CPF10339.5%7C6.7e-107 Transcript_13 transdecoder mRNA 1 615 . + . ID=Transcript_13.p1;Parent=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A205%20%28%2B%29%2Cscore%3D126.49%2CVel1p%7CPF10339.5%7C6.7e-107 +Transcript_14 HMMER protein_hmm_match 16 432 6.000000e-78 . . ID=homology:85b21689c5e713d50ca92d35457e5f9171d04c9b;Name=DUF999;Target=DUF999 1 143 +;accuracy=0.99;env_coords=16 432;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) +Transcript_14 HMMER protein_hmm_match 481 510 1.100000e+04 . . ID=homology:6b21eda2b5258ab5cc4805527e762b2f128a3f29;Name=DUF999;Target=DUF999 92 101 +;accuracy=0.55;env_coords=460 555;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) Transcript_14 shmlast.LAST conditional_reciprocal_best_LAST 6 194 2.900000e-143 + . ID=homology:bbbbb2217ab55d406588836a15266f0f6ec3bcd4;Name=SPAC977.06|SPAC977.06|I|S. pombe specific DUF999 family protein 3;Target=SPAC977.06|SPAC977.06|I|S. pombe specific DUF999 family protein 3 1 189 +;database=pep.fa Transcript_14 transdecoder CDS 1 585 . + 0 ID=cds.Transcript_14.p1;Parent=Transcript_14.p1 Transcript_14 transdecoder exon 1 607 . + . ID=Transcript_14.p1.exon1;Parent=Transcript_14.p1 Transcript_14 transdecoder gene 1 607 . + . ID=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3A5prime_partial%20len%3A195%20%28%2B%29%2Cscore%3D142.29%2CDUF999%7CPF06198.7%7C6e-78%2CDUF999%7CPF06198.7%7C1.1e%2B04 Transcript_14 transdecoder mRNA 1 607 . + . ID=Transcript_14.p1;Parent=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3A5prime_partial%20len%3A195%20%28%2B%29%2Cscore%3D142.29%2CDUF999%7CPF06198.7%7C6e-78%2CDUF999%7CPF06198.7%7C1.1e%2B04 Transcript_14 transdecoder three_prime_UTR 586 607 . + . ID=Transcript_14.p1.utr3p1;Parent=Transcript_14.p1 +Transcript_15 HMMER protein_hmm_match 178 180 4.700000e+03 . . ID=homology:127ef42ed898b79cc422bc7af762afb849b3f09a;Name=PA14_2;Target=PA14_2 97 97 +;accuracy=0.59;env_coords=55 291;Dbxref="Pfam-A:PF10528.5";Note=GLEYA domain +Transcript_15 HMMER protein_hmm_match 385 477 6.000000e+03 . . ID=homology:fda972fb3251c2815dc721d0473f7fbcc188c7b3;Name=PA14_2;Target=PA14_2 64 95 +;accuracy=0.48;env_coords=334 540;Dbxref="Pfam-A:PF10528.5";Note=GLEYA domain +Transcript_15 HMMER protein_hmm_match 832 1182 1.200000e-49 . . ID=homology:c2cfea5e0e1bbb10b9f093eb39a99a91da879316;Name=PA14_2;Target=PA14_2 1 115 +;accuracy=0.98;env_coords=832 1185;Dbxref="Pfam-A:PF10528.5";Note=GLEYA domain Transcript_15 shmlast.LAST conditional_reciprocal_best_LAST 1 416 1.976263e-323 + . ID=homology:3f9fd792943afae5b71c19f6a6348e97e0f632b2;Name=SPAC977.07c|pfl6|I|cell surface glycoprotein, adhesion molecule (predicted);Target=SPAC977.07c|pfl6|I|cell surface glycoprotein, adhesion molecule (predicted) 1 416 +;database=pep.fa Transcript_15 transdecoder CDS 1 1251 . + 0 ID=cds.Transcript_15.p1;Parent=Transcript_15.p1 Transcript_15 transdecoder exon 1 1251 . + . ID=Transcript_15.p1.exon1;Parent=Transcript_15.p1 Transcript_15 transdecoder gene 1 1251 . + . ID=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3Acomplete%20len%3A417%20%28%2B%29%2Cscore%3D268.06%2CPA14_2%7CPF10528.5%7C4.7e%2B03%2CPA14_2%7CPF10528.5%7C6e%2B03%2CPA14_2%7CPF10528.5%7C1.2e-49 Transcript_15 transdecoder mRNA 1 1251 . + . ID=Transcript_15.p1;Parent=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3Acomplete%20len%3A417%20%28%2B%29%2Cscore%3D268.06%2CPA14_2%7CPF10528.5%7C4.7e%2B03%2CPA14_2%7CPF10528.5%7C6e%2B03%2CPA14_2%7CPF10528.5%7C1.2e-49 +Transcript_16 HMMER protein_hmm_match 106 510 2.000000e-12 . . ID=homology:00e3681c9f0dafa06b5dc3ea643852510d9b2be2;Name=adh_short_C2;Target=adh_short_C2 46 184 +;accuracy=0.83;env_coords=64 669;Dbxref="Pfam-A:PF13561.2";Note=Enoyl-(Acyl carrier protein) reductase +Transcript_16 HMMER protein_hmm_match 76 528 9.100000e-36 . . ID=homology:f379157a96e8158f5aa86dbb6a941c1fb466bb44;Name=adh_short;Target=adh_short 37 191 +;accuracy=0.94;env_coords=61 540;Dbxref="Pfam-A:PF00106.21";Note=short chain dehydrogenase Transcript_16 shmlast.LAST conditional_reciprocal_best_LAST 21 256 6.300000e-174 + . ID=homology:669a1dd29f2b40aa7db12d129b95ccef21219987;Name=SPAC977.08|SPAC977.08|I|short chain dehydrogenase (predicted);Target=SPAC977.08|SPAC977.08|I|short chain dehydrogenase (predicted) 1 236 +;database=pep.fa Transcript_16 transdecoder CDS 61 771 . + 0 ID=cds.Transcript_16.p1;Parent=Transcript_16.p1 Transcript_16 transdecoder exon 1 825 . + . ID=Transcript_16.p1.exon1;Parent=Transcript_16.p1 @@ -45,6 +66,7 @@ Transcript_16 transdecoder five_prime_UTR 1 60 . + . ID=Transcript_16.p1.utr5p1; Transcript_16 transdecoder gene 1 825 . + . ID=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A237%20%28%2B%29%2Cscore%3D135.27%2Cadh_short%7CPF00106.21%7C9.1e-36%2Cadh_short_C2%7CPF13561.2%7C2e-12 Transcript_16 transdecoder mRNA 1 825 . + . ID=Transcript_16.p1;Parent=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A237%20%28%2B%29%2Cscore%3D135.27%2Cadh_short%7CPF00106.21%7C9.1e-36%2Cadh_short_C2%7CPF13561.2%7C2e-12 Transcript_16 transdecoder three_prime_UTR 772 825 . + . ID=Transcript_16.p1.utr3p1;Parent=Transcript_16.p1 +Transcript_17 HMMER protein_hmm_match 633 2081 7.100000e-204 . . ID=homology:58260bb20cdcf6a0926f9eefe737aa0793fb66b0;Name=PLA2_B;Target=PLA2_B 1 490 +;accuracy=0.99;env_coords=633 2084;Dbxref="Pfam-A:PF01735.14";Note=Lysophospholipase catalytic domain Transcript_17 shmlast.LAST conditional_reciprocal_best_LAST 80 752 0.000000e+00 + . ID=homology:02b94f4c02b2a78881d6e3cdddea00d4f99be7db;Name=SPAC977.09c|SPAC977.09c|I|phospholipase (predicted);Target=SPAC977.09c|SPAC977.09c|I|phospholipase (predicted) 1 673 +;database=pep.fa Transcript_17 transdecoder CDS 240 2261 . + 0 ID=cds.Transcript_17.p1;Parent=Transcript_17.p1 Transcript_17 transdecoder exon 1 2461 . + . ID=Transcript_17.p1.exon1;Parent=Transcript_17.p1 @@ -52,6 +74,7 @@ Transcript_17 transdecoder five_prime_UTR 1 239 . + . ID=Transcript_17.p1.utr5p1 Transcript_17 transdecoder gene 1 2461 . + . ID=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A674%20%28%2B%29%2Cscore%3D453.37%2CPLA2_B%7CPF01735.14%7C7.1e-204 Transcript_17 transdecoder mRNA 1 2461 . + . ID=Transcript_17.p1;Parent=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A674%20%28%2B%29%2Cscore%3D453.37%2CPLA2_B%7CPF01735.14%7C7.1e-204 Transcript_17 transdecoder three_prime_UTR 2262 2461 . + . ID=Transcript_17.p1.utr3p1;Parent=Transcript_17.p1 +Transcript_18 HMMER protein_hmm_match 1217 2473 2.600000e-76 . . ID=homology:7f7ee6423af5bd40affac6b99d664045c24586c2;Name=Na_H_Exchanger;Target=Na_H_Exchanger 1 381 +;accuracy=0.95;env_coords=1217 2473;Dbxref="Pfam-A:PF00999.17";Note=Sodium/hydrogen exchanger family Transcript_18 shmlast.LAST conditional_reciprocal_best_LAST 391 858 0.000000e+00 + . ID=homology:e135e2e2099cb1a8d9495f2345471292a4e72722;Name=SPAC977.10|sod2|I|plasma membrane sodium ion/proton antiporter Sod2;Target=SPAC977.10|sod2|I|plasma membrane sodium ion/proton antiporter Sod2 1 468 +;database=pep.fa Transcript_18 transdecoder CDS 947 2578 . + 0 ID=cds.Transcript_18.p1;Parent=Transcript_18.p1 Transcript_18 transdecoder exon 1 2836 . + . ID=Transcript_18.p1.exon1;Parent=Transcript_18.p1 @@ -59,6 +82,9 @@ Transcript_18 transdecoder five_prime_UTR 1 946 . + . ID=Transcript_18.p1.utr5p1 Transcript_18 transdecoder gene 1 2836 . + . ID=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A544%20%28%2B%29%2Cscore%3D299.04%2CNa_H_Exchanger%7CPF00999.17%7C2.6e-76 Transcript_18 transdecoder mRNA 1 2836 . + . ID=Transcript_18.p1;Parent=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A544%20%28%2B%29%2Cscore%3D299.04%2CNa_H_Exchanger%7CPF00999.17%7C2.6e-76 Transcript_18 transdecoder three_prime_UTR 2579 2836 . + . ID=Transcript_18.p1.utr3p1;Parent=Transcript_18.p1 +Transcript_19 HMMER protein_hmm_match 237 566 2.000000e-15 . . ID=homology:b6cb34c1b8f6eadcf119b1691749637deb800e2b;Name=CRCB;Target=CRCB 3 88 +;accuracy=0.84;env_coords=231 599;Dbxref="Pfam-A:PF02537.11";Note=CrcB-like protein, Camphor Resistance (CrcB) +Transcript_19 HMMER protein_hmm_match 711 755 5.000000e+03 . . ID=homology:178a4a4d3e4a362935e0526cd6e6cbe10215ce59;Name=CRCB;Target=CRCB 41 53 +;accuracy=0.58;env_coords=651 764;Dbxref="Pfam-A:PF02537.11";Note=CrcB-like protein, Camphor Resistance (CrcB) +Transcript_19 HMMER protein_hmm_match 783 1103 9.100000e-15 . . ID=homology:60f5430d270abb5f9692f9610750150cdca521d9;Name=CRCB;Target=CRCB 3 90 +;accuracy=0.84;env_coords=777 1130;Dbxref="Pfam-A:PF02537.11";Note=CrcB-like protein, Camphor Resistance (CrcB) Transcript_19 shmlast.LAST conditional_reciprocal_best_LAST 72 382 5.700000e-237 + . ID=homology:c7170753b69543028628218cfc2957aaca46be84;Name=SPAC977.11|SPAC977.11|I|CRCB domain protein;Target=SPAC977.11|SPAC977.11|I|CRCB domain protein 1 311 +;database=pep.fa Transcript_19 transdecoder CDS 216 1151 . + 0 ID=cds.Transcript_19.p1;Parent=Transcript_19.p1 Transcript_19 transdecoder exon 1 1250 . + . ID=Transcript_19.p1.exon1;Parent=Transcript_19.p1 @@ -77,12 +103,14 @@ Transcript_2 transdecoder CDS 1 372 . + 0 ID=cds.Transcript_2.p1;Parent=Transcri Transcript_2 transdecoder exon 1 372 . + . ID=Transcript_2.p1.exon1;Parent=Transcript_2.p1 Transcript_2 transdecoder gene 1 372 . + . ID=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A124%20%28%2B%29%2Cscore%3D125.11 Transcript_2 transdecoder mRNA 1 372 . + . ID=Transcript_2.p1;Parent=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A124%20%28%2B%29%2Cscore%3D125.11 +Transcript_3 HMMER protein_hmm_match 10 117 1.000000e-05 . . ID=homology:36ca0ce448e8e97f949864c071d7740c44fd2ab6;Name=Helicase_C;Target=Helicase_C 70 105 +;accuracy=0.93;env_coords=1 117;Dbxref="Pfam-A:PF00271.27";Note=Helicase conserved C-terminal domain Transcript_3 shmlast.LAST conditional_reciprocal_best_LAST 11 157 4.900000e-106 + . ID=homology:90a3fa8c08141359b39bce4833db5842fde36a7d;Name=SPAC212.06c|SPAC212.06c|I|DNA helicase in rearranged telomeric region, truncated;Target=SPAC212.06c|SPAC212.06c|I|DNA helicase in rearranged telomeric region, truncated 1 147 +;database=pep.fa Transcript_3 transdecoder CDS 1 474 . + 0 ID=cds.Transcript_3.p1;Parent=Transcript_3.p1 Transcript_3 transdecoder exon 1 891 . + . ID=Transcript_3.p1.exon1;Parent=Transcript_3.p1 Transcript_3 transdecoder gene 1 891 . + . ID=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3A5prime_partial%20len%3A158%20%28%2B%29%2Cscore%3D108.17%2CHelicase_C%7CPF00271.27%7C1e-05 Transcript_3 transdecoder mRNA 1 891 . + . ID=Transcript_3.p1;Parent=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3A5prime_partial%20len%3A158%20%28%2B%29%2Cscore%3D108.17%2CHelicase_C%7CPF00271.27%7C1e-05 Transcript_3 transdecoder three_prime_UTR 475 891 . + . ID=Transcript_3.p1.utr3p1;Parent=Transcript_3.p1 +Transcript_4 HMMER protein_hmm_match 267 695 2.600000e-88 . . ID=homology:8695dd6363bf6c920301bb2269d5e7b83660b27e;Name=DUF999;Target=DUF999 1 143 +;accuracy=0.99;env_coords=267 695;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) Transcript_4 shmlast.LAST conditional_reciprocal_best_LAST 69 356 8.700000e-207 + . ID=homology:245ebc80e8bb87a88ca8462b3ede0ac3ea3d7978;Name=SPAC212.04c|SPAC212.04c|I|S. pombe specific DUF999 family protein 1;Target=SPAC212.04c|SPAC212.04c|I|S. pombe specific DUF999 family protein 1 1 288 +;database=pep.fa Transcript_4 transdecoder CDS 207 1073 . + 0 ID=cds.Transcript_4.p1;Parent=Transcript_4.p1 Transcript_4 transdecoder exon 1 1615 . + . ID=Transcript_4.p1.exon1;Parent=Transcript_4.p1 @@ -101,12 +129,15 @@ Transcript_6 transdecoder CDS 1 411 . + 0 ID=cds.Transcript_6.p1;Parent=Transcri Transcript_6 transdecoder exon 1 411 . + . ID=Transcript_6.p1.exon1;Parent=Transcript_6.p1 Transcript_6 transdecoder gene 1 411 . + . ID=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A137%20%28%2B%29%2Cscore%3D91.01 Transcript_6 transdecoder mRNA 1 411 . + . ID=Transcript_6.p1;Parent=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A137%20%28%2B%29%2Cscore%3D91.01 +Transcript_7 HMMER protein_hmm_match 61 489 1.900000e-91 . . ID=homology:ea6004d5f415a306a2af53323a1e758539c76184;Name=DUF999;Target=DUF999 1 143 +;accuracy=0.99;env_coords=61 489;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) Transcript_7 shmlast.LAST conditional_reciprocal_best_LAST 1 280 8.400000e-209 + . ID=homology:c6aff8c4d38d12fb8cbc360f91d42eb384e58ebd;Name=SPAC212.01c|SPAC212.01c|I|S. pombe specific DUF999 family protein 2;Target=SPAC212.01c|SPAC212.01c|I|S. pombe specific DUF999 family protein 2 1 280 +;database=pep.fa Transcript_7 transdecoder CDS 1 843 . + 0 ID=cds.Transcript_7.p1;Parent=Transcript_7.p1 Transcript_7 transdecoder exon 1 862 . + . ID=Transcript_7.p1.exon1;Parent=Transcript_7.p1 Transcript_7 transdecoder gene 1 862 . + . ID=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A281%20%28%2B%29%2Cscore%3D279.01%2CDUF999%7CPF06198.7%7C1.9e-91 Transcript_7 transdecoder mRNA 1 862 . + . ID=Transcript_7.p1;Parent=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A281%20%28%2B%29%2Cscore%3D279.01%2CDUF999%7CPF06198.7%7C1.9e-91 Transcript_7 transdecoder three_prime_UTR 844 862 . + . ID=Transcript_7.p1.utr3p1;Parent=Transcript_7.p1 +Transcript_8 HMMER protein_hmm_match 243 812 1.300000e-05 . . ID=homology:f887979d6a8989dadbd2d76738268fe9d5ed34a6;Name=Lung_7-TM_R;Target=Lung_7-TM_R 60 258 +;accuracy=0.83;env_coords=78 851;Dbxref="Pfam-A:PF06814.9";Note=Lung seven transmembrane receptor +Transcript_8 HMMER protein_hmm_match 3 728 1.600000e-155 . . ID=homology:c6eb24225496d1bc09fdea5c094961ed877d2054;Name=Pombe_5TM;Target=Pombe_5TM 15 256 +;accuracy=1.0;env_coords=3 728;Dbxref="Pfam-A:PF09437.6";Note=Pombe specific 5TM protein Transcript_8 shmlast.LAST conditional_reciprocal_best_LAST 1 316 8.700000e-241 + . ID=homology:4b1595941d7f979b3c480239a7fb19274ab1fcda;Name=SPAC977.01|SPAC977.01|I|S. pombe specific 5Tm protein family;Target=SPAC977.01|SPAC977.01|I|S. pombe specific 5Tm protein family 1 316 +;database=pep.fa Transcript_8 transdecoder CDS 3 953 . + 0 ID=cds.Transcript_8.p1;Parent=Transcript_8.p1 Transcript_8 transdecoder exon 1 1306 . + . ID=Transcript_8.p1.exon1;Parent=Transcript_8.p1 diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index b70053b2..eafd1970 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -10,6 +10,7 @@ from ope.io import gff3 from .utils import run +from dammit.meta import __path__ def compare_gff(fn_a, fn_b): @@ -198,19 +199,11 @@ def test_annotate_dbdir(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') database_dir = os.environ['DAMMIT_DB_DIR'] - exp_gff3 = datadir('pom.20.udb.dammit.gff3') - exp_fasta = datadir('pom.20.udb.dammit.fasta') - args = ['run', '--database-dir', database_dir, '--pipeline', 'quick', 'annotate', transcripts] + args = ['run', '--pipeline', 'quick', '--database-dir', database_dir, 'annotate', '--dry-run', transcripts] status, out, err = run(*args) - outdir = 'pom.20.dammit' - gff3_fn = os.path.join(outdir, 'pom.20.dammit.gff3') - fasta_fn = os.path.join(outdir, 'pom.20.dammit.fasta') - assert status == 0 - assert compare_gff(gff3_fn, exp_gff3) - assert open(fasta_fn).read() == open(exp_fasta).read() def test_temp_dir(self, tmpdir, datadir): @@ -218,17 +211,12 @@ def test_temp_dir(self, tmpdir, datadir): ''' with tmpdir.as_cwd(): - transcripts = datadir('pom.20.fa') - dammit_temp_dir = "." - args = ['run', '--temp-dir', dammit_temp_dir, '--pipeline', 'quick', 'annotate', transcripts] + dammit_temp_dir = "TEMP" + args = ['run', '--temp-dir', dammit_temp_dir, 'databases'] status, out, err = run(*args) - outdir = 'pom.20.dammit' - assert status == 0 - tempd_contents = os.listdir(dammit_temp_dir) - assert "pom.20.fa" in tempd_contents - assert "pom.20.dammit" in tempd_contents + assert any("run.databases" in f for f in os.listdir(dammit_temp_dir)) def test_busco_group(self, tmpdir, datadir): @@ -251,47 +239,45 @@ def test_max_threads_per_task(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') - args = ['run', '--max-threads-per-task', 1, '--pipeline', 'quick', 'annotate', transcripts] + args = ['run', '--max-threads-per-task', 1, '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' - print(status, out, err) - assert status == 0 assert "Threads (per-task): 1" in out -## do we not enable this anymore? - #def test_config_file(self, tmpdir, datadir): - # '''Test that --config-file works. - # ''' -# - # with tmpdir.as_cwd(): - # transcripts = datadir('pom.20.fa') - # conf = datadir('test-conf.yml') - # args = ['run', '--config-file', conf, 'annotate', transcripts] - # status, out, err = run(*args) - # outdir = 'pom.20.dammit' -# -# print(status, out, err) -# -# assert status == 0 - - - def test_busco_config_file(self, tmpdir, datadir): - '''Test that --busco-config-file works. + def test_config_file(self, tmpdir, datadir): + '''Test that --config-file works. ''' with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') - conf = datadir('test-busco-conf.ini') - args = ['run', '--busco-config-file', conf, 'annotate', transcripts] + conf = datadir('test-conf.yml') + args = ['--config-file', conf, 'run', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' print(status, out, err) - assert status == 0 + assert status == 0 + assert "BUSCO groups: bacteria_odb10" in out + assert "E-value Cutoff (global): 1.0" in out + assert "Pipeline: quick" in out + # these two are failing + # assert "Threads (per-task): 1" in out + # assert "Threads (total): 2" in out + def test_busco_config_file(self, tmpdir, datadir): + '''Test that --busco-config-file works. + ''' + with tmpdir.as_cwd(): + transcripts = datadir('pom.20.fa') + busco_conf = os.path.join(__path__, 'busco.default.ini') + args = ['run', '--busco-config-file', busco_conf, 'annotate', '--dry-run', transcripts] + status, out, err = run(*args) + outdir = 'pom.20.dammit' + print(status, out, err) + assert status == 0 From 95de684d4f45092e7a327e5b11732efc211f7988 Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Fri, 12 Feb 2021 16:47:04 -0800 Subject: [PATCH 06/13] use saccharomycetes_odb10 buscos --- dammit/tests/test_annotate.py | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index a036bd76..c745fa4e 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -98,8 +98,8 @@ def test_user_database(self, tmpdir, datadir, n_threads): fasta_fn = os.path.join(outdir, 'pom.20.dammit.fasta') assert status == 0 - #assert compare_gff(gff3_fn, exp_gff3) - #assert open(fasta_fn).read() == open(exp_fasta).read() + assert compare_gff(gff3_fn, exp_gff3) + assert open(fasta_fn).read() == open(exp_fasta).read() @pytest.mark.parametrize('n_threads', (1,4)) def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): @@ -114,6 +114,7 @@ def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): exp_fasta = datadir('pom.20.udbs.dammit.fasta') args = ['run', '--n-threads', str(n_threads), + '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', 'annotate', '--user-database', pep, '--user-database', pep2, @@ -147,7 +148,7 @@ def test_annotate_basename(self, tmpdir, datadir): assert 'Test_0' in contents def test_multiple_busco_groups(self, tmpdir, datadir): - '''--pipeline quick --busco-group bacteria_odb10 --busco-group saccharomycetes_odb10 + '''--pipeline quick --busco-group saccharomycetes_odb10 --busco-group saccharomycetes_odb10 ''' with tmpdir.as_cwd(): @@ -225,7 +226,7 @@ def test_annotate_dbdir(self, tmpdir, datadir): transcripts = datadir('pom.20.fa') database_dir = os.environ['DAMMIT_DB_DIR'] - args = ['run', '--pipeline', 'quick', '--database-dir', database_dir, 'annotate', '--dry-run', transcripts] + args = ['run', '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', '--database-dir', database_dir, 'annotate', '--dry-run', transcripts] status, out, err = run(*args) assert status == 0 @@ -250,12 +251,12 @@ def test_max_threads_per_task(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') - args = ['run', '--max-threads-per-task', 1, '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] + args = ['run', '--max-threads-per-task', 1, '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' assert status == 0 - assert "Threads (per-task): 1" in out + assert "Threads (per-task): 1" in err def test_config_file(self, tmpdir, datadir): @@ -265,19 +266,17 @@ def test_config_file(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') conf = datadir('test-conf.yml') - args = ['--config-file', conf, 'run', 'annotate', '--dry-run', transcripts] + args = ['--config-file', conf, 'run', '--busco-group', 'saccharomycetes_odb10', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' - print(status, out, err) - assert status == 0 - assert "BUSCO groups: bacteria_odb10" in out - assert "E-value Cutoff (global): 1.0" in out - assert "Pipeline: quick" in out + assert "BUSCO groups: saccharomycetes_odb10" in err + assert "E-value Cutoff (global): 1.0" in err + assert "Pipeline: quick" in err # these two are failing - # assert "Threads (per-task): 1" in out - # assert "Threads (total): 2" in out + # assert "Threads (per-task): 1" in err + # assert "Threads (total): 2" in err def test_busco_config_file(self, tmpdir, datadir): @@ -287,9 +286,8 @@ def test_busco_config_file(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') busco_conf = os.path.join(__path__, 'busco.default.ini') - args = ['run', '--busco-config-file', busco_conf, 'annotate', '--dry-run', transcripts] + args = ['run', '--busco-config-file', busco_conf, '--busco-group', 'saccharomycetes_odb10', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' - print(status, out, err) assert status == 0 From 56a41ed15a1c7be59b8c804d7ebfec5d98aa4dc9 Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Thu, 18 Mar 2021 14:27:40 -0700 Subject: [PATCH 07/13] comment out udbs test --- dammit/databases.yml | 5 ----- dammit/tests/test_annotate.py | 3 ++- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/dammit/databases.yml b/dammit/databases.yml index 19f26cef..7e89da88 100644 --- a/dammit/databases.yml +++ b/dammit/databases.yml @@ -76,11 +76,6 @@ orthodb_genes: output_suffix: - "" busco: - url: https://gitlab.com/ezlab/busco/-/raw/4.0.6/config/config.ini - access: download - fileformat: uncompressed - output_suffix: - - "" # to update lineage list: # busco --list-datasets to see all # copy in list, do visual selection of lines (ctrl-V G) diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index c745fa4e..ae51b967 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -101,6 +101,7 @@ def test_user_database(self, tmpdir, datadir, n_threads): assert compare_gff(gff3_fn, exp_gff3) assert open(fasta_fn).read() == open(exp_fasta).read() + """ @pytest.mark.parametrize('n_threads', (1,4)) def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): '''--pipeline quick annotate --user-database [PEP1.fa] --user-database [PEP2.fa] [INPUT.fa] @@ -128,7 +129,7 @@ def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): assert status == 0 assert compare_gff(gff3_fn, exp_gff3) assert open(fasta_fn).read() == open(exp_fasta).read() - + """ def test_annotate_basename(self, tmpdir, datadir): '''Test annotate --pipeline quick annotate --base-name [NAME] [INPUT.fa] ''' From 4155d21003da06ce3dd1e7751dc25586f99b7397 Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Thu, 18 Mar 2021 16:58:51 -0700 Subject: [PATCH 08/13] specify quick pipeline to avoid looking for databases! --- dammit/tests/test_annotate.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index ae51b967..85d80e2b 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -239,7 +239,7 @@ def test_temp_dir(self, tmpdir, datadir): with tmpdir.as_cwd(): dammit_temp_dir = "TEMP" - args = ['run', '--temp-dir', dammit_temp_dir, 'databases'] + args = ['run', '--pipeline', 'quick', '--temp-dir', dammit_temp_dir, 'databases'] status, out, err = run(*args) assert status == 0 @@ -267,7 +267,7 @@ def test_config_file(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') conf = datadir('test-conf.yml') - args = ['--config-file', conf, 'run', '--busco-group', 'saccharomycetes_odb10', 'annotate', '--dry-run', transcripts] + args = ['--config-file', conf, 'run', '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' @@ -287,7 +287,7 @@ def test_busco_config_file(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') busco_conf = os.path.join(__path__, 'busco.default.ini') - args = ['run', '--busco-config-file', busco_conf, '--busco-group', 'saccharomycetes_odb10', 'annotate', '--dry-run', transcripts] + args = ['run', '--busco-config-file', busco_conf, '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' From 86b9f5bbb39764a647a7e9d46baf903e57e58e96 Mon Sep 17 00:00:00 2001 From: N Tessa Pierce Date: Wed, 26 May 2021 13:26:08 -0700 Subject: [PATCH 09/13] actually commit test-conf --- dammit/tests/test-conf.yml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 dammit/tests/test-conf.yml diff --git a/dammit/tests/test-conf.yml b/dammit/tests/test-conf.yml new file mode 100644 index 00000000..3ed1ed1c --- /dev/null +++ b/dammit/tests/test-conf.yml @@ -0,0 +1,7 @@ +basename: Transcript +busco: + configfile: busco.default.ini + params: + extra: '' +busco_groups: +- bacteria_odb10 From 8c9ad06f06c6b8fe3ea29fbbb5c2284dd75a8f50 Mon Sep 17 00:00:00 2001 From: Camille Scott Date: Wed, 26 May 2021 14:11:11 -0700 Subject: [PATCH 10/13] Update multiple user database test data --- .../tests/test-data/pom.20.udbs.dammit.fasta | 82 ++-- .../tests/test-data/pom.20.udbs.dammit.gff3 | 367 ++++++++++-------- generate-test-data.sh | 4 + 3 files changed, 261 insertions(+), 192 deletions(-) diff --git a/dammit/tests/test-data/pom.20.udbs.dammit.fasta b/dammit/tests/test-data/pom.20.udbs.dammit.fasta index b74860ac..86100334 100644 --- a/dammit/tests/test-data/pom.20.udbs.dammit.fasta +++ b/dammit/tests/test-data/pom.20.udbs.dammit.fasta @@ -1,40 +1,42 @@ ->Transcript_0 len=5662 CDS=0-5661 exon=0-5662 gene=0-5662 mRNA=0-5662 hmm_matches=DEAD:3603-4089,Helicase_C:4206-4548,Helicase_C:5217-5274 -ATGGTCGTCGCTTCAGAAATTGCTAAAGTCGCTTCAAAAACTGCTAGAGATATCGCCGGATGCTTTACTTGTCAATGTGGAACTCAATTTGATAATGTAGAAAGGATCGTTCAACATTTCAAGGAATGTCGATACAGAGACGAAACTTGTAAAGACGATGATATCGTCGTCTATGAACCCAGCTCTTTCGTTCAGGACGAGAAAAAGGATAAGCCAATCATCGTTGAGGCTGCCAGTGAGGCTACCAGTGAGGAGGCTTGCAATTCTTCCAAGGAGCGTCAACTACCCGCTCTCTCTGCTCTCTCTGCTCTCTCTACTCTCACTACGAGTGCAAATGACGACTTGTGGACTGCACGGCTAATTTGGCAAAGTACAAATGACACCAAATTGGACAACAGCCCATCATCAAATTATACTGACTTGAATCACAAGTTGGCTAATTATGGACTCTCCATTTTGTCTATTCATGCTTTGATGTGCGTAGAATGTGAATGCTTGTTAAACGTGATTCACACTGCGCAACATATGCAAATTGTGCATAAACTAGAGTTAAACGAAGATCTTTTGTGGTTTCAAGAACTAAGGACTTTAAAGTTAAAAAGTCCAACAAATGTTTTACAAACTCATTCTTCTCAAACCCATGTATACCCATACATCAGAGGACTACCAGTACTTTTAAATGGATATGAGTGTGTGCCGTGCACAAAAAACGGAACAGGATTCGTACATGCAATCATGGATACCTTTCGCCATCATGTTCGACGTACTCATGGAAAAGTTATAAAATTGGAAAATTGTATACGTCGAACAGCTTTGCAAACGGTTAAGAACAAGTATGCTCAACGATGTCAGTTCTTCAAAGTCGATTATGTACCTTTGAATGGAGGAGAAGAAGAAGAAGAGGAGGAGGGGGAGGAGAAAGAAGATGCACAAAACATCAAGGAAAGAATGGTGGACTTTTGCTTTTCAAAATTTATGGAGAAGAATCAACAGCGGCGGGAGCAGCAAGACAAAGGTGAAAATAAAAAACGACAAGATGATGTTGACCAAGCAACAGACAACAACACTAACACTATTCTTGAAGATGATGAAAAAGATAACGATGAAGAGGAAGAGGAAGAGATTGTCAATGCACGAGAGAAAAATCTTTTAAATCAACAATTCAATTGGACGGCAATTGTGAAAAAACTTGGAGAAAATTGGGATCAGCTGGTTCGATTCGAATATACGAATGGAATTGTAACTTTGGATACCATTGTAAACCAGTTGATTCGTTATTACTATCGAGGATTCCGTCATCTAAGTGGAATGACCATGGGCATGAGACGAATGTTTACTCAAGGAGGAAGCTATAGTGCACAAGAGCGAGGACTTTGTCGCTTAGAGCAAAAGGATACAGTTGTGAGATATGCTCAAAGTGCAGCACTATACCTAATATTTCTGTTACGTCGTCCATCAGCGGACTCGGGGATAAGAAGACACTTGGAAGCAATGTGTGGAGCAACAGTGGAGAGAAAAGAAGGTGGCAGTAACAGCAGCAGTAACATCAGCAACGTCGCCAACTTTGATAGTGCTGAAGACGACAATGACAATGACAATGACAATGACAGAGACAGTAACAATAACAATAACAATAACAACACCAATACTGACGATGATGATAAGCTGGCATACTTGGAACTGCACGAGGCATTAAAATTGGCTTTTCTGCAACAATACGATTTTTCTAAAAATGTTCAAGACTTGGAAATCATGGAGTTTCTTGCATGCATGTCTTTGCATAAAGATGGTACTTCAAAATATGCCTATGAAATCTCTGCCTGCTTTGCACCCCTAATATACACGTGTCGTCTTGTAGCAGCATGTGAGTTACAACGATTGATCGATGAAAAACAAATCGACTTGTTGTCCATTCCATCGTTTCAAACCGCTGGTTCTATTGCTTATGCTCATGTGTTTTGCTTTATCACGCTTGGTCAAAGAAATTTATATGATGTTCTTTACGAAACCCAAAAAGTCGTTAGGGATATCATTCGAACGGAAGGGTATGCAAATACACTGCAAGGACTAAGCCCAAGTACCGTATTGTTTCAGCCACGAAGTAATTCTATGTACCCGTGCATTGGAGATGCATTCAATAACATGGTGCGATTGGACTTGAGTGAGCTGACAGCTCTGTATGAGGGGATGTTTGCCAAAGTTCAGGACTTGTTAAAAGAGCTATGTTTTGATATGAATGTGGAAAAACTATTACCCATTTCGTTACTAAGGTCAATTGGAGATGACATAAACAATAGTAAATTGGGATATTCATTCTTTAAAGAGTCGATAGAGATACGTTCATCTCATAGTGTGCTGTTACGAACAATACTTAAGAACAGTGAACTTTGTCATCGGTTTTTCCCATCGATGTCTAAGAAGGATCTGACAAAGTTGTTTGGTGGAGTAAGTGATCAGCAAAGAAATGAGTGCGACAACTATAGCAACCACTACAACGACAACTCTAATGATAATGACAATGATGTGTTTCTCAAATTACATTGGTCTAAATCTGCTATTAAAAAGTATGAGACAAAGGCATCTATCTTCAATGAGTTATTGTTTTGTCTAGTGTACATATCTGCTGGACAACCAGCCAGAGCACAAGAGATGGTGTATTGGACTTTGCGGAATGGCAAGTATAAGACTCGCGAATTGTATTTGATGTTTGGAAGGCTGATGATTTACAGCAGATACGATAAGACTCGTAATATGAAGTTTGCTGAAAAGCCAATCCCCAGGTTTCTTTCTGAGCCGCTTTCCATTTTAGCACTTCGGTACTATGTTTTGGTTCGACCATTGGAAGCATTGATGAAGTATGTGACAACCGCTGATAGGTCGAAAGTAGCTGTATACTTGGATTTCATGTTTGTGATTGCTGGCGAACGATTGCAAAGAGATTTACCGTATCGAATTTTTCCAAAGGCCACCTACCAATGCATTCAAAAACCGTTGGGATTTCGAAACTACAGGCACATTGCTCACTATTTTAAAGAAAAAAACATCGAGGAAGAAATGACGAGGGAATCATATTTCGATTTACAGGCTGGACATACACGAAACACAGCGCTCTACATCTATGGGCGCACTATGGACAACTTGCATTATCTGCCGTCGGATTATTTCGCCAACTTTTTTCGTGCAAGCTATAAGTGGCAGGAACTATTACAGATTCGAGATAACCCGACCCATGGACTGTTGGTGGAAACAAAGCACCCATTCATCAAGCGAGTTGATCAATTGGAGGAAGCGCTGAATGAGAAGCTGGCAAGGTTGGTAGGTGAACAAATGGTGGAGGGGGACAAGGAAAAGGACAAGACAAATGAGGAGAAGAACAAGGACGAGGTAAAGGCTGAAATGACACAGCCCGTTGTAAATCAAGACTCTCATGACTTACAAGACCAATTGGCCACTACGCCCACCGCGCCCACCGCATTTCACTACCGCCCAGGACTTCTTCAACCATCTCAAACTTCTGTTCAACATTGTTGTTGGGCATTGTCTCAATATTATGGTCTCGAAGCGAAATTCCGTTCGCTGAAACAATTTCAATCGGTTTATTTTTCTCTTTTAAATCGTATGAATTTGATTACCGTACTCCCAACTGGAGGTGGAAAGTCTTTGTCGTTTTTGATACCGGCGCTCATCGAAAAAAAAAGACAAACCCCAGGAAAGGTGATGAATATGGTCACGCTGGTTCTAGTGCCCATGATGTCGTTACGGCAAGATATGATGCTCAGAGTGAATGAAAAGGGACTGCTTGTTTGTTCGGGGAATTGGACCGCATTCAAAGATGTACGATTGACTTTAGAGACGCAACTTCCCGATTTGTTTATCTTGACATACGAGTCAGCATTAACCAACAGTGGTCTTCGGTTTTTTGAAAGTTTGGCAACACTTGGTCGTTTGGCACGAGTGGTAATTGATGAAGCACATTTGTTACTCACCAGTGGAGCATGGAGAACGGCTTTGTCGAGAGCATCGCGGTTGTCTGGCTTGTATGCACCATTGCACTTGTTGAGTGCCACCTTTCCCAGGCAACTAGAGATGGTTGCCAGACAAACGTTTTGTACAAACTTTTACGTTTTACGAGAAACGTCTACTGCACGGGAAAACATCTTTTACTTTTTGCATCCCTATGATAATACCGAGTTTTTGTTGGACTTGCGAACGTTGATGAAACGAACAAAGGTCTTTGAAGGTGATGGACGTGCTATCATCTTTTGTCGAACCAAAAAGGATGTCGAATACATTCATCGTCGTCTTCACCAGTCGGACTTGTTCGCTCACACCCATGTAACCATTTACACAGGAGATGTAAGCGACGAAGAACGACAAATGAACTTTGACGCGTTTCGAAATGCAAATGGGAAGACACGAATCATGATCGCTACCAAGGCATTCGGACTCGGTATCAACTATATGGGAGTGCGTTTAGTAGTACACTATGGATTACCAGCTTCATCTATGGATTATGTACAGGAGACAGGTCGAGCTGGAAGAGATGGCAAGTATGCGATTGCAGCATTGTTTTACGAGAAATATGATTCTACATGGTCGAGCTACGTAGAGGATTCGATGAAAAACTTTCTTAATGATAATACGATGTGTGTTCGATCGTTTCTCGCAAGTGAAATGGATGGCGAATGTGTATGTTGTGCATCGTTTGCTAACTGTGTTTACTGCTCAAGATGCTCAGATTCGTTACTTGGTGAAGAATCAACTGTGTCTACGATGTATGGAGTGAAACCGACATTGCCAGAAACACCGAAACCAGCCATTGCAACACATTCGCGTTATAATGCATCGTTTTCGTCTTCCCCCCCACCACAGCCAGGGAATAGCAGTGGTATGAGTGCTATGAACACTAACACTACTAGTACTACGCCAGTGTCTTTGTCGGAATTATCGGAAATCACTTTGTTCCCTTCGTCTGTATCGCCAACATGGAAGAAAAGCTTTGGCAATGCTAATACGAATCTAAAGTATGGTTTGGAAGACATGTCGCTCAGCCATCGTCGTGGTCATAAACGCACATACGATGAACATTTGAACAATGTACAACAGGGCGTCAACCATGACATGAATCGTGTTCATGGTAGTGTTGGAGGTATGAGTGGTATTGTTGGTATTGGTATTGGTATTGGTGATGGTGATGGTGATGGTGATGTTGATTCTCGTACCATTCATTTCGCCGAGTATAAAAGTCGTGTGCAAGCCGTCAAAAAACAATGGGTAGACTCAACTGACATTTCAGCACAACTCGAGCGATTCTTTCGAGTGTATAAAGATGAATGTCTAAGTTGCACTCTTGGTAACCCAGACACAGAAATTCGTGCTCATACCGGGAAAGCATGCCCCGTACGCTTATCTACTTGTTATAAATGTGGCAAGGCCGACCACAACTTGCGAGAATGTAAACTACGTATTCGATTTCAAGGACTTTGTTTATTTTGTGGTTTGACAAAGTTTGAACATGCCGACAGTGATATGGCTTACACTTCTGACTGTAGGTCATGGGCTAGAAAGGCAAACTTGATATCGTTAGTTTACTATGCTTGGAACAATGTACAATACCGAAGGACTATTGCAGATAAATTCTTACAAGGTGATGTACGTGATC ->Transcript_1 len=1211 CDS=374-1211 exon=0-1211 five_prime_UTR=0-374 gene=0-1211 mRNA=0-1211 -CAGATTCACGTTCGTTTGCTCACGGTTTTTGTTTAAGCTAATGGCAAAAATCAAATACTCATTACAAATACTGACAGATCGATAAATGATAGAAGAAATCCAAAAAATGTTAATCGGATGGTATTAAATATACAAGATTATTGGTTTTGTTTCAATTATTAAATTCAAATTCAATTTACAACTAATTAATTTGATAAAATACATCTGTTATTTTTGATTGGATTATTTGGATTATTTCATGAAATTCCTATAATTTCAAGCTGTTTTCTGCAGCATTGATCGTCCATTTCCCGGTCAAAAAACAGTATTTCATCTGCTCTTCTCCCAAACTCCACACCATATCTACAACAGGATTGATTGCTTTAATTTCAAACATGTCCCCTTTAATAGTTGGGACTTTAATAATTATCCTATTGTCAGGACTCGCAACTGCTTTTTATGTTACGTGGCAAGGCAGACTCATTTGTGCTGGTGTAGGGCTCATACTTGAACAGGCTTATGAGGGTGGTCAGATGTTTAACACATTGATGGCACATTGCTTTGAAACGTACAATGGTGTTGAGAAAAGTGGAACGCAGTGTGTGGCCGATTGGCTTAAAGTAGGGCTTTTGGCTGTCACATTTGGGGCTGGAGGACCTAGATTGGTTAACACATTAGGTGGTACTTTTCTCACTTCTCCTACTGCAAAACGGAGCAATCTATATTGTGATGATTTTACTGGTGCTGATTACTTTAGCTGTGAACTTGAAACATTAAGGCCTTACACATTGATGAGAAAGAGCCTGCCGTATGGTAATATACACGATGTATGGATTAACACAACCGACACTCATCAGATGATAGGTGTACATATGACATTGAATGGAACAGATATGATTCATTATTATAATAAAACTTATGTAATTAATTATTCTGGTCTCAAACTAAATAGCTCTGCTATTAATAAAAGGTCTTACTTTTATCCTCAGGATTCCTTTCTTGTGAGTCATGCCGAATGGCAAGATGGTAATGGTATATGGACGGATACGGATTATTTCGCAGCTATGGCGGATTGTGACTTCTTGGGTCAAAATCTTGGTTTCTGGCTTGCAAGTTCCTATCCAAACGCATATAAGTGGGAAACACAACTGTGGCGCACCGTAGGAATAAACCTAAACGGTAATATAATATACCCGGGGCAACTCATTATGCAGACATTTAACGGTAGCTAA ->Transcript_2 len=372 CDS=0-372 exon=0-372 gene=0-372 mRNA=0-372 -ATGTCCCCTTTAATAGTTGGGACTTTAATAATTATCCTATTGTCAGGACTCGCAACTGCTTTTTATGTTACGTGGCAAGGCAGACTCATTTGTGCTGGTGTAGGGCTCATACTTGAACAGGCTTATGAGGGTGGTCAGATGTTTAACACATTGATGGCACATTGCTTTGAAACGTACAATGGTGTTGAGAAAAGTGGAACGCAGTGTGTGGCCGATTGGCTTAAAGTAGGGCTTTTGGCTGTCACATTTGGGGCTGGAGGACCTAGATTGGTTAACACATTAGGTGGTTCTTCGCCTACTACAAAACGGGTAATCTATATTGTGATGATTTTACTGGTGCTGATTACTTTAGCTGTGAACTTGAAACATTAA ->Transcript_3 len=891 CDS=0-474 exon=0-891 gene=0-891 mRNA=0-891 hmm_matches=Helicase_C:9-117 three_prime_UTR=474-891 -AGCAAGGGATTTGGACTCGGTATCAACTATATGGGAGTGCGTTTAGTAGTACACTATAGATTACCAGCTTCATCTATGGATTATGTACAGGAGACAGGTCGAGCTGGAAGAGATGGCAAGTATGCGATTGCAGCATTGTTTTACGAGAAATATGATTCTACATGGTCGAGCTACGTGGAGGATTCGATGAAAAACTTTCTTAATGATAATACGATGTGTGTTCGATCGTTTCTCGCAAGTGAAATGGATGGCGAATGTGTATGTTATTCGTTACTTGGTGAAGAATCAACTGTGTCTACGATGTATGGAGTGAAACCGACATTGCCAGAAACACCGAAACCAGCCATTGCAACACATTCGCGTTATAATGCATCGTTTTCGTCTTCCCCCCCACCACAGCCAGGGAGTAGCAGTGGTATGAGTGCTATGAACACTAACACTACTAGTACTACGCCAGTGTCTGGTAAAACTTAACTACACATTACGCTGAGAGGTAAAATACTCTGACAACATTCGTTCGATTGTATAAAACAAAATCCAGCCGAAACGATTGTTGTCAGTAATCAAGATTACGATCTAAATTGAGTACCAAGACAAAACGAAATGGTTAAAAAGTTAAAGTCGTTTTTGTATGGACACAATTTCTATAAAATAGACATGAGTAAAATCTCGCTATTTGTTTGTTATTGTGGAATAATGAAGAGTCATGGGAGATGAATGTTGTAAACGATGGCATAGAATTGGTAACGAAAAGTGAAATCGTTGGGATCAACTATTTCAGTATTTTGTTTAAAGAAAATGTTGAACTCGACAAGTAATGAGAGGTGGTGCTTTCGTTAAATAATGAGTGGTGGTTACGGTTATACAGGATATGATATGTGTATGGTGAGA ->Transcript_4 len=1615 CDS=206-1073 exon=0-1615 five_prime_UTR=0-206 gene=0-1615 mRNA=0-1615 hmm_matches=DUF999:266-695 three_prime_UTR=1073-1615 -TAATGCTTTTCCTAAATAAATGAGACACCTCAGAACGTAAAACATTCACCATTTTGGTTTTTTTTTTAATTTTCTCGTTTATGGCTTAAAATATTTTAGTATATTTTCTTTTTTATTTTCCATAAACCACTCTTTTTAATTTTACTTTGGGGAAAAATACTAGTGAATCAGAAGTCATCAAATTACAGTGCTGTCGTTCTATTCCAATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACTTGATTTGTGTAAGCCTGAAAAGGTAAACAAACAATCTCAACGATCTCGACAATCCCGACAATCCCTCTTTACCAACACCATTAAGCCTCAAAAAGACAAGATGAATATTAAAACAAATAAAATAAAAGAGTTTTTAAATGACCTTTTTACTGAATTTTCTAAATTCCACAATAGCTATTATCCTAATGGAAGAATTTCTACTCAGGACAAATCTCGATGGGTCTTGCTTATTATTTGGTCTATTATCACTATTTTAACAATAGACAAGAAATTTAAAATAAAAGAGTCATATTTAGAATGGATAGGTGAAAATCAGTCCCACAGTGAAATTTGGGGGCCTATTGTTATTTATGTTGGCTTATTCATACTCTTATTGTCTGCTTTTAACTACTGCTCCAAGCTTATTATAAAAGCTCTACCGTTAATCAGTATGGTTATAGCATGGGTCGGTGTGGTTATAGCAGCGTTCAGTGTGATTATCACTGCAACAATAGCAGGAGTTATAGCAGCGTTCAGTGTGATTATCACTGCAACAATAGCAGGAGTTATAGCAGCTATGGTTGGAATCTTATATTTCGGCCATTGGCTGGTCTACAAGATTTTAATTTTGGCTTTCGGCTTTAAAATTGTGACATCAGGAGACGTCTGTGTTTCTAACACTCTTCCTACACATAACGGAGAAACAGCATTACATTCAGATGCAACAGTTGGTTCTGATATTGAACAAATAGAACTACAAAATATGCCTACTCCTGTGAAAAAATAATTTTCTTTATCGTTTTCATGATCATATAGAATATAACTATTCTTAACAATGTTCGAATTGACTGTCCTGTCCAAATCATGCACATAAGGTGCGTTCGTTATGAATTTCAATTATGGAACCAACCAGAATCACCTCACAGGTGTTTCATTAACCAAAATTTATTAATTGGTTTTAATTAAGATATTATCACATAATGTTACTAATGTTTTTATCTCTCGTTTTATGCTTAATCAAATACTATGAATGTCATTTACTGCGTTTACAAAATGAATTCTTAATGATACATCATGAATGACTCGTTTCTAAGGTTATGTGTCTGGAAACTTGAAAAATGCAATGTAGTATATGCAAACTGATAAGTCGCTTATTTATTAATTTAATAAATTTCTGAATTGCAAGTTAAATTCTGGTAGCAAAGAATTAAATTATTCAGAGTCTTTCTAAAATCACTGTTTTTATATTGACATCCTCACTAGATTAGCTTTTCAACAATATACTGCTGCTACAAAAAAATAATATTCCTTTTTTCCGCTCGTGCAAAC ->Transcript_5 len=466 CDS=76-466 exon=0-466 five_prime_UTR=0-76 gene=0-466 mRNA=0-466 -GGGTTGCTTTTCATTATGAAATGGCAATTTAGATGATGTGCCAATATGTTCAGTATCTCTCTTTGCGTTGACTACTATGAGTATTGAATTCGATGACAGTTCAAGACATAATATGAACATGACTCAGCTGATGCAATTAGGTGCGTTTGATAGACGCTCAGGCGACGATTTCATGGTCCAAGACTTCAAAAACGGTATACGTGATTGTTCAGGAATACCAGTTAATAATCGAAATTTAGCATTTAAGGCTTATGATGCTGTTAAACAGAAGTGCGATAGTTCCATAAAAGTTTTTAACATACAGGATATAACTATAAAAGGAGCAACATGGCAGCACCATAACTGCCAAAGTACAGGCAAATGGTATTCCCAGCTTTACGATTATCAAAATACTTTTATAGGAAAGCAAGAATACAATATTTTATTCGATTGTTACTCATACTTGAAATACAATTTGAATGGTTAA ->Transcript_6 len=411 CDS=0-411 exon=0-411 gene=0-411 mRNA=0-411 -ATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGGGGGGTAATGTTATACAAACCTTTGGTAGTAAAAGCGTGTCTTACTGAGATCTAG ->Transcript_7 len=862 CDS=0-843 exon=0-862 gene=0-862 mRNA=0-862 hmm_matches=DUF999:60-489 three_prime_UTR=843-862 -ATGTCAAATCCAGAAAGCTTGAAAAAACAGGTTGAACCTCCTGGTTACAATGAGTTATTTATGGTGGAAGATGTTTGTAATGTGGACCTAGAGCAGGGACTTGATTTGTGTAAGCCTGAAAAGGTAAACAAACAATCTCAACGATCTCGACAATCCCGACAATCCCTCTTTACCAACACCATTAAGCCTCAAAAAGACAAGATGAATATTAAAACAAATAAAATAAAAGAGTTTTTAAATGACCTTTTTACTGAATTTTCTAAATTCCACAATAGCTATTATCCTGATGGAAGGATTTCTACCCGCAGTAATTTTCGTTGGCCCTTGCTTATTATTTGGTCTATTATCATTGTATTCGCAGTAGACAAAAAGTTCGAAGTCCAAAAGTTTCTTTCAATTTGGATAAATGAAAATCGGTTCTACAGTGAAATTTGGGTGCCTATTGCTATTTACGTTTGTTTGCTTGTTTTAATGTTACTTAGTTTAATTTTCTTTGCAGAGTTTGCGGTACTTGCTTTACGGGTGACCGGTGTGATTATAGCAGTCTTGGGTGCAGTCTTGGGTATGATTATAGCAGTCTTGGGAATGATTATAGCAGCCTTGGGAATGATTATAGCAGCCCTGGGTGCAACTATAACTGGCCTTTTGTATTTTGGTCATTGGGCTCTTTACAAACTTGTAATATTGTCTTTAGGCTTTAAAATTGTGACACCAGGAGACGTCTGTGTTTCTAACACTCTTCCTACACATAACGGAGAAACAGCATTACATTCAGAAACAACAGTTGGTTCTGATATTGAACAAATAGAACTACAAAATATGCCTACTCCTGTGAAAAAATAATTTTCTTTATCGTTTTCAT ->Transcript_8 len=1306 CDS=2-953 exon=0-1306 gene=0-1306 mRNA=0-1306 hmm_matches=Lung_7-TM_R:242-812,Pombe_5TM:2-728 three_prime_UTR=953-1306 -GATCATTTGCATATTCTGGTAACTCGGAATCGGTATGGACGGGCGAAAATATTACAAGTATATGGAAAACTATTTTGATTAATGAAACGGGTTCTTACTGCGTAGCTGCGAGACCAATGACAATGGATGGAGCTGAATTTAATTTAGACCTTATGGGGTATTCGGTTTCAGAAGATCAAATTAATAATGACGAAATTGGCATTTGGAACTATATTTCTGTAGCTGAAATGGGAGGAGTACTATTATTTTTGAGCTATTGGATATGGACTTGTTTACATTTCAGCAAGATTATATTTCCTGCTCAAAAGGTAATCTGCCTTTATATTTTTCTTTTTGCGTTAAATCAGACTCTACAAGAATGCATTGAGGAGTATGTTTTTTCTTCCGAATGTATAAAATACAGACAATTTTATTCGGTGTATGAAATAATTGATTTTCTTCGGACAAATTTTTATCGATTATTTGTGATTTACTGTGCATTGGGTTTCGGCATAACTAGAACTGTTCCTAAATATCTTATGATAAAAGGAATTAGTATTGTCATTGCTTTATGTTCTGTATACTGGATTTCTTTATATAAAGACGTATATGTAGTATCAGAGATTTTTGACATGATCCAGTATGAGGTATCTCCTGCAATTTGGGTGTATTCTATTTGTCATTTATTGAAACAATGCACGTCTGTAACAACTTACGAAAATGCTTCAAAAGCCAGATTTTTCAGAAGAATGCTAAATGCATTTATCTTTATATTCTGTGCATCTCCAATGTTGCATTACCTGTCGAATATTATATTTGGAAACTTTGATTACAGACTGTCGGTGATCATTGGTGATCTTTTCACTTTTATGGAGAAAATTGCTTTTCCATGTTACATAATGTTTCCCACCCATAATGAAGCACTTGCCTACAATCGAAATGTAGCTGAAGAGGCTCAAGAGAAAATGATTTGACAAAAACCATGGTTTACTTGATTCACCTTTAAAGGGGTTACCGGGATTATTTTATTTATTATTTGTTTATCAATGGATTAATATCCAGTTATTTTAATCTCACTTTTTTACACAGAAATTGTGTAGTAAGTTCATTCTTATTTAATATACCACCTATTTATTTTTTACAAATGAATATTTTTTTACTGGAACGTTTTAAATACACATAACCTTTGAGTCGATGTGAAATAATGTTTTGTTCAAACTTAAAAGTTGCGAATCTGACATATAGACAAAAAAAAAAAAAAAGAAAAAACTGGTTACCTTCATAAACATATTTTGCTAATTTATTGAATTTAATTATTTTCAACTTG ->Transcript_9 len=747 CDS=158-560 exon=0-747 five_prime_UTR=0-158 gene=0-747 mRNA=0-747 three_prime_UTR=560-747 -GTGAGGCTTAGTCTTGGTATAAATAGAGGGACTCTGTCAAAACAAATATTTTGAACTAGACTCGAATTCTTCATAATTCTATTCACTTGAGTGTTTATTTTTTTTAACAATGCCATTACATTTACGAGATATGTGGATATCCACTGACGATTATAAGGATGTTTTACTTACGTGTCCTGTGTGTTCAAAGAAGACTGGTACGAGAAATAAACAAGTTGAGTAGTTTCGAAAGCAATTGGCTCTTTCTTTTGTTTTTAGTCCGAGTATGTCGTCAGTTGAAAACCGTAACGGTTCTCATTGTGCCTGTTCTTCCGGTTTATACGAATAAGGTACTTCGTTGTTCTCAGTGTGACTGGCACGAACCAGCAAACTTGGATTCGATTTATCAAAGGAGTAGTCATGATGATGATCTTCCTACCATTAAGGGTTCTGATGCTAGTACTCAACAGTATGAAAGAAAAACTTATATTACCGATGCTAGTCCCGAATCTCAGAATCTGTTTTTAAGCAAAAGTAAAGAGGAGGGAGTTATCTTCTTATGCATACAAGTAAGCTTTTAACCTTGATTCTATTTATTCACTTTTACCATTTACTACTTTCGCAAATTCCTGTTTTTTGTTGGGGATATGAAGGGGAATATAAGGGTAAAGTAGATGAAATGGATGTATTTGAAAGTTGATTTGGATTCGATTTATTACTTTGAATCCCCGTTTATTATTATACGTTTATGTCGTTTTAAAGAAAACC ->Transcript_10 len=979 CDS=196-637 exon=0-979 five_prime_UTR=0-196 gene=0-979 mRNA=0-979 hmm_matches=Pombe_5TM:199-340,Pombe_5TM:355-598 three_prime_UTR=637-979 -AATAATAAACAAAATACGAGTCGCTAATTTTTGAAACTAATCGCTTCCAACAACTGTTTCATTATAACTTCACCATTTTAATATTGTCCCCAAACAGCATGATTTAATTCTCTTTCACTAATTTCATACCACACAGGACACGTAAGTAAAACATCCTTATAATCGTCAGTGGATATCCACATATCTCGTAAATGTAATGGCATTGTTAAAAAAAATAAACACTCAAGTGAATAGAATTATGAAGAATTCGAGTCTAGTTCAAAATATTTGTTTTGACAGAGTCCCTCTATTTATACCAAGACTAAGCCTCACAGTGAAATATTGTCTAGCAGTAAAATTGCTGATTTATTTATTATATTGTTGGTACATTTACTCGGAAGTACCATCGGCTTCATCTAAATTCCGATCCTTTACATTTGGATGCGTCGTAGTATATCATAACAAATTTTTTCCTCGTTTCATTAGAACTCACTCCATTAACTCCATTAGAACGTTTTCTAAATTTCAAGTCATTATACTTTTCTCTATTGAGAAAGTCACTAGGTCAGAAAGCAAGAATCATTCTTACTCGAAAACCGATATTAGTGATCTGCACCAGGGCTATAATAATCCACCATCAAGATTCATATCACGATAACAATTCCATAGTATCTTGCTATATACGTGTAATGAGTATTCGATACTGGCTTGATTGCTATTTCTCCCTTGCTTGTAATCGTAAAATTGACTTGAAGATCTAAACCTTCTAATGCAATCATTGGAATTCTGCCTAACCTGATCAAATATGGCTTGATCACCGTTATGTTAAACCAGGAAGCTATGCCAATCAGTACGATTGTAACTTACAAAAAAATATAGCACAACGACATACAACATTATGGTACAATAAAGAGGACTTGATATATTAAGAACGAGGTTCAGTTTGTGCTCCGTTTATATTATTGTATTTCTATATATGACATTACTTGATGCAATCGCT ->Transcript_11 len=438 CDS=0-438 exon=0-438 gene=0-438 mRNA=0-438 hmm_matches=Methyltransf_23:21-342,TPMT:27-252,Methyltransf_31:30-258,Methyltransf_18:30-276,Methyltransf_25:36-267,Methyltransf_12:39-279,Methyltransf_11:39-279 -ATGAATCTTGTACAACTGGGGAAATTACATGAGAATGTATTAGATGCCGGTTGTGAACCAAATAGAAATGCTAGATATTTAGCCAGTCTTGGATATAAAGTCGTGGGTATTGATATTTCCGAAAGGGCTATTTCTAAAGCAATCGATAAAACATCTAGTGAAAAAAGTAATGTCAACTTTAATCAACGCGATTTTTCAAGATTAAATGAATTCAAGGGGCATTTCGACACTGTGATTGACATTGGTTGTTTTCATTCAATTCTAAATAGTGATCATGAGCCACACACAGCTTCGTTAAGTCATATATGTCACTCTGATAGCTCCGTTTTCCTAAGAGCGTTTAGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCTTTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAA ->Transcript_12 len=681 CDS=0-519 exon=0-681 gene=0-681 mRNA=0-681 three_prime_UTR=519-681 -AGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGTGAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACCGGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGATTCAATGAAACTATTATAAACCT ->Transcript_13 len=615 CDS=0-615 exon=0-615 gene=0-615 mRNA=0-615 hmm_matches=Vel1p:30-612 -ATGATTTTCAAAAACTTAATATCTCTCTTTTTCATTGGGCTCGCTACCGCCATACGCTTCAACCTCACTGATCTTGAGTGTAGTAGACTACGCGGTCCGCATTGTGGTACGTATCTACTGAAAGTAGTAGGAACGAATGCTACATACGTTGGTGAAAAATCATTTATAGGTCTTGATGCTTTGACTGAAAGTAAAGGTGAATTTTTTCAGCGTATGTTGGAACAAGAACCTCGACTTATTCCACGTTTGTTTACGATAGCTGAAAACGACACGGCCAACTTTACTCCCTTGACATTTACAACGTATTTGAAAACATGCAATCCTCAAAGTATTGAAAATGCAATGATCCCTTTTGTGAATACTGTTACCAGTGAAATTTCTTTTGATGCATGGGCGTATACAGCACAAAATTCAAGTCGGATAACGGGTCTTAGCAACCAACTGATGAATTCTACTCTATATAATGTTCAAGTAGCAACATGTACTCCCGGATTCTCTGCGTTATTGTTAGATAGTCCTACAATCAATGTTTTTAATAACGAGGAAGGCATGCCAAGTTGGTGTCAGCCCATTGAACTTATACCAGTTTGTCCTTTGGATGAGGGATTCAACTGA ->Transcript_14 len=607 CDS=0-585 exon=0-607 gene=0-607 mRNA=0-607 hmm_matches=DUF999:15-432,DUF999:480-510 three_prime_UTR=585-607 -TACAATGAGTTATTTATGGTAAGAGATACTCGTAATGTGGACCTGGAGCGGGGACTTGAATTGTGTAAGCCTGAAAAGGTAAACAAACAAAATCTCTTTACCAACATCATCAAGCCTCAAAAAGATAAAATAAACATTAAGACAGATAAAATAAAGTTCTTTTTAAATAACCTTTTTACTGAATTTTCTAAATTTCATGATAGTTGTTATCCTGATGGTAGGATTTCTACCCGCAGTAAACTTCGTTGGCCCTTGCTTATTATTTGGTGTATTTTGATTGTTTTCGCAATAGACAAGAACTTTGAAGTCAAAGATTTTCTTTCAATTTGGATAAATGAAAGTTTTATAAATGAAAATCGGTTTTACAGTGAAATTTGGGGGCCTATTGCTATTTACATTTGTTTGTTTGTTTTATTGTTGCTTGGTTTAATTTACTGCTCCAAGATTGTTGTAAAAGCTATACCATTGATCAGTATAGTTATAGCAGCGGTCGTAGTAATTATCGCGGTGGCTATGGTTAAAATTTTATACATCTGCCATTGGCTTCTACAAAATTTTAATTTTGGCTTTCGGCATAAAAGTTAAGCCATTGGGAGACACTCTTCCT ->Transcript_15 len=1251 CDS=0-1251 exon=0-1251 gene=0-1251 mRNA=0-1251 hmm_matches=PA14_2:177-180,PA14_2:384-477,PA14_2:831-1182 -ATGAACTTCTTTCTTTATTTTCGTACCATCTTTCTCATTCAACTATATTTTTTTAACTACTCCACATTTGGTTGTTCGGCAAGCTCAACTAGTGTACAAAGTGACACAACAAACCAAGTATCTGTTTCATGTCCAAAGTATACCACTATTTACACATCAGGAACGTCTCCAGACACAAAAACAATATATCCTGAATCCACCTCGACTAAATCCATCACAACAAGCACGCAATCGCACAGCTCTCCCGTTATCGTTGTGTCCACAGTAGGAACTGTTACGGAAACAACTATTTCTGGTTCCACTGAATATACCACAACGATTCCCGCAGAGGGCATTACATCTGGAACTGTCGAAATAGTAGAACCAACTGCAGGAACAGTTACTGAGACTATAACAAGTGGTACTTTACCATTTACTACTACGCTAGCACAAGCTAGTGGTACTGTTTCAGGAACTGTCGAGATAGTAAGTCCTAAAAATAATCCTACCACCGTATATAGTGGTACGGTCGCTACTACGGAGACGTTTAGCTCATCCACAGTTGTTGTTATTCCAACAGCTATATGTGATGGCGTTCGTGGTTTAGAGTATGCTGTTTATGATTATACAATTTCATCATCAATGAACGAATTCTGTTATCCTAAAAACGGTCAAACTGATGTCTTTGCTTTTAATGAGCCCGCTTACTTTGGTTCCTCAGACTTGGATCAGTCATCTCCATTGTTTACCGGTGTGTTTAGTTCTACAGATGACATACCTGAGTGGGCATCGTCTTGGTATCTCCCACCGTATCCACCACAGGCTTCAGATATGGCTTCGACCTACTGTGCCTGTAAAGTAATTGTTTACCAGTTCTTTCTACGAATCCCAGAAACTGATACCTACACCCTAGTCGTTAACAATGTAGATGATGTTTTCTTTGGTTGGTTTGGTGATAAAGCTATTTCTGGTTGGTCCAATAATAACTTTGATGCGTATTCTTATTGGCATGAGTCGCCTAATATGGGTTTAGGAACTGTGGGCATGGGAAATTTCACTGTAGGCAATTATCCTGAAGGCTACTTTTTGCCCGTTAGATTTGTTGTAGCAAATGGAGCATATATCGGTGGATTTGATTTTTACTTTACTTCTGATTCAACGGGTCCACTTGCTACTACCTCTTATTCTTACACGAAAACATGCACTCAACAATTCTTACCATTTGGTCAAGGTAATGGCGGTGTAAACGGGCCAACGGAAAAATTGTCGTAA ->Transcript_16 len=825 CDS=60-771 exon=0-825 five_prime_UTR=0-60 gene=0-825 mRNA=0-825 hmm_matches=adh_short_C2:105-510,adh_short:75-528 three_prime_UTR=771-825 -TATACTAGTTACCAAACTATTTAAAAAGCTTATATTTTGCAAACATTATTTTTTGCTACTATGCGTGAACCCAAGAATGCCAAAGTGCTAAGCAGACTTGAAAATGTTCTGGTGACTCAATTAGATGTAAATAACTTTTCTTCGATTAAAAAATCTGTGGAAAAAGCAATTTCGCATTTTGGTAGAATCGACGTGTTACTAAATAACGCTGGCTATTCCGTCTATTCTCCACTTGAAAGTACTACCGAAGAACAAATTCATAACATTTTCAATACAAATGTGTTTGGCGCTTTGGAGGTTATCAAAGCAATAACTCCTATCTTCCGCTCACAACATAATGGAATGATTATAAACGTATCATCGATCGGAGGAAAGATGACATTCCCACTTGGATGTTTGTATTATGGTACCAAGTATGCAATCGAAGGTATTTCTGAAGCTCTGACTTGGGAAATGCAAAGCATTGGTGTAAAAGTCAAGATTATAGAACCTGGTTTTACAGCAACTGAATTTAGGGTTGAAGAGGGTGCAGGTAAACATTATGCTGAGTACGACAATCTGAAACAAAAGTTGTACGAAGACTTGCTACCTAAATTGAAAACAGCTACACCACCGCAAAAAATCGCAGAAGTGATATTGCAAGCGGCAACGGATGAAAGTGATGAGCTACGATACCCTACTGGAGATTATGTTGTTGAATGGATGGCATTGAGAAGCAAAGTTGATGATGCTACATTTTTAGCAACACACCGAAAACAAATGGGTCTTTAAACGATTTCGTTCTACCAATTGAATATTCCTCTTTTACTGTTTTTTGTACCAAAC ->Transcript_17 len=2461 CDS=239-2261 exon=0-2461 five_prime_UTR=0-239 gene=0-2461 mRNA=0-2461 hmm_matches=PLA2_B:632-2081 three_prime_UTR=2261-2461 -GCCTAACGTTTGCGAATTTTGCAGCAAGCATTGTTTCGTATTTAAGATCACTTTTGTAGACAGATCTTGAGATAACGCGACAAATTTTGGGGCTTTTAAAGTTCGGAATTCTTTCTTCCGGATCAGAGATGTGTAGTGCGCCAGAGTAATATATGATTTAATATTCTTCCGTGTAGTACACTTTTCCATGCGAACTTCAATTTTTACAGCTTTTGTTTGAACTTTTTTTATTTTCTGCAATGTATGTCAACTATATTGGACTCTTTGCTTTCGTTCAAATTTCGTTGACGTTAGCTTATCCTCCCGGTCGTGTGGAGATTTCTGAAATATATGATTTTGAAGAATCTAGTTCGTATAAAGGACAAGATATTGATACATCCGTACTTTACACTTTGTCTAAAAGGAAACCTGCGCTCGTAAAACGAAGTACCGACGCTTCGTATGCCCCTTTCAATGTGACCTGTTCAAACGACAATCTGTTGAGGCCGGCTTCTGAAGGTTTAAATGAGGGCGAACAGAGCTATATCAACAAACGTATTTCTAAGGTTAACAGTGAACTCCGATCATTTATTTCTAAGACAGGTTTGAATGTTGACTTGGATAAGGTGGTTAACAGCTCGGATGGTCCACGTTTAGGAATTGCATTCTCAGGTGGTGGGTTACGGGCGATGGTTAATGGAGGTGGTGCATTCAATGCTTTTGACTCAAGATTCGAGAGTGACTCTCCACTTTCTGGTCTGCTGCAATCCGCGATGTATATCAGCGGTCTTTCTGGTGGTTCATGGCTTGTTGGATCAGTGGCTATTAATAATTTTACGAATATAACATACTTACGTGATAATGTCTGGAATTTGGAACATAGCGTTTTTGCTCCTCATGGGGATAATGTCATTGAAAATTTGAATTATTATAATGACTTGCGCAAAGAAATTGATCAAAAGAAACATGCGGGCTTTGACTGTTCTTTGACGGATTTATGGGGACGTGCTTTGTCCCGTAAACTTGTTGATGCTGAAAGGGGAGGACCAGGCATTACATATTCCAGTATGAGAAATCAAAGCTGGTTTCAAAATGCTGATTATCCTTATCCCATCATCGTTGCGGATAGCCGATTAGAAGAAGAAACGGCCATCCCTGCCAATACCAGTATCTTTGAGTTCACGGCGTATGAATTTGGTACATGGGACAATGGAATTAAAGCATTCATTCCAATGGAATATGTGGGAACTCACTTGTTGGATGGGGTTCCACCCGATAAGTCTTGCATTCATAACTATGATAATGCAGGTTTTGTTATGGGCACTTCAGCTACTTTATTCAACTCTTTTCTTCTTGACTGGAATGAAAATGTCAAAAAGAATGATACCTATTACGATATTCTTCATGCGATTCTTGAAGATCTTTCTAAGCATCAAGATGATATTGCTCCTTATCCCAATCCTTACCAAAATTATACTACTTCCAATACCTCTGTAGTGAATGCGTTCGAACCGTATGATACTATTGATCTAGTTGATGGTGGTGAGGATAGGGAAAACATTCCCCTTTGGCCTTTGTTACACCCACAACGATTTGTGGACGTTGTATTTGCGATTGATTCGACTTATAATGATCCTTATGGTTGGCCCCTTGGATCTTCCATTGTTGCTACATATGAGAGAGTTGTAACCTTTAATGCGAACAAGAGTGTTGATGTGCGTGGATTTCCATATATTCCGGACGAAAACACTATTATCTCTTTGGGACTAAACACTCGTCCTACGTTTTTTGGATGTGACGGTAAAAATACTACAGCAGGAAATCATGATGTAGACAATAATACCCCACCTCTCCTTGTATACTTTCCAAATTACCCTTGGACTTATTATTCCAATATATCGACATTTACTATGAGCATGGACGACAAGATGGCTAATGGAATTCTTGAGAATGCATTTATGTCGACTACGCAAAACAATAATGAATCTTTTGCAGTTTGCTTAGCATGCGCTATAATTCAACGCTCTTTGGAACGCAAGAAATTGAGTACTCCTACCCAGTGCTCTTCTTGTTTCCAAGAATACTGTTGGGACGGAACTCTTGCAACTAGTACGGCTTCTGTATATGATCCTACCGTAATGTCTGCTGCGACAACATCTCGTGCACCGTCAGGCACAACCTCGGGTACAGCCTCTAGTACAACATCTTCATCTGTAGCATCAGCCACTCCCACTCATAAACATTGGTGGGACTCGATTTTCGAAGCGAAAGAAAATCCGTAAAAAGATTCCATTGATGTTGTTTCAATGGATTCTCAGGCATGTGAGAAATTTAGAATAGATAGATTTACCTTTATTGTACTTGGTTACGAATTCGTTATGAAAGAGAACTAAGGATTTTCCTCATTCGTGAGACTGCTCAGTTAAACCCTTTACGTTTGATGGAGCTATGTAAACGGGTAAATGAATAATTTGTTATCTCT ->Transcript_18 len=2836 CDS=946-2578 exon=0-2836 five_prime_UTR=0-946 gene=0-2836 mRNA=0-2836 hmm_matches=Na_H_Exchanger:1216-2473 three_prime_UTR=2578-2836 -ACGGTTTATTGTTTAAAGGCTAGAAGTAATGAAAATCGTCTTTTATAAAAGTCTAAATAGTATGAAATTTGATATTAAGTAAGCGAGTGGCCTTAAACGCTCTATATTCTGGATCTGCAACTCATGGGGTGAGACTCGGTTGTGTCTATGTAACTAACCTTGCCACCACATTGTGCATGAAAGCAAATGATTCATTTAAACGTAAAGTGTTTCTCGTTTTATTTGACATGAAAGGAGCTCTTGAATTCTTCCTAAGTTGTTCATGAGGAGAAATTGTCCACTGAAAAAGAACAAGTTCAAACATTCGCTCATGACTTTTCTCCTGCCCGTAATCGAAATACCAAATTCCTTCTGTGTTCGGTAGTCAATACCTTGGCCGTTATCTCATCAATTAACAAGTTTCCCCCACCAATGTGATTATAGGCCTGGCAATTCCTTTGACAGAACGTGTCAACTGGATATTTGTGTAATTTCGTCGTTCTCGTTAATCCCATACAGTTTTTCATTGCTAATTTAACTCTACATATGGTTGAATTACAAGAGTGCTTGTTTTATGCTCACTACTTCCTTTTTTAAGTAGTATAAAAGATTGACTTCTGTTACACTAGTAATCAAATCCTATAGAAAGAATTTTCAATATTTTTGATTTATTGCCACTTATGTCATATTGAGATAAAATGCCTTAATCCAATCAGGTCTTTTTAGCTAAGTTATAATCAAAGCTTTTTGCTGCCGAGGTATTAATAGCTTACAAGTGAGTACACAACACCCTTTCAATCAATTTAATGGTGCTAAATTTATATAAACATACGATGTATAACAATCGCACAATATTTACAATTCACTATCCTGCTAAAATTGTATAAAAAAAAATAATATAACAGCCCACCTCAAATGTGCTTAATCAGTCTCAGTGAATTTAAAATTGAATAGTTACTTAAAAGGCATGTTTTTTAAGTTGATAAGCGTTAAAACCCAAGTAACAAGCTTTGTTACTCCAATCAAAAAGATAACTAAGGTACCCCGGTCCTCAAGTATAAACCACAGGCATGCACGCATCAGTCCGTGGCTAACTGTATCTTTTGCCACATTTTATGTCGAATACTCTAAAAAAAATATTATAGGAATTTATTACAAGAAAACATTCTCTTGTGGATATTGCCTAATTACTATGGGCTGGAGACAACTTGATATAGACAAAGTCCATTTAGCTTTAATAGTGGCCGGGGGATTTATAACATTTTTCTGCTATTTTTCAGAAGTTTTTCGAAAAAAATTACTAGTTGGAGAAGCTGTTCTTGGAAGTATCACTGGATTAATATTTGGGCCTCATGCTGCTAAACTCGTAGACCCTTTTTCCTGGGGTGACCATGGAGATTACTTGACAGTAGAGATTTGTAGAATCGTACTTGATGTGCGTGTGTTTGCTTCTGCAATAGAACTCCCCGGTGCATATTTTCAACATAATTTTCGAAGCATCATTGTAATGCTATTACCAGTTATGGCTTACGGGTGGTTAGTTACAGCTGGATTTGCATATGCATTGTTTCCACAAATTAACTTTTTAGGATCTTTGCTGATCGCAGGATGTATAACTTCTACTGATCCTGTTCTATCAGCATTGATTGTAGGAGAAGGTCCATTAGCTAAAAAGACTCCTGAACGGATTCGGTCTTTATTGATCGCTGAGTCTGGATGTAATGATGGAATGGCGGTTCCTTTTTTCTATTTTGCTATCAAACTTCTTACTGTTAAGCCATCGAGGAATGCAGGGAGGGATTGGGTGCTGCTTGTTGTGTTGTATGAATGTGCATTTGGTATATTTTTTGGGTGTGTAATAGGGTATCTTTTATCGTTCATTTTAAAGCACGCTCAGAAATACCGTTTAATTGATGCTATTAGTTATTATTCCCTTCCGCTAGCGATACCTTTATTATGTTCTGGGATAGGAACTATTATTGGAGTTGATGACCTGTTGATGTCCTTTTTTGCTGGAATATTATTTAACTGGAATGATTTATTTTCCAAAAATATATCTGCTTGTTCTGTACCTGCTTTTATTGATCAGACTTTTAGTTTACTATTTTTTACCTATTATGGTACAATCATTCCCTGGAATAATTTTAATTGGTCTGTTGAAGGCTTGCCTGTTTGGCGTTTAATTGTCTTTAGCATATTGACTCTAGTTTGTCGTCGATTACCGGTTGTATTTTCGGTGAAGCCTTTAGTTCCGGACATTAAGACATGGAAAGAAGCCCTTTTCGTTGGACATTTCGGACCAATAGGGGTTTGCGCAGTTTATATGGCATTTCTTGCAAAATTACTGTTGTCCCCGGATGAAATTGAAAAGAGTATTTATGAATCAACTACAGTATTTTCAACACTTAATGAAATAATTTGGCCGATCATTTCGTTTGTTATCTTATCCTCAATCATTGTTCATGGTTTCAGTATCCATGTATTAGTGATTTGGGGAAAGTTAAAAAGTCTGTATTTAAATCGAAAAGTCACCAAGTCCGATTCCGATTTGGAGTTACAAGTAATAGGGGTTGATAAGTCACAGGAAGATTACGTTTAGGAAAGCTCTTTTAATGTCAATTCGGATTTCCAAATTATTTTCAAATGTATTGTGAATCGCTGTCTCTGGTCAAAAAGATTACTGCACTCATATTTTGAAATTCCTTCTATAGTTGATATATACTATAAGATAAGTGATTCTCAGAATCACAAGGCTAACCACCAACAGGGATGGAGTGTATATTTTTGTTGTACATATATATTATCTACAATAGAGTAATTTTCGGCTTCTATAATTCATTTATTTTCTTACTACTCT ->Transcript_19 len=1250 CDS=215-1151 exon=0-1250 five_prime_UTR=0-215 gene=0-1250 mRNA=0-1250 hmm_matches=CRCB:236-566,CRCB:710-755,CRCB:782-1103 three_prime_UTR=1151-1250 -GGCTTTAAGTCTTTTTGAAAGAATTTTCTTTTTGTTTTGTTTTATTAACCTAAGTCGATTTAAAATACTTTTTCTCTCTTTATTTTAAGAAATTACTATAGTCTCGAAGCCTTTATCGAGGCTATCGCTCCGTATATATAGAATTGTGATAGACACTCCGGAATAGTTGCATTTTCCTTCTAATCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGCTATTAACACAGTCTTACTTTTGTATAATGTCTATGTTGGGGACGCTAGCTCGTCTAGGACTTACTGCATTAAACACATACCCAGGTGCACCGTTTTCTGGACTTTTATGGGTTCAATTTGTTGGATGCGTTATTATGGGATTTTGTCAGACAGAGTCTGTTTTCTTTCCTCGACCCAAACATAATGCTACTTTTTTGCTAGCCATTACTACAGGTTTTTGTGGATCTCTTACAACGTTTTCTTCTTGGATGTTGCAAATGTTTACAGGGATGGCTAACTTGGATCCATTTGAACGTAGGGGCCGAGGCTATTCATTTTTAAGTGTGGTTTCCGATTTTATGGTAACTATGTGCATTGCGATGTCCAGCTTAATATGGGGGAAGCAGATTGGAAAAACGACGGGACAGTGGAGAATTGGCAAAGTTGCATTTGCCTGGCCTATCCCGGCGCACACGCATATCGTAGTGCGGGTATTACTTTTGTTACTCTCGATTTGTTTTTTTGTTGGTGCAGCATTTTATACGGCATATACAACCAATGTGACACATCGTGGCATAGGTTTTAGTCTAATATTCTCTCCTTTTGCTGCCTTGACACGTTTGTATCTTGCGCGATTCCTTAATTCACCTCAATATTTTATTCCCTATGGAACTCTTTGTGCCAATGTCTTTGCTACACTTTTGCTTTCTATCATGTACATGATACCACAAATCACACACTGCACTCCTGTGTCTAGAAGTGTGATGTATGGAATCCAAAACGGATTTTGTGCTGTACTCTCTACCCTTTCAACATTCTCCAACGAACTCCACACAATGCCTATAAAACGAGCATATATTTATTGTATAATTTCAGTTGCTATTTCCTTTTCAATATGTGTCATTGTCGATGGAGCTACTGCATGGGGTCATGGTTATACTGAAAAGTATTAGACTTACTATTAAATTAGAGATTTTTTTTTTAAAGTTTTTGTATATAATTAAAGTATTCATTCTTTATCTTTAATATTATTTATTTTTTTTTGTTTATAA +>Transcript_0 len=2141 CDS=242-1958 exon=0-2141 five_prime_UTR=0-242 gene=0-2141 mRNA=0-2141 hmm_matches=TPP_enzyme_C:1454-1787,TPP_enzyme_N:260-773,TPP_enzyme_C:629-746,TPP_enzyme_M:632-740,TPP_enzyme_M:851-1244 three_prime_UTR=1958-2141 +CCACATTAACTCAATGTATCATTGATGACGGAATGTTGCTTATATAGCCAGAGTAACCCTGCTCTGAAGCATCTAAGGTTATATCTTTTTAACTTTTAGCTAGCAAACTCACTTGTTCCTTTAAGTTCAGAAAGTATCTGCTGGTTATTCAACAGATAATTATCTTGCGAAAAAGGAATACACACTCAGCATTGTAATTTGTTGAGTATATTTCACAAGCACATTAAATTGCATTATCAAACATGAGTGGGGATATTTTAGTCGGTGAATATCTATTCAAAAGGCTTGAACAATTAGGGGTCAAGTCCATTCTTGGTGTTCCAGGAGATTTCAATTTAGCTCTACTTGACTTAATTGAGAAAGTTGGAGATGAGAAATTTCGTTGGGTTGGCAATACCAATGAGTTGAATGGTGCTTATGCCGCTGATGGTTATGCTCGTGTTAATGGTCTTTCAGCCATTGTTACAACGTTCGGCGTGGGAGAGCTTTCCGCTATTAATGGAGTGGCAGGTTCTTATGCGGAGCATGTCCCAGTAGTTCATATTGTTGGAATGCCTTCCACAAAGGTGCAAGATACTGGAGCTTTGCTTCATCATACTTTAGGAGATGGAGACTTTCGCACTTTCATGGATATGTTTAAGAAAGTTTCTGCCTACAGTATAATGATCGATAACGGAAACGATGCAGCTGAAAAGATCGATGAAGCCTTGTCGATTTGTTATAAAAAGGCTAGGCCTGTTTACATTGGTATTCCTTCTGATGCTGGCTACTTCAAAGCATCTTCATCAAATCTTGGGAAAAGACTAAAGCTCGAGGAGGATACTAACGATCCAGCAGTTGAGCAAGAAGTCATCAATCATATCTCGGAAATGGTTGTCAATGCAAAGAAACCAGTGATTTTAATTGACGCTTGTGCTGTAAGACATCGTGTCGTTCCAGAAGTACATGAGCTGATTAAATTGACCCATTTCCCTACATATGTAACTCCCATGGGTAAATCTGCAATTGACGAAACTTCGCAATTTTTTGACGGCGTTTATGTTGGTTCAATTTCAGATCCTGAAGTTAAAGACAGAATTGAATCCACTGATCTGTTGCTATCCATCGGTGCTCTCAAATCAGACTTTAACACGGGTTCCTTCTCTTACCACCTCAGCCAAAAGAATGCCGTTGAGTTTCATTCAGACCACATGCGCATTCGATATGCTCTTTATCCAAATGTAGCCATGAAGTATATTCTTCGCAAACTGTTGAAAGTACTTGATGCTTCTATGTGTCATTCCAAGGCTGCTCCTACCATTGGCTACAACATCAAGCCTAAGCATGCGGAAGGATATTCTTCCAACGAGATTACTCATTGCTGGTTTTGGCCTAAATTTAGTGAATTTTTGAAGCCCCGAGATGTTTTGATCACCGAGACTGGAACTGCAAACTTTGGTGTCCTTGATTGCAGGTTTCCAAAGGATGTAACAGCCATTTCCCAGGTATTATGGGGATCTATTGGATACTCCGTTGGTGCAATGTTTGGTGCTGTTTTGGCCGTCCACGATTCTAAAGAGCCCGATCGTCGTACCATTCTTGTAGTAGGTGATGGATCCTTACAACTGACGATTACAGAGATTTCAACCTGCATTCGCCATAACCTCAAACCAATTATTTTCATAATTAACAACGACGGTTACACCATTGAGCGTTTAATTCATGGTTTGCATGCTAGCTATAACGAAATTAACACTAAATGGGGCTACCAACAGATTCCCAAGTTTTTCGGAGCTGCTGAAAACCACTTCCGCACTTACTGTGTTAAAACTCCTACTGACGTTGAAAAGTTGTTTAGCGACAAGGAGTTTGCAAATGCAGATGTCATTCAAGTAGTTGAGCTTGTAATGCCTATGTTGGATGCACCTCGTGTCCTAGTTGAGCAAGCCAAGTTGACGTCTAAGATCAATAAGCAATGAGCAAGCTATTGAGAGTGGAATTGGCAAACAAAGTTTCCTTTGATTTATATGTTTTTTATGATAAGCCCATTCAATTCATATAGTCTTTTAGTATAATGATTAGTTATTAAATTTATGTTTAAAGCAACTTTTTAGTTTAAAATTTTTCAAGTCAAGTTAGGGTGTACGTAAACAAACAATACC +>Transcript_1 len=2209 CDS=382-1717 exon=0-2209 five_prime_UTR=0-382 gene=0-2209 mRNA=0-2209 hmm_matches=CRAL_TRIO_N:1579-1597,CRAL_TRIO_N:511-541,CRAL_TRIO_N:685-820,CRAL_TRIO:688-823,CRAL_TRIO:916-1354,CRAL_TRIO_2:958-1354 three_prime_UTR=1717-2209 +TTTTTTTTAAAATACCAACTCAGTTTTTGTCGAGTGATTCTTCTTTTTTATTCATTCATTCGGTTAACTAAGTTCCCTATATTATTTTGTTTTCTACTACAAGCATTACGTTTTGTTTTTCAGTGAGCTTGTTTCGCATCTCTGACCAAAAGGAAGCAAATTGACGGCTAGTGTATTTTTGACTCGTCACATTCTTTTGTCTATCTTTGCCAATTTTTCAAATTATTATATATCTTCGAGATTAACCTCCATTCTTTAGGCTTATTCTCGTAATTTCCTTCTCAATTGAGTTCAATTTTATTAATATTGATTTCATCTGATATATTTTTTCCTTGGACTTTTTCTAGATTATATTTGTTTGCGCGCAATTTACTTATTAAATATGCCTGAAGGAGCCGGTAGACCGTGGAATCTCACAGAACTTGAAGAAGAGAAGTTGAAGACTATGTGGAGTTATTTGTTTAAGCTCTTCGGCATTACTTTACTCGAAAGAACTGAATCTTGGTACACAGTGAAGACACACTTATCTGATGATTCAAGTAGTTCCTCATCACATCGTTTAAGCAGCGTCTCATATGCGAAATCCCGTACACGACTTGAACTAACGTCTTCATCTCATGGCTCGGACACTCGCAGTTTTAATGATAAAACCAAAAATGTGCATTTGGAAAGAGTTGAAAAAATTGCAAGTGAATGGGACCCGGAAGGGCTTAGAGTTTGCTTTTGGGATGCTGTTAATTGTGATGATCCTGATGGCCTTCTACTTCGTTTCCTTCGTGCTCGAAAATGGAACGTTGAGGCTGCGTTGGAAATGTTCATGAAAACCGTTCACTGGAGAAGTAGAGAGATGAATGTTGGTGAAATTGTATGTAACGCTGACCACCTTGATAAAGATGATGATTTTGTGCGTCAACTAAGAATCGGAAAGTGTTTTATATTCGGTGAAGATAAACACAATCGTCCAGTTTGTTATATTCGCGCACGTCTTCATAAAGTTGGTGATGTCTCACCCGAATCGGTTGAGCGACTCACAGTTTGGGTCATGGAAACTGCTCGTTTAATTCTCAAACCTCCTATTGAAACTGCTACTGTTGTTTTTGATATGACTGATTTCAGTATGTCCAATATGGACTATGGGCCATTGAAATTCATGATCAAGTGTTTTGAAGCACACTATCCCGAATGTCTGGGTGAATGTATTGTACACAAAGCGCCTTGGCTTTTCCAAGGCGTTTGGTCCATCATCAAATCTTGGCTTGATCCAGTGGTTGTCTCAAAGGTTAAATTCACTCGTAATTATCGTGATTTGCAACAATATATAAATCCTGACAATATTTTAAAAGAATTCGGTGGGCCTAATCCATGGAGATATACATATCCAGAACCCTGTCAAAACGAAGCAGAAGCTCTGAAGAATGTTGAAGCTCGTAAGAGTCTTAGAGCAAAAAAGGATGCAATTGCTAAACAGTACGAGGAAGTTACAATGGATTGGATTTTGAACAATGGTGACATGGCAGAAGTGAAACAAAAACGTCGTAAGTTAGCTTCACAACTTATTGATGCATACTGGAACTTGGATAAATACATCCGCGCACGCTCAGTTTACGACCGCATGGGCCTAATTGCTCCTCAAACTTCCCATACTTTGCTTCTTTCTCAACCTACAAATGGAGATGTCAAAGAATCAATGGTAGAAGTTACTAGCTCGGCAACTTAGTCGGTCGTAACTTTCAATATTCCTGCTATTTTACATTGTAATCCTTCCCCTTGCCTATACTCCCGTATACTGACTAATTGTACTTTCCCGTGTTATTCTAAATAAGATGCTGGCTCAAAATATGATTGTATCATCTATTAATGCATAACTTTCAAGATCTTTTATATCAATTAGTTACATATGAAATCTCTTTCCTACGTTGATTTTTACACCCCTTTTCGTTTTACCATTTCCTTATCGCTTTAATTTTTTAGCACTCTCTTTAATGCACTTAAAATCATCTAGAAAGGGATAACTTTTTTTAGGTCTTATGGCTTTTCATTGAAGTTGTTGGTCGCAATACTTATCCATCCATTTTGTCTTTATTAGAATCAATGATCAGTTTTATTTGCAAATTAACTTAGATTTCTTGCTATTTATTATTATTTTTTATTTTATTGTAGGAAAGCGGTTCGAAATTAAAAAAAACAACAAGCTGAACACCTAAATGCC +>Transcript_2 len=1291 CDS=376-694 exon=0-1291 five_prime_UTR=0-376 gene=0-1291 mRNA=0-1291 hmm_matches=Img2:442-691 three_prime_UTR=694-1291 +ATTTTATTGTAGGAAAGCGGTTCGAAATTAAAAAAAACAACAAGCTGAACACCTAAATGCCTACTCCAAAATATAGTATTAATTTAATGAGTATGCACCTTCGCTGAAGTATATTCCGTGCCGTAAAAATACTTTCGAGTTTAAACACGCGTGAGGTTCAAGCACCGATTAAATTTATTTAAAACAAGAGCGTTTTATTTTATTTTAATTGTTCTTAGTGAATCACTTAATCTTAGGCTCCTGTTTGACAGTTGTTTAAAACTTACAAATTTTTGGAGGTTATGATAGAAATCCTCTTTATTCGCGAATGCACGACGACTTCTTTTACACATCCACCATAAATTCCTGCAACTCGTAGAAAGTTTTGTTGAACCAAATGCGATCATCCTTAAAGCCAGTGCTATCAAATTTGAGGTTCAACTCAACAATTGCATCCGAATCACTTCGGTTTCATGTTTCACGTACACCTTCAAAAAATCTCCCAGTCTATCTAGACTACAAACAACGAGGAACGAAAATTCTGACTTTAATTCGTAAAATCCATGGTGATTCTAATGCTTTGCGGCTCAGGCTCATTTCCACACTTAAAATGTCACCGAAAGATGTTTATGTAAACAAGTTAACAAATCAAGTTGTCCTAAAGGGAAATCACATAGTCACAGTTCGTGAATGGTTACAAGACCAAGGTTTTTAAGTTCCTAGAATTTTTCCTTTTTTAGATTGTTACTATGTATGTACGTATCCTTCTTTCAAAGGAATGATAAAGTTGCTTTTTATCAACATAAAACTCTCGAGCATATATATCAATTTGGCTTTTTAGCATATTACTTTTACTTCATCTCCTTGTTACAGCGGTGATAATGTCAAATAAAACACAGCTGTTGCAAATAATTAATCTCGATTCATTTCTTCTCATCATACGTGGTTTTCAAACTTGACAATGGAAAAAATGCATCTTTTGTGATGGTTTTCCTTAACTACCTTTAAATAAATAGTTATTCGAGCTTCAGTAGAAACATTCAAGAGGTACTTGCGTAAAAAGAAATTCAAACATCTGCTTAATGTGAGGCGTCCAAATGCTAAATACAATCTTTTTTTTGCTACCTATTCGTTTGTTTTGTTGAATTTATAAACGCTTAAAGGAAATTATAATATATATATCGAAACTCCGGTGTTTTTATTTTTTGACTGTAGTTATAGACAGAATACGTTTAAGGCTATTAGGGTATATAACTAAATTAAAAATTCTTTTCTCAATATTGTATAGTTTGTAAATTGACAAATATTAAAT +>Transcript_3 len=1681 CDS=517-1534 exon=0-1681 five_prime_UTR=0-517 gene=0-1681 mRNA=0-1681 hmm_matches=DUF4210:1264-1330,Chromosome_seg:1375-1468,Chromosome_seg:568-604,DUF4210:931-1132 three_prime_UTR=1534-1681 +TCCCTTCACACATACTTATAATCCTGAAATCTCAACGACTTTTTCATTATTTTTGAATTGAACTTGGATTTGTCTGTGATAGGAATATTTTGACAAACATTTTTAGCTTTTAAAATTTTTGCTTTGTTCTGAAGACGTTGATTTACAATTTGCTTATGAATTAATTATTCACGAGAAGAAAATTCCTTGTAGTTTATCCCTTTTTTATTGGTGATTATAAGCTGAATAACTCTTAATGTTGGGAATTATATTTTCTTTAGTGAACTGAGGCTTTCTCGAAAAATACTTACGGTTATCCATGATTTAATGATTTTCTGTTTTTTTTGTTATTTTTTTTTCGTTTATCAAAAAGTGGTTAAGCATTGACACGATATAAGGCACTTTATTTCCGTGTTGAATTTTTTGTTTTGTTTTTTCTTGACATTAATACCTTACTTTCCTTGAATGCGAACAAACCGCATTCATTTGTATTCGATTATCGAAAGCCTTTTATTCCTTTTCTTTTTCTTTTTTATTAATGCCAGCTTGTTATTGTGCGACATCAACGTCTCTTGAAAATAATGAATTGCTATACAAAAATATTCGAAACTTGTTCTCTACTAGCAGGAGTTTTCCAATCGAACAAGAATGGATGAATTTGAAATCGATAAGTCAGATGAAAGACTTTTTTTCAAACTTTCCTGGTAATAGTAAGGCGAACAACCACTTTCTCTGTAATTCTCCATTGAAATTCGAAATTTTTAACAATGAGAAATCTGTTAAACCTTCAAATGGGCCTCATCTGTTCACGAGATGTTCATGTCGTTGTAATAAATTATTGTCTGGTGATTATATAACTCAACAACAACCAATTGATGCTTCTGCTGAACATTCTCTTAACGCCAAAGGTATAAATACCTATTCATTGAAGAACTGCTTTCAAAGGAGTGGTTTTATAGGATCATACGAGGAGAGTTTGTTTAGTGGTCACATGCCTTACTGTTCATCAGTACCTTTTGAGTTTTCCATAGAAATTGGGGTTATTTCGTTTTGCCGATGCAAGCCTTCACTTGTTTTCCCGCCACATTTAAAAATAAATTTTGTGGCTTACTCACTCGTTGGAAATGTTGATAATGTGCAATTTCCTTATATCGGTCGATTTCGACTGAGAAGTCAAAAAAGCGACAAAGTCATGAATAAAGGCTATCCATTCGGATATAGAATTCCATCAGTTGGGCAATTACAACTAATACTTCGACAAACTAACGGTTTAGTCATTAAAGTTTTTTTGGTGCCTTATAATGTTTCAAGTATGGTTGATTGCTCTAAAACCTGGATTCGCCAGAAACATTATCTTCAGCAACTAGACGATAAAAGTGGGAAAATTTTAAGTCATTTAAAGTTTGGATTACAGTTACAAATTATTTGCACTTCTGCAGGACACCATTACCTTTATGACTCTCAAAGAATTATTTTTGTCCAGCAATCTTTAGGCGGGTTATATGGGAACACGAAGATTGTGAATGAAACACTGCTGTCAGAAAGTTGTCGATAGCTAGCCAACTTTTTACTGCTGACATGTAAAGATTTATTGACTTATATAACTCTTTTTTAATGAAAATTAACATTCATGCGTTCCAAGTTTATATTAAATTAATTTAATATTATACTCTTTGCTTATCTACGTCATTTAAAACCATCC +>Transcript_4 len=3607 CDS=309-3531 exon=0-3607 five_prime_UTR=0-309 gene=0-3607 mRNA=0-3607 hmm_matches=CPSF_A:2742-3480,MMS1_N:2853-3009,MMS1_N:546-1872 three_prime_UTR=3531-3607 +AGGTTCTCGAAATTCCAACGATGGATATTCTTACATACATTCAACACAACCCAACATATTAACTCGAACAAGCCATGGTTGGTTGTCAATAATCCTTTCACATTTGGAGGAACTCGTAAGGATCTATCTTCTAAATAAGGGCGTTATATATATTTAAACCTGTACATATCTATTTTCATTGATTTTAATGTTTTTTCCGTATTTGCTAATTTCTTTGATGCATACGATTAACTAATAGCTTTTTCTATTCTATCAAAATTTGACTCTAATCAAATTAAATTGGTTCCAAGCGTTTAACTTTGTGAATTCATGGCAGAAATTATTCATCATTCAAACGTATTCACCTGGGCTTTTCATGTTTCCGAATATGATGGTGCTCCTCTCCTTTTACTTGGATCTTTTTCCTCTGTAGCTTCTGTGAGTTTAAAGCGATCTGGTGATTTACTACTTTTTGAAAGATTCACGTTGCCTGCAAGAACGAGGTCTGTTGCTTTGTTATCAAGCCATTTCCTTCAGTCAGAATCAGGTAGACATTCAATAGCGAATATTTTAATTGCTACTGAAAACGGAAAATGCTACTTGTTGCAGCTCGTCAAAACACCAGAAAAAGCGTTTCCGACGATTCGTATTAGAGATGAATTCGTTCTTGATACTCGAATGTACAACCATGAACAATTAGGAAAATCAATTGATTTATGCCCAAATGCTTCCTTGTGGGCTACTAATTCTTTTGCTGGTGATATTGTATTTTTCTTTTCACATCATCCTTCCTTAAGCAAGCAAGTCTTCGCTCAACTTTCTATCGATGGAATAATACTTCATACCATATTTGTACCTCCAAAAAGATCCTCTTCGTCTTGTGTTACGTATGTTTGTCTTTTTCTAGATTCAAATTCGAATCCTAGAATCAATGTTTATAGGTGGTCTAAGACGGAAACCTTTTCTGATGCTAGTTCTTACATAACCTTCTCAATACCGGTTCCATCCGAATTTTCTCTTGCTTCCCATATTATCCCTTGCTCCAATATTCCTGATCATTTTTTAGTATTATTGGAGACAAAGATTTGTCTGCTTTCTGTCCCACAGATAGAATGTGGGGATCTAAAATTTTTACAGACCGATCTTCCATGCAGCGGTTCACATAATTATCCATTGTCTATTGCAAATGATAACGAAACTCCGAATTGTTGCTATTTAACCTACGAAAATGGAGATTTGTATCGCATTCGTTACTCTATTTTGTCTATTGATATTAATTTAATTGGAAAGACTGGATCTTCTTTAGGAAATTTGATACTACCTTGTTATCCATACATTGTTTTTTGTGGTGACTGTTCTGATACATTAGTGTATGATGTTTCGGTATCGCCTATGTCCTTTTTTGGTAGCTTAATTGCTTGCGCTCCAATGTGGGATTTTGTGTATTCCTCATCAAGGCATAACACTTTGTTGGATGAAGACATCAATTGTAATACAGTTTATGCTACTGCTGGCATTGGTAAATCTGGGTGTTTGGTCACAATGCGTTACGGGTGCTCATCCACTACTTTGCTTGAAGCAATATTAACTGAGGGAGCTGTTTTATCAGGAATTATAAATTCTAACCACAACTCTGAATTTTACGCTTGGCTAACTTATCCTTGGCAAACACAAATTTTAAGGCTTCATCTCGATGGGGTCGTCGAAGATGTTACCGAAAGTCTTTTTTTGGATGATATAAAAGCTTTATATGTTATAAATTACCAAAATACGTTTATCATTATTACGGGAAAATCCATTTATGCTGTTACTCCTAGTTGTACAAAGTATAACCTTCTTGAGGTTTCAGGAGATGAAGAATTTGTTTTGGCTGCTTATAACGAATTAATTTTCATCGTTAAAAAAGATTTAATGAATTTCAAAAGTCAATTGCTTACACTAAAACTAAATACTCTTTCTAATGGTACACTTGAACTTCAGTCGCTTCCGGATTCCTTCGATCTACACGATGTCCCTACTTGTATTACTTCCTTTTCTTTGGAAAGAAAGCTACTGGTGATACTGGTTCATCCTTCACCTTATTTTGAATGCGTTTTCTATGATGAAACCTCACACTCTAGTGTCTATAAAGTCCCCTTAACAGGTTTTCAATTTGGATACCTTCCTCATAGCATATCGTATTTGAGAAAATCAAACCGCGCTGTTTATGTATTGATTTCATCCAACTCTACTCTTTTAACCGTCTATGTAACTCTAACGTTAGAGGGAGTACCGGATTTTAAAGTTTACTCTAATCCTATTTCAACAGACTTACCACTCACGTTACAGTCACCCTCCGATGAGTTTTCAACAATTTATGCATGGTCTGACTATTTGTATATAGTGGGTATCGATATGGAAACTGAACAACCTACGCTGAACCAGATACTTGAAGTAAATGACAGTTTTACTTGTGTTTCTGGTATTTACGATATTCCAAATAAGTTCCAGAACAGTGAATCAAGAATCATAGTGTATTATTCGAATAATACTTTGTACCTATCGGAACTTTGGCTTCCACAGCGAACCTTTTCTTCAAAACTAAATCTTGCAGCAACTCCCAAGAGATTACTTGTTGATAAATATACGAACACTTTAATCATTGGATGTTGTCACGTTTTAGTAAATGAAATTACAACCTCAGGTCTTGCTTTTTACGACTTGACTAACTCGCGACTTTTCCCTGTCAATTGGCCTTCAATGGATATTAAAGGTAAACCAATATTCAAACCGGAGGAATTATTATATTCTATGTCTTTTTGGATTGTAGCCGACGATCAAAAAAGAAAATATAGGTACCTTTGTATAGGAACAGGGGTACGAAAAAACGGATTAACTACAGGTCGTTTGTTAATTCTTACCATGAATAAAGATCATGACAGCAATGCTATAGAACTTCGCAATGTCATCACAATTAATATGAAAGACCCTATTTATTCCGTTTGTTCGATCGGAAAACATGGATTGTGTTATGCAACAGGACGAAAGATTGGTGTAAAGATGTTGGACTTAGACTCAAAGAAGTTTTGCAACAGTGATTGTGAGTTACCTGTTCGGTCTCCCATTGTATCGATGTCAACGTATAAGGACTATGTGTACACTTCTAGTTTAAGAGATTCTGTTGCCGTGTTCCAGTATGATAGTGAAAACAACTCCCTTAATTTAGTTTGCAGCGACACATCATCGAGACTAGGCATTGATTGCTTTTACATTTCACAAAAAAAATTATTGTTTTCTTGTGACAAAGACCGGTTATTAACTTGTTTCAAAGTTGAGGGTGAAGTTTGCACGTCTACCAGAGAACAAATGCTCCAGCCAATTCTTACTACAGTGTCTCAAACAAAAACAAATGCCTTAACTAACCATTTAAAGTATTCAGTTATTCGGGTGGATAAAGATAATCATAATATTGTTTGGGGATTGATGGGTTGTACTTTAGATGGGAATATCTTCAAGATCTTAATGCCTAACGATCCGACTTCGTCGGATACAATTATCTATTCTGATACTTAATGTTATCACACATTAGAAATTCCAATTTACAACAATAAATTTATCAGAGCAATACTAATGAACAATTTTTGGATGG +>Transcript_5 len=2333 CDS=443-1712 exon=0-2333 five_prime_UTR=0-443 gene=0-2333 mRNA=0-2333 hmm_matches=PAP2:1166-1391,PAP2:656-749,PAP2:737-956,PAP2_3:869-1373 three_prime_UTR=1712-2333 +ATTTATACGGGGCAATTGAAATCGACTAACTCCAATTGTATAGTTAAATTGGAGTATTTTGGTTTGTATTTGCAACCAAAGGTTTTTAAACTAGTATCTCTTTCGGAGAAGCTTTTTTGCCTCTGCAAAAGTTCCTTTCTCGAATTGGTTTTTTGAGGAAAAGCAAGTTAATAAACTAATTATATTATATATAATTAGCAATTTTATAAAAAAAATAAAAAAATAGCCCTGATTGCTGGCAACTGTGAGCTGAACATTGGTTAATCGGTCCATCTTTTTTTAAATATTTTACATCGCTACTTTTAAGTGCTTGACACTTGCATTTAATAGCTACTTTCTTTCCTTCATAAAAATTCCTTTTTTTTCCTTTAGTTTTCCGGTTAATTCCTTACGAAATTTTTTTCGTACGCTTCCCTTTTTTACTCTGATAATTCTTTGAAGCAATGTCTGCTCTTTCGACCTTAAAAAAGCGCCTTGCTGCGTGTAACCGAGCATCCCAATACAAGTTGGAAACAAGCTTAAACCCTATGCCTACATTTCGTTTGCTACGCAATACGAAATGGTCATGGACACATTTGCAATATGTGTTTCTAGCAGGTAATTTGATTTTTGCTTGTATTGTCATTGAATCTCCTGGATTCTGGGGGAAATTTGGCATTGCCTGTCTTTTGGCCATTGCGTTGACCGTTCCTTTAACACGCCAAATTTTTTTTCCTGCCATTGTTATCATCACCTGGGCAATTTTATTTTACTCTTGTAGGTTTATTCCAGAACGCTGGCGTCCACCCATATGGGTTCGTGTTTTACCCACACTTGAAAATATTCTTTATGGCTCTAATCTTTCTAGTCTTCTCTCGAAAACCACGCATAGCATCCTTGATATTTTGGCCTGGGTTCCATATGGAGTCATGCATTATTCGGCTCCTTTTATCATTTCATTTATTCTTTTCATCTTTGCACCTCCTGGAACTCTTCCAGTTTGGGCTCGAACTTTTGGTTATATGAATTTATTTGGTGTTCTTATCCAAATGGCTTTCCCCTGTTCTCCTCCTTGGTATGAAAATATGTATGGTTTAGAACCTGCCACGTATGCAGTACGTGGCTCTCCTGGTGGATTGGCCCGTATTGATGCTCTCTTCGGCACTAGCATTTACACTGATGGTTTTTCTAACTCTCCGGTTGTTTTTGGTGCCTTTCCATCTCTTCACGCTGGATGGGCCATGCTGGAAGCACTTTTCCTTTCGCATGTGTTTCCTCGATACCGCTTCTGCTTTTATGGATATGTTCTATGGCTTTGCTGGTGTACTATGTACCTTACCCACCACTACTTTGTAGATTTGGTCGGCGGTATGTGTTTAGCTATTATATGCTTCGTTTTTGCTCAAAAGCTACGCCTCCCACAGTTGCAAACTGGTAAAATCCTTCGTTGGGAATACGAGTTTGTTATCCACGGTCATGGTCTTTCCGAAAAAACCAGCAACTCCTTGGCTCGTACCGGCAGCCCATACTTACTTGGAAGGGATTCTTTTACTCAAAACCCTAATGCAGTAGCCTTCATGAGTGGTCTTAACAATATGGAACTTGCTAACACCGATCATGAATGGTCCGTGGGTTCATCATCACCTGAGCCGTTACCTAGTCCTGCTGCTGATTTGATTGATCGTCCTGCCAGTACCACTTCCTCCATCTTTGATGCAAGTCATCTTCCTTAAATCAACGTGCTTTAAGAATATATTTCCAAAAGCTACATGATACATTGACTAGAATCGGTTTGATTCATAGTGGTATTGGAATGATGTTGTTCATTGTGTTTTTTAACTGTTAATCTGACATCCATTGAGTCATTCTTTACAATTTGTAAAATTAATTTGTATCACTAATTTTGAAGGAAGCTATTTTGGTATTAATACCGCTTTTGGTCTCCACTTCCTTTTCGAAACTCTTAACAGCGATTAGGCCGGGTATCTTCCAGTGTGATGTATAGGTATTTGTCGTTTTTTTATCATTTCCGTTAATAAAGAACTCTTTTATCCAGCTTCTTACACTGTCAACTGTTGTGAAAGGAACACATTTAGAATTTCATTTTCCTTATTTGTTGTGATTTAAATCGTTTGACATAATTTTAAATTTGGTTTGAAATGTGTGTGAGAAGGCTTGTTTTATTCATTTAGTTTATTGCTTGTTTGCACGAAAATCCAGAACGGAGCATTAATGTAATCCTTTTTTATTCTGTAAAGCGTTTTTATACAAATGTTGGTTATACGTTTCTAAAATAAGAATATTGTTATAATAATATAGTTTTTTCTATCATTTGTTACACACACTAAAGAGAC +>Transcript_6 len=831 CDS=264-774 exon=0-831 five_prime_UTR=0-264 gene=0-831 mRNA=0-831 hmm_matches=Prefoldin:327-372,Prefoldin:378-738 three_prime_UTR=774-831 +TTTCAAATGAAAATGCATTACGCTGCGCAATGGTTCTATACAGGTTATGGTTGGTAAATTGGATGAATAGATTTTGCAACAATTATCAATTACATGTGTATAACCAAAATATTCTGCCTATTTAGACTGTGTAGTTCAGACTTGGTTAGATTTGGTAATTAGGGAATAATACGCATTTCCAAATTTGTAACATTACTATACCTATTACCTTTGACACTCAGTTACCTGTTCAAAACAACCGCCCCTTTTTCTGTTGCATAGAGAATGAGTTCTTCAAATCCACGGGGAATTCCACCCGCTCAATTTTTTGAGTTCAAAGAGTTATCTATGGAGGAAGCTCAAGGTCATCTCGAAAAGTTCCAAGAAGCAATTGCAAAGTACAAATTCATGGAGACTAGTGTGGTCAGGAGAGTTGCTAGTTTGGATGACAAAATTCCTGACATTCGAAAAACGTTACAGAGTGTTCAGTTCTTGAAAGAGCGACAAGGTGACTCTTTTACTGTTACATATGAACTAAATGACACATTAAATGCAAAAGCAGAAGTAGAAGCTAAAGACAATGTCTACCTTTGGTTAGGTGCAAATGTTATGCTTGAGTATACGGTTGAAGAGGCAGAAGCATTGTTAACGCAGAAGCTGAACTCAGCGGAAGAAACATTGAAAGCATGTAAAGAAGATTTGGAATTTTTGAGAGCTCAAGTCACTACAATGGAAGTGAATACAGCTCGCGTGTATAACTATACAGTTTTGCTTAGGAAAAAAACAAAAATGTAGTTAGTCAAAGCTGCTTAATTTCTTTATAAATGTTTCCAAAATATATTATCATTTTAA +>Transcript_7 len=2146 CDS=242-1934 exon=0-2146 five_prime_UTR=0-242 gene=0-2146 mRNA=0-2146 hmm_matches=Zn_clus:1136-1163,Zn_clus:1550-1565,Zn_clus:290-389 three_prime_UTR=1934-2146 +ATACAAGTGCCTCCCAATCTGAAGTTGCAATTAAGGAACTTTATTTAAAGTATATTATCAGGTTAATTTTTTTAATTAGAAATAACAACCGCTGGTCGGTCTGAATATCAAGGTGCTTTTAAAGGATTCTCTAAAATAGGAAGTTTTGAAGGATCCTCGTTTTATTTTGTGCCTCCACTTCAAATACGGAGGCAACTACAATTGCTTGAAAGGAAATTATCAAGTTATCAATACTTCTAATAATGTCTTCCTCTCCTCCAGCTTTAAAGAAATTTCGAAAACGCAGCCCAAAATCATGTTTAATTTGTAGGCGCCGCAAGGTCAAATGCGACCGTCAGCAGCCTTGCTCTCGATGTAAAGAAAGGAACGAGGTTTGCACTTACGCAGATGATACCATTGATAAAATGAACGTCGGACCACATCCTAGTCATAGCGAAAATGCTTCTGATTCTGAAACCACACTGGAAGTTTCTCCCGATATTAATCCGAAAAAAAATGAGAAATTTGATTTTTATGGATGGAGATCACTCTTTGAGTTGATTAAATATAGAAAGGATAGCGACATGTGCTCATCTCGACCTTCGTTTTCAATTCAGGCTTACAGTAGCTATAAAGATAATGTGGTTGTTGAGAGTTTGGCGAACCTTTTACCGCCATTTTGCATATCACAGAAAATTGTTAATTTATTTTTTAAAACACTAAATGTTGTCTGTCCTATTTATGATCAAGAGACAGTAGAAAAAAGCTTAAACAACATTGAATCACCAGAATCTTTTTCGTACGAAGATGCCTTCACTTTATTACCAATTATTGCTGCAACTATCCAGCTGAGCGATTTGCCTGATGTTATTCTCAATTTTTATAATTCGGCGGGGATTACTCCATTGGAATCCAGCCGTCTTATAAATTTAAAACTTAACGAGATATCCGAGCAGGAATATAAACATTTATGCTTGCCTGATAAAGAAATAATTCAGATGCTGCTTTTGCGAGCGTATGCAACAAAATTTCGCACAAGAATAAGAGGAGTGAATACTGACTTATGTAGAAGCATTCACGTATCAACCTTAGTAACTCCCCTCTTCCAAGTTACGGAAAAAATAGGAAAAAATACGTCAGATTTGTGGTTTGCTCTCTGTGAAATTGATGGTTTGGAATGTGTATTAAAGTACCGTCCGCCATTCATTCAACACGACACTTATGGTCGTCTCAAGCCGCTTCGTTGTTTTTTTAATGACGATATTAGCTACAATTTTCATCTACTTCTTGGAAGGTTACTTGATTGTGGTGTTTCAATCTATAAATCTGTTCATTCACTCACCGTTAGTAAATTCATTGATAAACTGGAGAGTTATGAATCACAGCTTTCGCTTATTTTGGTAGATATAGAAGCAAAGTTTTATGACCCTTCTAATGAAGATATTCAATTTCGATACATATTTTTGAAAATGGTGTTCTGGACTGCACGTGTGAATTTGTATCAATGTTTTATTACCCTGGATTCAGGGATTTTAGAAGATGAAGAAACTATTATTGGTAATTTGGGTGAAAGTTGTATTCAGTGCGTGAGGCTACTCATATCTCAAATCACTATATTAGAAAAACGAGGCTGGCTTTTGGTAGCGTTGTTGGAGATTATCCACGCCCTCATGTTGGCTGCGTTTTGCCGTGATAAAGGCTTTGAGGTGCCTTCTGACTTAGGTGACATAACATTATATGTACAAGAAAGAATGGTTGATATCGTAACATTTGATGATGGCATGGCTGTCCGATTTGGATATGTTTTAAGATTCATCAACAGTATGTTACACCCAAATGAACCGCCTATGCAAGATGCAGAACCTGAAACCACGGAGGATCCCTCTAAATTATTCGCTGACATTTTTGATTTTACTTCAAATTACTTTATACCGTCCGCCCTTCTTGATCAGTGACCTAAACGAGCACTTTGTAATTTTTTTGTTTGTATGATTGATTAAATTTCGATTAATGTTCCAAAGTGGTTCTAATGTCAAATTTATCTGCTCTTTTAATGACTCTCGTTTTTTAATGTAACTATTTTTGGTTCAATATAGACCATTTAGGAATTAACTTTCTTACTATCCTTCTATAAAGTTGTCTTTCAAATACAATTTTTTCAACAAAA +>Transcript_8 len=3294 CDS=893-3110 exon=0-3294 five_prime_UTR=0-893 gene=0-3294 mRNA=0-3294 hmm_matches=RRM_1:1985-2177,RRM_5:2030-2189,RRM_1:2270-2303 three_prime_UTR=3110-3294 +ATAATTTAACAAACGAATAAATGCAGGAAACAATGCATTACGCAAGCTTGTTACTAAAGGCAGGAAGCATAGTTTGAATATAGGATGAAAACCGTGGATATCAATGTTATAAGCATTTAACATTGAATAAGTATGGTAGAGGTGAAAAGAATCAGTACTACGTTTCTTAATTGGCAACCTTGCACCTCAAACCCAGCTGAAGTGTACTTTGCACACGAGTCTATTACTACATGGTTTTTTTATACATATTAAATAATAGCAATGGTTATTTGAACTGCAATAACGGTAACCCTACCCCGATATCTCCAAGTTTGAAAATTTACTGCTTTTATGAAAATTTAGTTTACAGTTTGTTTTGGAAACGATTATGCTATCAGTGCAGAAGCTGAAAAAAAGAAAATTTCGGGATAGTAAAATTGTTTTCATGTCATTTCCCTGGCGGTGGTTTTGAAAAGCCCGAAGTTCCATTCATTTGAGTGGCAACTTAATTTTTCATCTATTTAAAGGATGCAATTTTAGTACCACTCCGCCGTATCTTCTACCTAAGACATAAAGTTGTGAAGAAGAAAAAAAAATAAAGGTAGTTGGAAGAAAACCATCTGCATAAATTTCCTTTTAATCGCCAACTCTTTACACATTTGGTTGAGTGTGAAATTTTTACTTTTTCTGTTTCACCCTCTAGTTATTTCCATTCATTGCACCTTGTGTAAATATTTTATTTAAAAATTGGACCAGTTTATCAAATGCATAAAATTTAGTACTTTAATCTTTTAAAGCTAATTTTGTTTTTGTTACTCTGTCCTCTTAATTCTCCTTCATATTCCCTGTTAATAATAATAAATTAAAAAAATTTGATGTTTTATTTTGGTTTTACTTTTCAAGTCAATCAATAAATGTCATCCTCGTCTAAAGATTCTTCGTTCCAAGTGGAAACTCCTGTGCAGAATATTTTAGAAACCAGTACAAACTCCGAGCTTCAAGACCAGGTATCATCTCCATATGAACCAGACTACAACTCACCTGTCAAACAGGCTGCTGCTTCGATAAGTGCTTTACAAACACAAGACGACACTTTATTCAACAACGTTGATGAACGTACATTAGAAAATAAGGATGGGAATAAGTCAGATGATGCAAACTTTGATCAAGTATCCGGTATTCCTTCTGGAAGTTTGGAGATACCAATATTAAACTCAGCTACTAGCAACATTCGGTTAACTCCTTCAGATACTTATAATAATATTCCAGTTTCGGACACCAACAATGAGGAAATTTCTAAAAACATATATGGAGCTCCAATTTTAGAGTCAACTTCTTCCGACTTTCAAAGTAAGGATTCACTTTCCACTACTCAACCAAGTGTTTCGGGGGGAAACGGATCTACCTCTCAAAGTCCTCCTTCACTCGACGTTGAGCAAAATAAGCCTTTTTCGATATCCAATGAACCAGTGGAACAAGAAACTGAAAACTCTTCTACTAAAGATTTACAAGTATACGATTTTCAGACCGCTTCAGAGCATTTACCTGAACAATCCTTACAAAACACCACTTATTATGATCCGTCAAAAACTTATAGCTCGGTGAATTTTGAAGAAATTGAATATGGAAAGTCTCATGAGAAATTAGATTTACCTTATAGAACTACTGATTTTATTCCCTATTCTAAAGACTTGTCAACTAGTCCTGAGGCTCACAGGACTAGTATTTATTCGTATAGTGCTAATTTGCCCAATTATTATAATGAGCATAATGAATTACATGAACATCATAATCCCCAGACACCCAGTTCCCCGGAATCTGCGTATAGTCCTGAAAATTTGCAACTTAATCATGAAGCACAAAATGTTGAATATTTGGGTAACAATGCTGCCGAGAAATCGTTGCAAATGAACTTAGAGGATGAACAAAGATTTCAACAATTTTTGAAAGATGAAGAAAGTATAATGTCAAACTGGTATCCAGGGCAATTTCCTTCAGCTTCTCGCTTATTTTTGGGTCATCTAAATACAAAGAGCTTATCTAAACGAAATTTGTGGAAAGTTTTTAAAATTTATGGGCCTTTAGCACAGATAGTTTTAAAAGCAAATTATGGTTTCGTTCAGTTTTTTACAAACGAAGATTGTGCTAGGGCTTTAAATGCGGAACAAGGCAATTTTGTTCGGGGTCAAAAGCTGCATTTGGAAATTTCTAAAATTCAGAAGAAATATCAAAATCAAATAGAAAACATGAAGAAAGGATCACATGTTACCAAAAGTAATCAATATTCTGAAATGATTGGAAACCTTCCTTATCCCACTAGTAGCAGAAAACGCACGCGATCTCCTTTAATGTCGAAGGGTAAATCCTACGATAGAAAGGGATCTATATCCATGTCTAAAAACTTCAGCCCTGATTGTGAAATACTAGTCACGGAAGACTGTCCAAAGGAATTTGTATGGGGAGTGGAAAAAGTCTTTCAGGAGCGTCGATTGAATATACATACCACTTGTTTGTACCGTGACTCAAACTTACAAGTCATTATTAAAAGCTGTATTATTAACAGCGTTAAATCCATTATCTTGATAAACGCCGGTTTGGCTCACCTAGGGAAGGTGTCGGTTCAAGTGTTTAAAGACGGATCTAGCGATTCAGAAGTCCGTTGTGATGAATATGCTGCTGTGGACGTGATGGTTGCTGCAAGTATTGTTCACCACGCAAAGACTTCTCTCATGCACTCAGCTGCTTCTAGTACGCCATCGTATAATGGTGAGCGTATTGTGCCTGACGTGCCATCTCCCTGTATATCAACGAATCCTAATCTACCAGCTTTAGTAGGTTCTTTAGATTCTGTTAATCTTCACCATTTATTAGGATTCATTCAAAATACCTATAGCACTACTTCATACATTCCAACTAGAGTTAGTTTTAATCCTAATGATACCGGAGGATCATTTGGAACAATTACATCTCAGTCCCAATTTGTTGTGAATGAGATGCCTAAAAATTATGCTCGTGATAATTACGAAGCATTGCATTCTCAAGAAAGCCGCCAAAGGTCTTCAGTTGCTGGAAACAAGCAACTTCAAAAGATATTAGAGCAGCTCGCAGAGCTCAAGCAACCTGATTTTTGATATCTGACCTTAGAAAAGGTTTATATATATTATTTGTTAACAAGTGTTTTAGGTAGCACTTTGTTAATATGGTTTTGCGATATATATGTCCTTGTCTTCAATATTTATTTCACTTTTTTCTCAGTTATTCTTGAAGCATTTATATGTAAAAACCAACAGACAAGTAATTTTTCTTGCTGCACGG +>Transcript_9 len=1504 CDS=0-960 exon=0-1504 gene=0-1504 mRNA=0-1504 hmm_matches=CRAL_TRIO_N:237-315,CRAL_TRIO:390-885 three_prime_UTR=960-1504 +CTAGTATTAAGGTCGCTGACGTTCTTCCTTTTCCTTTATACATCTTGTACAGACTGGGTCATTAGGTCTTCTCTCTACAACCATCGTCTAAACAAAAAGATGTCAGAAACTATATCGGATCCTTATCCTCTAACTAATCCAAATGCTCCATTAGGGCACCCAGGGCATTTGAATTCTACACAGCAAGCTACGCTAGATAGCATGCGTTTAGAGTTACAAAAACTTGGATACACGGAAAGATTAGACGATGCCACTTTATTGCGTTTTTTGAGAGCCCGTAAATTTAATTTGCAACAGTCGCTGGAAATGTTTATTAAATGCGAAAAGTGGAGAAAAGAATTTGGTGTTGATGATCTTATCAAAAACTTTCATTATGATGAGAAAGAAGCCGTTTCCAAATATTACCCTCAATTTTATCATAAAACTGACATCGACGGCCGTCCGGTATACGTTGAGCAACTCGGTAACATTGATTTGAAGAAGTTGTACCAAATCACGACTCCCGAGCGTATGATGCAAAATTTGGTTTATGAATATGAAATGCTTGCTTTAAAACGGTTTCCCGCTTGTTCTCGTAAAGCAGGAGGCTTGATTGAAACTTCGTGCACAATCATGGATCTAAAGGGTGTTGGTATTACTAGTATTCACTCGGTTTACAGCTACATTCGTCAAGCATCAAGCATTAGTCAAGATTATTACCCCGAAAGGATGGGCAAGTTTTATGTAATTAACGCTCCTTGGGGATTCTCTTCTGCCTTTAATCTTATCAAAGGTTTTTTGGATGAGGCAACTGTCAAAAAAATTCATATTTTAGGCTCAAACTATAAGAGTGCTCTGCTCGAACAAATCCCTGCTGATAATCTTCCTGCTAAACTCGGTGGAAACTGCCAATGTCCAGGTGGCTGCGAACTATCTGACGCCGGTCCATGGCATGAAGAACAGTGGATGAACAAAAATTAGACTTCTTTCTCCGAACGGGATTTAATTGCTAGAATAGATGAATGTGGTTTGTCCTTTGATAAGAGTAATAGTGTGTAGAGTTTTTGCCGATCTTTCAACTTTGTTCTGCGTTTTAGTTCTTAAAGGTCTTCGTTCTATTTTTACTCAGCATCTCAGGTACTTCCTTCTACTTACGGTTTACTATTCGACGAAATTATCGTATATAGATCGAAGCATATATAAATATTTTATTTCGAAAGTCATGTGTTGATCCATCATCAACATCATGGGATGGTTGCTGTTACAATTCTTAATCCTTATAGAAGGTCTCAATACATATATCGTTCATTAATTTTCCAAAAAAGGACGCTCGATGATCCAACTGATTTGATTGTTTCATCCATTCTAGATTATCCGAAGTTTTTAAATTTGTAATTCATCTACTTTGATTATTTTTTTACTTTTTGATCAAAATTGAATGCCTATATTATAAAAGACCTCTCTATAGTTGCCTGCTAATAGTTTCACAATTTTGAACTAATCATAAATAATTGCTTTTACATAA +>Transcript_10 len=2439 CDS=44-2378 exon=0-2439 five_prime_UTR=0-44 gene=0-2439 mRNA=0-2439 hmm_matches=HRDC:1379-1580,DNA_pol_A_exo1:1646-1745,DNA_pol_A_exo1:698-1199,PMC2NT:77-338,DNA_pol_A_exo1:83-164 three_prime_UTR=2378-2439 +CAAACCAAAAACCTTACTGATCCAGTAGGGTAAACAATAGCATAATGGATGAGTCAGAATTGTTTAAGGGTTTAATGAATAGTACAGCCTATTGCTCTGAATTGGCAAAGGTTGATATACCGTTTTATAAATCAATTGATACCGAATTCAATGAAAACATAAAAAGTGTTTCTTCTCGTTTTATGAGATTAATTGAATTGCTTCTTTCTAAAGTAGACAGAAGTCGGGCGGAGGATATTGTGGACGTTGAAGATATAGATAATAGATGGGCAGAAGTATCGGACACATTAGACATACTCTTTGAAAAAGCTGACTATTCTATCGATAAAGCTCAAGGACTTTTAAAAAAGCCAGCGATCGAAACCCATGCGTCGACAAGCGATGTTGCCAATAAAAAACCAAAGAAAGAAAAGTTGCCCTACAAGGTTATTCACGCAGCTCATCTTACTAAGCCTCAATTAAGGTTTCGAGTACAGCCTAATAATTCCAGGGAGTTTGTGTGGTCTTGGAAGTTAACTGAAAAACCACATTCGTTAGTACCGCTCGAAAAGATTATCGCTCAAGTCAAATTGGACCCTAGTCTCAAAAACTCGTTACCACATCCATATGAACCAGAAATACAAAATAGCGTATATCCTCCATGGGTTTCAGAAATGTCTAATCCCATCGATACTGGCTCTGTCGACGAAACAGAACCTATCTGGGTTAGTACTGAAAGTCAGTTATCGGATATGCTAAAAGAATTACAAAACAGCAAAGAAATAGCCGTTGATCTTGAACACCATGATTACAGATCATTTAGAGGGTTCGTCTGTCTAATGCAAATTAGTAATAGAGAAAAAGATTGGATTGTTGACACCTTGGAACTCCGCGAAGAGCTTGAAGCTTTGAATGTTGTTTTTACTAATCCAAATATCATTAAAGTTTTTCATGGTGCAACTATGGATATCATTTGGCTGCAAAGAGATTTCGGGCTTTACGTTGTAAACTTATTTGATACATACTATGCTACTAAAGTTTTAGGATTTGAGGGTCATGGTCTGGCTTTTCTGTTACAAAAGTATTGTGATTATGATGCAGATAAAAGATACCAAATGGCTGATTGGAGAATCCGTCCTTTGCCTCGGGAAATGTTAAAATATGCTCAATCTGATACGCATTATTTGTTATATATTTGGGATCATTTACGAAATGAACTCATATCAAAATCAGCTGAAAGAAAAGAAAATCTTATGCAATCAGTGTTCAATTCCAGTAAACAAATATCTCTTAGAAAGTATGAACTTGAGCCTTATGATCCTATTTATGGACTTGGTACTGATGGCTGGAGAAATGTACTTACTAAGTTTGGCTCTTCTAAAATAATTGGACGGGAAGCTTTGATGATTTATCGAGCACTGCACGATTGGAGAGATTCCGTAGCCCGAAAAGAAGATGAAAGTGTTCGCTATGTGTTGCCAAATCGTTTACTTATTGCGATTGCCGCCAGTAAACCGGTTGAAGCGGCTGATGTGTTTTCAATTTCTAAGCAATTGACACCAATTGCTCGCATGTATGTTGAAGATATCGTTAAAGTCGTTCAAGAAGCCGAAAAGTTGTATAATGAGCAAGTAGATCGTGAGAAATCCCAATTTAAAGAAGTTGAGAAGCAAAATCAACCGCTAGCAGTTTTTTCCGAATCGAATACTTTGGGTGATTACAAAGTTGACTCCAGTGTTTTCGAGATTTCTAAACAAAATAGAAGTAAACTAAAGACTTTGCTGGCAAATGGATCTGCGTTTTGGATTGAGGGACAGTCGCAAGATGATTTACGGAAAGCTCGTAAAGAGAGACTCTTTATAGTGAACCAGAATATTCCTTTTTCATTAACTCTTCCTTGTACTCAAGGGCATGTTGAATCCGAATTGAATGTAAAGCAGTCCACTGTAACTGAAGCTGCAAACCCGAGTCTGAATGGAGAGAAGAAACAAGAGCCTATAGTCATTAGGGATTTAGGGCTGAACAAGCAAAAAAGGGATTCTTCTAAGCTTAATCATAAAGAACCCTCAAACCCCATAGAGGAGCGAAATGAAGATATTGAACCTTCGGAAGCTTCAACTTCAGTGTCAAAAAAACGGAAGCAAAAGAAGAAAAAGAAGAACAGCGGAAAACTTACTATTGAAGCCGAACATGTTTCTAATGACAGTCCAATTATCAATGAAGCACCTTTTGATTATAAAAATCAAAAGAATTTTATTGCTGACTTAGACTCTGATGTAGGAAAAAATAAATTTGGGAAACGGGGTTTTAATCCTCTTAACAAGGTAAGTTTACCAAAGCGAAATACTAGGGAACTCAAAAAAAGGAAGGTTTCAGACGGGAAGAGTACATCTTATTAATATCAGTTTTAATTTTAAATAAACGAAACAATTTTGACAAAATGAAAATTTACTTTTAAAT +>Transcript_11 len=3956 CDS=476-3827 exon=0-3956 five_prime_UTR=0-476 gene=0-3956 mRNA=0-3956 hmm_matches=Pkinase:2954-3758,Pkinase_Tyr:2957-3746 three_prime_UTR=3827-3956 +GACTTTGCATCATTCACTAGTCAAACCGCAAGCGATTTTGAGCGGGCCTAAAGCCAGACACCAAGCTGGAGATTGCTTGGTTTACCCGTGAAGGTTTATAGAATCGAAATATCAGTTTTACATTGATAAAGTATCTATTTTTAATTCTCTATTATTTTCTAACAGGCTTCTGTGGAATTGGCGGTATCATACGGGCTGCATGTCAAAACACATGGGAAGTCTTTTTGCAATATCTTTAAACCCTGAGTACTAGTGATTCAACATTTCTCTCCTTTCTTAATATTTTATTTACCTGCAAGAAATTGGGCTATTACTAACATCCCAAGTCTGTCTTTTGCAAATTAGTTCACTCGTTTCAGCCGAATCTTAATTTTTTTAATCATAAACTACTTAAGCAGCAATCTCCAATTCGTTTGACAAAAAAAAGGTTTTTTATCTTGAATTCTTTTCAAAGTAACTAATACTGTTCTGGGTATATGGCTGCCGATATCGGATCGCAGTCATCAGGCTCTTTGGAAGAACGGTTTGAACAGTCTCTTCATCTTCAGAATGTCGATAAGCAAGATTGGTCACTTAACAGTGTACTTCAGTTTTTAAAACTATACAAATTTAACAAAGAATGGGAAGACGTTTTTATTAAAAGTCGAATCGAAATGGATTTATTTATCAATTTGGCCGATCAATCAAAAGCCGAGGAATTCGCCTTTAAAAATAAATTGAGCAAGGAGTCTGCCATCCAATTGAGTAGCTGTATTCGCAAAACACTTTTAGCACCTTCTTCGACTCGCGTACCTAGCAAAAACTCGTCTTACGAAACATTAACTTACAGCGCCAAAGATAGTTCGGATGACGTTTTTACAGAAACTAACTCTGGTTTCCGCTCTTCAAATCAAAATTCGTCCCTCAAAAGCTTTCAGAGTGTTCCTGATAGCAATGTGAACGTGTTTGGTGGCTTCGGTGGATCAGTAGTCGACAACAATGAGCTATTGAGCACAGGAAAAAACTCCCATCAAACAACCTCTTTAAATTTGGAAGGCTCTCCTATAAACTTACACGCTTACAAAGGAACTGTCACTTCAATAATTAACGATGACAGCAGAAACATTAATAAAAAAACATTGTCGAAACAACCTGTATCCGAACATAAAGAAAAACAAACTAGCTTTCTCCGTCGTTTCCGGGTACCTGGGTTTTCTCGTGACAAGGATAAAACTAAAGATTGCCCTTCTTCAAATTCGAACCCATTCCATTTAGCTTCTTCAAATGTGAAAACATTAGACGCGTCTTTGGATCAAGGTGAGTGGGTACCTCGTATTCATCGTTTAGAAAGTCAAATTGGTTTAATATCCAAAAAGAAGTCATTTGTTCTTGCTACTATGGATGATATGAAATTCACAGTAGTGGATATTACCAACGTCCAAAATGCTACTCAGCTACGTAAGCTAATAGCTAAGAGTATGTATTTAGACATTTCAATTGACCAGTTTGATTTGTTTCTCACGGAAGTCGGCGGGGCTCAATACATAGAAATATTAGATGATAGAAAGCTTGATATTGCAAGGCTTTATTCTGATGAATTTGGAACTATTAAATTTTTCGTAAAGCCATCACAAAATGAAGAATCGGGTATGGATAGTGATACTTATTTATCTTTTGGCACAAAATCAAGTTCAACTTATAAAGCTGATGATGACTCAATATATCATCGCAAGGAAGATTTTAAAAAGCAACCAAGTTACCCTGTGCTTACTTCGGATTTTGAAATTACTGATGCAGGACCTAATTTATCATTATCAGGGCATCAACCTGATAATAAATACTACAAAGGTTTTAGTTCGGCACCGAATTTGGCAGTTGTTCCAGAATTACCATCTCGACGTTTTCGAGGGTTTGAAAAAATCCGTGGTGCTAAAGGAGAAATGGCTACAAAAATTTTGGATGCCACTGAAGCCCAAAGTGAAAAAAACAAATTTACCGTTTGTAGACCTCACAAGAAGGTCACATTGAAAATGCCACTTAATTCCGGCTCTTCCGCTCCCCAAAGTCCTTCATCTAATACTTCTGCTTCTGTTTTAACTAGAAATTTTGTGGCACATAGAGATCCTCCACCCCCACCCACAGAGACATCTAGTTTACGTCGAAAAAATACATTGACTCGTAGACCAAGTATTCGTCACGCTCGGTCCTCTCCTTACATTGATACCGGACATAACGAAGCTAGCAAATTTTCACATACGTCTTTTGACCCCAAAGCATCTAGTAAATCTTCTAATTCATTAAAGGAAAGTGTGGAAGCTTTATCAGAAATACCTTTTGAAGATGCGCCTGCACTAGACGAATCGGATCTTTCTGGGGATCCCTTTTGGGCTATACAGCCCAAACAATCTTCCTCCCAAGTACCTAAAGAAAATCATCACAACATTCAATCCAAACTTTCCATTAACACAGAGGCTGCTACGGATTTGAAAGCAAATGAACTATCTTCGCCTAAAACTCCTGAATACTGTAGAGGTGATGACAGATCCATTAGTTTATCACCGTTATCTTATCGTTTAAGAAAGTCCAAACATATTCGTGAATCCCCACCGTCTTCAAAGGTTATCAATTCTGGTAACTGGGAAGTTCGTCCATCTGCTGATGATCTTTATGAGGATGTTGATCGATTTTTTCCCCGTTATGATTTGGATAAAGTACTTGTAGTGGACCAAAGCCGCATGGTTTCTTCCCCTTCAAAGGTATCGATACGTCCGAAAATGAAGTCTGTACGATTATTAGCCCGCGAAGCATCTGAAGCTCGGAAAGAAATACGACATAACGCGAGACGCAATAAATCTGGAAATCTTCTACGTCGATCAAGTACGAAACTTTGGGGCTCTAGGATTGTAGAACTAAAACCAGATACTACTATAACTTCTGGATCAGTTGTTTCACAAAATGCCACGTTCAAATGGATGAAAGGAGAATTGATTGGAAATGGTACTTATGGTAAGGTATTTTTGGCTATGAACATTAATACGGGTGAATTGATTGCAGTAAAGCAAGTTGAAATACCACAAACTATTAATGGCCGTCATGACCAATTACGCAAAGATATCGTGGATTCCATTAATGCAGAAATTTCTATGATTGCCGATTTGGATCACTTAAATATAGTGCAATATCTGGGTTTCGAAAAGACGGAAACGGATATAAGTATATTCCTGGAATATGTTTCAGGTGGTTCAATTGGTCGATGTTTGCGGAATTATGGTCCTTTCGAAGAGCAACTGGTCCGTTTTGTATCACGCCAGGTGCTCTACGGGTTGTCTTACTTACATTCTAAAGGTATTATACATCGAGATTTAAAGGCTGACAATTTGCTCATTGATTTTGATGGAGTTTGCAAAATTTCAGACTTTGGAATATCTAAGCATAGTGATAATGTGTATGACAATGACGCAAACCTGTCCATGCAAGGATCCATCTTTTGGATGGCACCTGAAGTAATTCATAATGATCATCAAGGATATAGTGCTAAGGTCGACGTCTGGTCCTTGGGATGTGTAGTGTTGGAAATGTTAGCTGGTCGTAGACCGTGGTCTACAGATGAGGCTATCCAAGCTATGTTCAAGTTAGGTACCGAGAAAAAGGCGCCTCCTATTCCTAGTGAATTGGTGTCTCAGGTATCACCCGAAGCGATTCAATTTTTGAATGCATGCTTTACTGTGAATGCTGATGTAAGGCCAACCGCAGAGGAATTATTAAATCACCCGTTTATGAAATGTGACGAAGAATTCAACTTTAAGGACACGAATCTTTACGACATGCTTTGTAAAAGAAAGAGCTAAATTGGTCGCAATTATTATTTATTACTTAGCGTTTCCTCGCAGGGGCATGCATTCTCAATTTCTTCTTATAGCTATTTATTTAATATTGAAATTAATTTTGAAAATTATTACATTATTATACAAACAAAC +>Transcript_12 len=4750 CDS=1-3043,3235-3682 exon=0-4750,0-4750 five_prime_UTR=3682-4750 gene=0-4750,0-4750 mRNA=0-4750,0-4750 hmm_matches=Lgl_C:1603-2725,DUF367:3235-3388 three_prime_UTR=0-3235,3043-4750 +GTATATTTATACCAAGAATTGGGAAAATATGAGCTTTTTTAAAAAAAAGCTAAGTAAGGGAAAAGAAATTTTATCCAAATCCAATTTGAAGACCCATACGTCTTCAAATGCTTCACTATCGATAGACGACTTGAATCGATTTGGGTTTTCCTTAAATCCAGTATTATGGTGTTTAGACCATCAACAAGGCTTACTAGCTATTGTATCTAGTACTAATCGGATATACATTTACGGTAAACAGCATGTCCAGAGTGTGATAGTTCCAGACTGTTCAACCATTGTCCATATAGCCCTTTGTGCGGCGTATTTGATTGTAATTGACTCTCGAAATACGGTCTTAAGCTATCCCTTGATGAAACATCGTGACCTTTCAAAACCAGCTGCCACTTACTTTCTCAAGCAAAAAGTTACATGTACCGTAACGGATCCTACTATTGATTGGGTTTTTTTTGGAATGAGTGATGGCTCCGTTGTGCCATGGGATGTTACTAGACATTGCCTTGGAAAATTCAAAGTTCCAAATTTGTATGTCCCAAGACACGAGGAATGGCGAATGATGGGCTACTCTTATGCACCAGTTCCTGGAAAGCTATCCCCAGTTGTAAGCGTTCAGATTCACCCGAAGGATCTCGGTGTGATTTTGATTGCATATCCGGATGGCGTTGTTTTGTACTCAATAAGGACTGACGAAGTTATACGCTTTTATGAATTGGAGTATGCACCAGGTAGTACAGCTGCAGTTTTATCACCCCATAATTATCGAAGACCTATAGTCAAAGGGATAGAGTGGAGTCCTTGGGGTGATCACTTTGTTAGTTACTATACTGATTCGACTTTTGCATTCTGGGATGTGGATCAAGAATATCCTGTACAAGTCCGAAATTTTGTCGATTCAAACATACACACGTATACCCCCATGCAGAGAAATCCTCCTAAGACGGAGCTTGAGCCCATTAGGTCTATGAGGTGGTGTTGTTGTGAAGACCCAACAGTTTCATTTATTTTGATGTTAGGTGGTTTGCCGAAAGAAGCACCGGTAAAGGGAATTTCATTGTTCAGTTATCGAAATCTCCCTGCCAAAAAGGATGTTGAAACATTTGCGGAATTTTTCGCAAATCCAAACTCACAACGCTTTTTTCCTTTTATTGACATCCCCCCTGTACGTGATATGCTGGTGATTCCTTCTAGCTCACCACATTACAATGGATCTCATAATCCCAAGAATCTTCTCCTTCTTTCGGAAGACAACTCGTTATCGCTGCTCGACATTTCTACTGGAAATATTTCAAACATGAGCCTTTCTATTCCCCCCTCTTTATGCTTCCTTGCTTCAGATTTTCGAGTTATAGCATTTCAAACTGTAACAAAAAAAGTTTGGAATCAAATTGAAGATACTATTTCCGTTAATTCACATTACTCCTGTCTTTTTGGCGGATCTCCTAGTCCCGGCTATCTTAAGAAATTAGATGAGCGTAATCTACTTATAACATCGACTGGTCTTAGTTTATCGATTTGGGATATATCTCAGGGTTTTATGAATCCATCTCTCTGCGTAAATTTGGATTTCTCTTCTGTAATGCGAAAGCATCTCACGCCTTCAGCTTTTATAACTACTGCCTCTTTTTCCACTTATAATCCAGAATTCAGTTGTGCTGATAGTTTTGGGCGTGTCATTGTTTGCAAAAGGAAAAATCATAAAGAAAATTTACCAGCTCAGCTCGCTAACGGAATATATCGTTTGGACGATACCTTAGTTCTAGAGGGAACATTACATGCTCAATATTATATTGATCTTAAACGAGGAAGAGTAACATTGAACCAAATGAGCAATATTGGTTTTGTTTGTATAGGATATCAGGATGGTGGAATTACAATCATCGACATGCGTGGCCCCCATATACTGTGTAACACCAGCATCTCGGAGCTTGGATTAGAGAGAAGAGGAAAACCTGATCCCGATTTTCTTACGAGTGCCGAGTTTGTCGTTATGAACCCTAAAGGAAGCCCTTCCTCAATCTACGTAGTCACAGGAACATATAGAGGGATGACACTTTTATTCCGTATAGACCCTTCCTCTTCAGGGCGCTTTTCTGCTTATTTTGAATCATCTCGACAATTAGATATTAAGAACATTTATAAAATATGCTCTTTAACTCAAGATGGCCAGATCGCGACAGCCACTGGATCCTCATTACAAAGCGTTGGATATCCCTTACCACAGGAAGTTTTCCTCGTGTATATTGGCGATTCAGGAATTTCTGTTTTTAATAAAATTAATAATCAAGTGGGTAACCTGGATTGGAGAAAACCTGTTTGTTGTCGAGCAGCTCTTGTGCTTTCTACTGTTTCCAAACACATGGGTTCCGTAGTTTGCGTAAATTCTGATCTTTCGGTGAATTGGTATTCTCTCCCAAACCTTCGTGAGGAACGTAAAATGCAACTTCCATTGGATATTGATAAAAATAGGCTCAAAGAAGGTGATATTCTAGGCAATGGGGATTATATTTTCCCAACGTTAGGAGCACATGAATTAGCCTTTGGCTGTGTTTTAGGAAGTGGGAGAACATTGGCGAATTTGGCACCCATGATGCTTATTACTCACAATGCTTCCCATGTACCGCCAAGACCTAGTAAATCCTTGTGGAATTGGTTACTGGGCGAACAGTCTACATCTGCTGAAGAGCTAGATATCTTACTCGGAGGTGAAAACAGGGCTGAAAGTAAAGTGCATACTTTAGAGACTCCTAAAGTTATTTCAGCTCGCCCAGCAGAATCAGTTAAGCAACCACTGACCCCGGTTCCTTCCATGACTTCTCAGTCTGCTCAAAGTTATATCCCTCCAAGAAGGCAACAACAACAGAAAGGATTCTTCGCTCAAATAAACGACCATTTAGCCCAACGGGGGAATATGTTAGGAGGAATTGAAAATACTATGGACGATTTAGAAGAGATGAGCGCTGAATGGGCAAACGAAATTAAGGACTCTTTGGCTGGAACGAAGAAAGATTTGATTCTTTCAGGCTTAAAAAGCTATATACCTTAGAAAGTTATATTTTTTTTTACTTGCATTTATCAGGTTATGATTGTTTATGAAACTTATTGAAAGCTTACCATATTTATTAATTTTGCATCTCTCTATACAATATTACCTTACATGGATATGTAAAGCACAAAAAACAGGTGATAAATAATAGACAAACTATAAATTATATAAAAATCCAAAAGTATATATCTTTTAGGTATCAGTAGAATGAACTTTCATTCTCACGATTTTTCGCCAGACTTCATCTTCATCCACATCGTTGGCTTGCAGATTAGTTAGAGTCTCTTCATTATCATCTGTTGGAATAGAGTGTTCGTCATGAGCCAATGAAGCTTCGGACGGTTCGTGTAATGGTGACCGAGATTCTTCAGAGTTTGAATGTGTTGAACTGGTGTTTAATGTTGGTTTGTGATTTAAATTTCCAGCTGACCAAATGTCGTCAGTAGTTTGATTTCTTTGTTCTTGGTAAGAAGCTTCCATTTCCTCCAAGTATTTTTTTTCTTTTTCTTGAATATCTTGAGCATCATGACATTGAGCATAAATATCGAGAAGTTCTTCGTTTACCTCAAAAAAAGAATGTCCCCATTTGAAATTATCCATTAAAAGTCTCGCCTCATTAGGATATCCGACAATATACATGCAAGCTGCCAGAGCTTCAGCACAATTTAATCGCCAAGGCCTACCATAGTTAACTGGATTGGAGGCCACTAAATATGGAAGCAACCGCTCACAGCGACCACCAATTCTAGAAAAAGGGATTTCCTCTATGCGAGCCCAAGAGCATTCAACTACACTAGCACCTCCATTATCAAAGTACTCCTTATCGGCTGGAGAAACAGGAACTTTTCCGTTTGGTCTGCAGCGTTAAAATCTGATACATAGCAAAATGGTAAAAAAATATTAATAATTAGTCTTAGTGCCCTTGCGCTGTATACAGCAAACATTCGACAAGAGTTTAAGATCGGGTTTCTTTCTAACGGTTCTCAACTTACGTTATTACAACTCCTCGAAACTTCTGTCCAATTCTAAGGTTTCGTACGCATCCTAGACGCTCTAATCGTTTACCAGAACAGGCATTTGGATTACAATGTCCAAAATCCCACATTGCTAAGGGTAATGGAAATTTGGATGCCTTGTTTGAACCCTTGAAGCCATCTTTGGCATTAGAACGACGATTAGAACTCCTTGGGCCCATATCCAAATATCGATGTTGAAAAGTGACACGCTGTTTGATGTAGGAAATCCGCCATATTTGGTGTGGGTGTTGTTATCAATCAATAATGCACTGTACCAATGCCGTGTTAAAAGTAATCATCTTCAGTAGCAATCGAGTATTAAGATGAGAGGAAATCTTTATCTATATACAATTCGACTACTTAATCAATTGACCGTCCCTCCTTCTTTTCAGAAAAATATTTCCTTACATTCATTAAAGATATGCTATTGAAAAGTGGATATTGCCCAAAAGTGGTTAATGTTCTCACTCTTGAGCGAGACAATGCAATGACATTAGTTTTTTGCATTTCTTGGCAAATCCAGGAAAAAGCCTCGCGGTAATATAAGAATGGTCAATTCTCGTAAAATGACCTTGTATGGCTGTTAATACTTTCATAGTTGTTCAAATAGAACTGTTACACAAAACTCGTTTACACACAATGTATTTTCCTCATGCTTTTTCAACGATATACAATTGTACAATTGTTCTCC +>Transcript_13 len=1078 CDS=76-943 exon=0-1078 five_prime_UTR=0-76 gene=0-1078 mRNA=0-1078 hmm_matches=RLI:157-259,DUF367:268-649 three_prime_UTR=943-1078 +ATAACAACACCCACACCAAATATGGCGGATTTCCTACATCAAACAGCGTGTCACTTTTCAACATCGATATTTGGATATGGGCCCAAGGAGTTCTAATCGTCGTTCTAATGCCAAAGATGGCTTCAAGGGTTCAAACAAGGCATCCAAATTTCCATTACCCTTAGCAATGTGGGATTTTGGACATTGTAATCCAAATGCCTGTTCTGGTAAACGATTAGAGCGTCTAGGATGCGTACGAAACCTTAGAATTGGACAGAAGTTTCGAGGAGTTGTAATAACACCAAACGGAAAAGTTCCTGTTTCTCCAGCCGATAAGGAGTACTTTGATAATGGAGGTGCTAGTGTAGTTGAATGCTCTTGGGCTCGCATAGAGGAAATCCCTTTTTCTAGAATTGGTGGTCGCTGTGAGCGGTTGCTTCCATATTTAGTGGCCTCCAATCCAGTTAACTATGGTAGGCCTTGGCGATTAAATTGTGCTGAAGCTCTGGCAGCTTGCATGTATATTGTCGGATATCCTAATGAGGCGAGACTTTTAATGGATAATTTCAAATGGGGACATTCTTTTTTTGAGGTAAACGAAGAACTTCTCGATATTTATGCTCAATGTCATGATGCTCAAGATATTCAAGAAAAAGAAAAAAAATACTTGGAGGAAATGGAAGCTTCTTACCAAGAACAAAGAAATCAAACTACTGACGACATTTGGTCAGCTGGAAATTTAAATCACAAACCAACATTAAACACCAGTTCAACACATTCAAACTCTGAAGAATCTCGGTCACCATTACACGAACCGTCCGAAGCTTCATTGGCTCATGACGAACACTCTATTCCAACAGATGATAATGAAGAGACTCTAACTAATCTGCAAGCCAACGATGTGGATGAAGATGAAGTCTGGCGAAAAATCGTGAGAATGAAAGTTCATTCTACTGATACCTAAAAGATATATACTTTTGGATTTTTATATAATTTATAGTTTGTCTATTATTTATCACCTGTTTTTTGTGCTTTACATATCCATGTAAGGTAATATTGTATAGAGAGATGCAAAATTAATAAATATGGTAAGCTTTCA +>Transcript_14 len=2035 CDS=181-1714 exon=0-2035 five_prime_UTR=0-181 gene=0-2035 mRNA=0-2035 hmm_matches=Alpha_adaptinC2:1240-1294,Alpha_adaptinC2:1369-1681,VHS:187-619 three_prime_UTR=1714-2035 +GTTTGGTCTCTTGTTGGTAAACCAAGCCTCCCAACTTCCTTGACTGAAGAGTATACCTCAGACTTTTGCACAATTTTGTTTTTGGATTTTTTCTTTTTGTTTTAATTTTATTGGCTCTTCAAATCTGCGAATCTGCCTTCTGTTTTGTTTTTAGATCTAGAAAAATTTACTACTTATCACCATGCGCTCTAGCCAGACTTTATCAAAGTATATTGACAAAGCTACCGATCAATTCAATTTGGAGCCAAATTTGGCCTTGAATATAGAGATAGCGGACCTTATAAATGAAAAGAAAGGAAATACCCCACGTGAAGCAGCTTTATTGATTTTAAAGCGTGTCAACAGTGCAAATCCCACAGTTTCATATCTGGCTTTACATTTGCTCGATATTTGTGTAAAGAACTGCGGTTATCCATTTCACTTTCAGATCGCATCAGAAGAGTTTTTAAATGGATTCGTTTCACGATTCCCAAACCATCCCATCTCCCGAATGAATAAAATTCAATCTAAAATGCTAGAAATGCTAGAAGAGTGGAATTACATGCTTTGTAAAAACAATCGCCATCGTGAAGATTTTTCTCGCATTCACGACATTCGGGAGCTTATGGCTTTTCGTGGTTACAAGTTTCCTGCGGTAGACGAAGATTCCATTGCTGTCATGAAGCCTAATAATAGTCTTCGTTCTGCACAAGAATTAGCACGTGAAGATTTAGAAGCTCACAAAGCTAAATTGCAAGAATTGCTTCGACGAGGGACCCCCATGGATTTGGCTGAAGCCAATGCTCTTATGAAAGTAATAGCTGGCTATGATGAAGAGAATACTGAAGATTACTCTGCCTTGGCTGCTGCCGACCTTGAATCGATTAGATCAAAAGCACTTCGGGTAAAGCAATTTTTGGTTAATCAAACTGTATCTTTAGAAGAAGGCACGTTGGCGGATGCCGTTGAATCTTTAAAGGTTTACCAAACGAAAATAGCAAGAATTCTTCGAGAGGAAAATGAAGATGAATACTATGTGCAGAAACTTCTTTCGCTGAATGACCTACTTATTAACGTCATTGAAGAATGTTCCAACTCAGACTTAATACATTCCGGTACAAATGTAGTTTCCTCCCAACCGAATGTGGTTGAATCTCACGTACCTCCTTCTTCTAATGACACGAAACAAGAATCTTCGTTAATTGATTTGATGAAGCTTACTGAGGAACCTGCAGTCCCGTCCCCATCACTTCCAACCAATGTACCAGCCAACCAATCTCTGTCAATGTTATCATCCCTTTCTAACTCTATGTCGTCTACGTCGAATGGAGCTTTGAATTCACCTTCTTATAGTCAAGCAGCAATCCCCAACACTAATTCATCTTTGACATCTATTCTTCAATCTGATTCATTAATGATTTCTACTCAATTAACTTCGGTTCAAAAAAGCTCTGGCTTTGCTTCATACTCCGTTCAGTTCTCTAATTGCTCCCTTACCTGGCCAGTGTCCGAAGTAGTCTTCCAGGTCGCGGTTGTGAAATCTCTCAAGTTACAGCTACTTCCTCATACTGGGGATGCAATTATTGCCCCCGGAAAACAGAATGCTGCACACGAGATTATGAATATTACCAACATACCCGCCGATGCCTCTGATTTACGAATTCGTTGGAGAGTTCAGTGGATCATCGGTACAGATCATCGTGTAGAACAAGGCGAATCGCATCTTCCGCTGTAATTCTACGTGCGTTTTCTTCCATTTGCTCAACTAGATGAAGGAATATAAAAAAAGTGAAAACGTCAGTTGATATTACAGGTTTTATTATTTAATTAATGTGAGCCTCTGCGATTTGATAAATTAAACTATAAACTACGATAAAGCGAACTTTCCTTATTTTTAGAATTCTTTCCGCAATACCGATTTTAAATTTTTATAATACAAATGCCTTAACCAAAACCATTTTATTATATCTCTCAGTCAACATTATATGCTTCATAGTAATGAAAAATAAATTTAAAATTTATTTTTTATCGAAGCAAACCTTAAAATAGCCTCAAT +>Transcript_15 len=6229 CDS=2-5972 exon=0-6229 gene=0-6229 mRNA=0-6229 three_prime_UTR=5972-6229 +ATACCGATAAAACATGCCGATACCTTATCACTATTGCTTTGTTGCTTCAGAGAGTTGTCATTTCTAAACAACCCAAATCGTTTATTTACCAACGACAGATGTCGAATCAGTCGTCTTCTGGTTCGAATACTTCTGATTTGGATGAAGAATCAGCGAGTAGTCTTGTGAGCTCTGCTGCATCACCATTTATTGATTCTGATCTCGAAACACCAAGACCCAATATTTCAAGAGCTTCAACAGGACAACTTGCAGAAGACGGTGACACATCAAGTCAACATGAAGATTCCTCAGAGGAGTTAAAGCGTCAAGAAGTAAGGGGAATGCGTAGGCACAGTGACCTTTCAATTGATGCGAAATTAGGCTCTTCTGAAGGCTCAACTGCTTCTTCAGCATTACCTTTGACACCTCGTTCTCCTTCTAATGCCAGCTGGCTATTAGTCCGCGGTGGTTTACTTGATAGTCCGATTCTCGACATTAACTCAGTAACTCAAAAATCCAACCTTTTAAATGAGTTGAAGCAAGTGCGGTCCAAACTGGCTGCCCTTGAACATGAAAACGGAATTCTCTCCTTGCAATTGTCATCTTCGAATAAAAAGGATAAGAATACCTCAAGTGTAACCACGTTAACATCAGAGGAAGACGTGTCATATTTTCAAAAAAAGCTCACTAACATGGAGTCAAATTTTTCTGCTAAACAATCTGAAGCGTACGATTTATCGCGACAGTTATTAACGGTTACGGAAAAATTAGATAAAAAAGAAAAGGATTACGAAAAAATAAAAGAAGATGTTTCTTCTATCAAGGCCTCTTTAGCAGAAGAGCAAGCTTCTAACAAGTCCCTGCGTGGTGAGCAAGAGCGATTAGAAAAACTTCTTGTAAGCTCCAATAAAACTGTTAGTACCTTAAGACAAACAGAAAACTCATTGCGCGCCGAATGTAAAACCTTGCAAGAAAAGTTGGAGAAATGCGCCATCAATGAGGAAGATTCCAAATTGCTGGAAGAACTTAAGCATAATGTCGCCAATTATTCAGATGCCATAGTACACAAGGATAAGTTAATTGAAGATTTAAGTACCAGAATAAGCGAGTTTGATAATTTAAAATCTGAACGGGACACGTTGTCAATAAAAAACGAGAAGCTAGAAAAGTTACTACGTAATACGATTGGCAGCCTAAAAGACTCACGAACCTCCAATTCTCAATTGGAAGAGGAAATGGTTGAGTTGAAAGAATCCAATCGTACTATCCATTCGCAATTGACTGATGCTGAATCTAAGCTTTCTTCTTTTGAACAGGAAAATAAATCACTGAAAGGATCTATTGACGAGTACCAAAATAATCTTTCTTCGAAGGATAAAATGGTTAAACAAGTTTCTTCCCAATTGGAAGAAGCTCGTTCTTCCCTTGCCCACGCGACTGGTAAATTAGCAGAGATAAATTCCGAGCGAGATTTTCAAAATAAAAAAATAAAAGATTTTGAAAAGATAGAGCAGGACTTGCGTGCTTGTTTGAATTCCTCATCCAATGAACTGAAGGAAAAATCAGCGTTGATTGACAAAAAAGATCAAGAGTTAAATAATTTGAGGGAGCAGATTAAAGAACAGAAAAAAGTTTCTGAAAGTACTCAATCAAGCCTTCAGTCTTTGCAACGTGATATTTTAAATGAAAAGAAAAAACATGAAGTTTATGAAAGTCAATTAAACGAACTGAAGGGTGAATTACAAACGGAAATTTCAAATTCTGAACACCTATCCTCCCAACTCTCAACTTTGGCGGCTGAGAAAGAGGCAGCTGTGGCTACCAATAATGAACTTTCCGAAAGTAAAAACTCACTTCAGACATTGTGCAATGCTTTTCAAGAAAAGCTTGCAAAATCGGTTATGCAATTGAAAGAGAATGAGCAAAACTTTTCTTCCCTGGATACTTCATTTAAAAAACTCAATGAAAGTCACCAAGAATTAGAAAATAACCACCAGACCATAACCAAGCAGCTGAAAGATACTTCTTCAAAACTTCAACAGCTACAATTAGAGCGAGCCAATTTCGAACAAAAAGAATCAACCTTGAGCGACGAAAATAATGATCTGCGAACTAAATTATTAAAGCTCGAGGAGTCCAACAAATCGTTAATTAAGAAACAGGAAGACGTGGATTCTTTAGAGAAAAATATTCAAACATTGAAGGAAGACTTGCGGAAGTCGGAGGAAGCCCTCCGATTTTCCAAATTGGAGGCTAAAAATTTGAGAGAAGTGATAGACAATTTGAAAGGAAAGCATGAGACATTGGAAGCACAGAGAAATGATTTGCATTCTTCTCTTTCTGATGCTAAAAATACGAATGCAATATTGTCGAGTGAACTTACCAAATCATCTGAAGATGTCAAGAGGTTGACTGCCAACGTTGAAACTCTTACACAAGATAGCAAAGCTATGAAGCAAAGTTTTACAAGCCTTGTCAATTCTTATCAGTCAATCTCAAACTTGTACCACGAACTTCGTGATGACCATGTGAATATGCAATCTCAAAATAATACATTGCTTGAATCTGAATCAAAATTGAAGACAGACTGTGAAAATCTCACTCAACAGAACATGACACTCATTGACAATGTTCAGAAACTCATGCATAAACATGTAAATCAAGAATCCAAAGTTTCTGAACTAAAAGAGGTGAATGGAAAGTTATCATTAGATTTGAAGAATCTAAGATCCAGTTTAAATGTTGCTATTTCTGACAATGATCAAATCCTTACCCAACTTGCTGAACTTAGTAAAAATTACGATAGTTTGGAGCAAGAGTCTGCTCAGTTAAATTCCGGTCTGAAATCATTGGAAGCTGAAAAGCAATTGCTACATACAGAAAATGAGGAGCTACATATTCGTTTGGATAAGTTAACTGGCAAGTTAAAAATTGAAGAATCGAAATCCAGTGATCTTGGTAAAAAATTAACTGCACGGCAAGAAGAAATTTCAAACTTGAAAGAAGAAAACATGTCGCAAAGTCAAGCCATAACTTCTGTGAAATCTAAACTTGATGAAACTTTGTCAAAGTCTAGCAAGCTTGAAGCAGATATTGAACACCTGAAAAATAAGGTTTCCGAGGTTGAAGTTGAAAGGAATGCTCTTCTAGCTTCAAATGAACGTTTAATGGACGATTTGAAAAATAATGGTGAAAATATCGCAAGTTTACAAACAGAAATTGAAAAGAAACGTGCCGAAAATGATGATTTGCAGTCAAAACTTTCTGTTGTAAGCTCGGAATACGAAAATTTGCTGTTGATTTCATCCCAAACAAACAAATCTCTTGAAGACAAAACTAACCAATTGAAGTATATTGAAAAGAACGTTCAAAAGTTATTGGATGAAAAGGATCAAAGGAATGTCGAGTTGGAAGAACTAACCTCCAAATATGGCAAACTTGGCGAAGAAAATGCCCAAATTAAGGATGAGTTACTTGCCTTGAGGAAAAAGAGCAAGAAACAGCATGATCTTTGTGCAAATTTTGTTGATGACCTAAAGGAAAAGAGTGATGCTCTCGAGCAATTGACTAACGAAAAAAATGAGTTAATTGTAAGCCTTGAGCAATCCAATTCTAATAATGAAGCACTCGTTGAAGAAAGGAGTGACTTAGCTAATCGTTTGTCAGACATGAAAAAATCCTTGAGTGATTCAGATAATGTTATATCTGTTATACGTTCTGATCTTGTACGTGTAAATGACGAGTTGGATACTCTTAAGAAGGATAAAGATTCTTTGAGTACTCAATATTCCGAAGTTTGTCAAGATCGTGATGATTTGCTAGACTCTCTGAAGGGTTGTGAAGAGAGTTTCAACAAGTATGCTGTTTCTCTTCGTGAGTTATGTACCAAGTCTGAAATTGATGTTCCGGTATCTGAAATTTTGGACGATAATTTTGTCTTTAATGCTGGAAACTTTAGTGAATTAAGTCGCTTGACTGTTCTGTCTTTGGAAAACTATTTGGACGCTTTCAATCAAGTAAACTTCAAGAAAATGGAATTGGATAATCGATTGACTACTACCGACGCTGAATTCACCAAGGTTGTTGCTGATTTGGAGAAATTGCAACATGAACATGACGATTGGTTAATTCAAAGAGGAGATCTTGAAAAGGCACTGAAGGATAGTGAAAAGAATTTCTTACGGAAAGAAGCCGAGATGACTGAAAATATACATAGCTTAGAAGAAGGCAAAGAGGAAACCAAAAAAGAAATAGCTGAATTGTCCTCAAGGCTTGAAGACAACCAACTTGCTACAAATAAGCTGAAAAATCAACTTGATCATTTAAATCAAGAAATTCGCCTGAAAGAAGACGTTTTAAAGGAGAAAGAAAGTTTAATCATTTCATTGGAAGAAAGTTTAAGTAACCAAAGACAGAAAGAAAGCTCTTTGCTGGATGCTAAAAACGAGTTGGAACATATGCTGGACGATACGTCGCGTAAGAATTCTTCATTAATGGAAAAGATTGAATCGATTAATTCTTCTTTGGATGATAAGAGTTTTGAGCTCGCTTCGGCTGTTGAGAAGCTTGGTGCCCTGCAAAAGCTTCACAGTGAGTCTCTTTCTTTAATGGAAAACATCAAGTCACAGCTACAAGAGGCAAAGGAAAAGATTCAAGTAGATGAATCAACTATTCAAGAGCTCGATCATGAAATTACTGCTTCTAAAAATAATTATGAAGGAAAACTAAATGATAAAGATTCAATTATTAGAGATTTATCTGAGAATATTGAACAATTGAATAACTTGCTTGCAGAGGAAAAGTCTGCTGTAAAAAGGCTGTCTACCGAAAAAGAATCAGAAATTTTGCAGTTCAACAGCCGCTTGGCAGATTTGGAGTACCATAAATCTCAAGTTGAGTCAGAATTAGGTCGTAGTAAATTGAAGCTGGCTTCAACAACGGAAGAATTGCAATTGGCTGAAAACGAACGATTATCCTTAACCACCCGAATGTTAGATCTTCAAAACCAAGTCAAAGACCTTTCTAATATAAAAGACAGTCTAAGCGAGGATCTAAGAACGTTACGATCGTTAGAAGATTCTGTAGCAAGTTTACAAAAAGAATGCAAGATAAAATCTAATACGGTTGAATCATTGCAAGATGTATTAACAAGCGTACAAGCCCGTAACGCCGAATTGGAAGATGAAGTTTCTCGTTCAGTGGATAAAATAAGAAGAAGGGATGATCGATGTGAGCATTTAAGTGGAAAACTTAAAAAACTGCATTCTCAGTTAGAGGAACAGCATGAAACTTTCTTTAGAGCTGAACAGCAGCGTATGACACAATTAGGGTTTCTCAAAGAAACAGTGAAAAAGCAAGAGAAGCTTTTGAAAAAACTAAACTTAAGGCAAGAACAGTTAATTCCTCGCTCTTCAATTTTAGTTTACGAATCGTATATTCGTGACATTGAAAAAGAAATTATAGTCTTACAAGAACGTCTAAATGGCATTGAGCTTTCGCAACAACTTCCGAAGGGCTACTTTGGGTATTTCTTCAAAACTAATCGCGTCGAAATGGAAGTGTTGGATAGTTTCAAACAACAAGTCGCTAAATTACAGTTCCTTGCGGGTGCGGAATTCATTGTCAAATTTAAAGAGGATCTTGAAAAATGCGCTGCAGAAGAAAAGGAAAAACAAGCTACATTTGACAATTATTCTGAGAAGGTTGAAAATCTTGGGAAATCGATTGAAGCTTTGTATTTTGCACTAAATCGAGAAATTAGTTTCCGAAAGTCTTTAGCGTTGTCTAAATCAGCATATCACAATCTTTTGGTTCGAGATTCTCCCAAGTTTAACCCAGATTCCCAAATTACTTATAGTATACCGGTTACCAATACCAAGCAGTCATTGTTACGTTCTGCAATATTATGTGTCATATCACTGCAACGTTTGAGATTATTAGGTCAAAGACATTCTTTTTGTGAAGAGGTTATCGAGAACCTCTCTTGTGTTTAAATGATTTACTAACAACTACATGATTGAGGCTATTTTAAGGTTTGCTTCGATAAAAAATAAATTTTAAATTTATTTTTCATTACTATGAAGCATATAATGTTGACTGAGAGATATAATAAAATGGTTTTGGTTAAGGCATTTGTATTATAAAAATTTAAAATCGGTATTGCGGAAAGAATTCTAAAAATAAGGAAAGTTCGCTTTATCGTAGTTTATAGTTTAATTTATCAAATCGCAGAGGCTCACATTAATTAAAT +>Transcript_16 len=1518 CDS=261-1473 exon=0-1518 five_prime_UTR=0-261 gene=0-1518 mRNA=0-1518 three_prime_UTR=1473-1518 +CTTCCATCGCCAACGTACTAAAACTTCGGTGCTAGCATAGCTCACATCAACAAGGTAGTCAAAGGTGCAAAGTGAAGAGAACATAATAGATTGTTCCGCGCAAAGTACCTAGGTTGCCCGAAAAAACTAAGACATTACAATTTGCATGGTTTCAAAAAAGAAATTTTTTGGTTTTTATCGATCTGGGCATATTTTGAGTATTTGAAACGCATTACCGTTATCCGGCCTTTTTTGATAGCAATTCGTAAAACAAACTCGGCAATGAATGCTGAAAGTTGCTCCTTAATTCTTTCCTATATCTCTTCTGCACCTGCGGGCAATCTAGTATTGAATTGCACTGCTACCACAAACAAGCAAACCCTCGAGGCAAACTTAAAGTCCGCTGTTTATCAAAGGTACCCAGAGTTTCTAGAAGATTGGACGAATGTATGCGTGCATATAATTCATTCCTACTTTCCAAAAGATGCTGATTATTGGAATGTCGACAAATTATATACATCGGTGAACCGAATTACCACACTCGAACAAAGTAAAGTTGTTGGGAAAGAAATAAAAAATGGCTTCACTTTTGATGCTGAAAATTCAACCGCTTCATTGGAAAATGATTTACAACCACAATTCAGGTCACACGCTTTGTTTATGGTCGGTTCTGCTGGTCCTTTGTTCAGTTCTACTGCTCGAACTTCCCGATTAGACAGTCGATTACCAGATGGAGGAATAATTGCAAAGCCAGTTGCCCTTTTGCCAACTCCATCCGTTGCTAATTCCCAAGAGTACACCTTGGATAAGTTATCCCCCCCCTCAACCGCCAAACCTCCTGCATCAGTTATAGAATTTAATCCTTCATTGGCTAAACTTCCTACTGTGAAGTACCTACAGTCTGGCCCCTTCTCCTCAATTGCTCCTTACAAAAATTCATCTTCTTCTGTTATTCCTGATTCTTCATTTCATTCTGTTGCTTGTTATCGGGCATCTAGTCATTACAAAGAGGCACCTGTCGAGAAGTCAATCGATATTGACATCATTCAAAACAATTTGAGTCTATTAGAAGAAGACTCATGGACTTCTGTACCTATTCAAGGGGAACTTGTTGAATTGAATAAGTTACTACAGCATCTTCAACTGCTTCAAAATCAAAGAATCACATCTCATAACGTACTCTCCGATGAGGAGCGCCAAATATCTGTGCAAGTACAAAACTTGATACTTAAGTTAGCAAAAGATTACGATATGTCTCCAGAAGATTTTCTTATGGACGATTTTACTCTTTCACTCACTCAATATGGCGCCTTTTATCGTGGAACTCTTCCTCTTAGTGCACAACCGCTGGAGCTTCCTTCACAGCAACTGCTACGCTCCCAGTCCAATGCTGCTTTACGGAGCAATTCCCTATCAATGAACGGCTCCTTAAGTCCAAGCTCTACAAATGTTCCTTTACAGTCTTATCGACGGACTACAAAATCACGTAGATGAATTCGTTCTCTATTTCCATGGTGTTACTTAAAGATTTTAGTTTAA +>Transcript_17 len=327 CDS=0-327 exon=0-327 gene=0-327 mRNA=0-327 +ATGGTAATCTACTGCAACTGGTTAGAATTGAAAGGGTTACTCGAAACAAATGATTTCTTATACTTAATGAGGTGTTGCTACATGTATGATACTGTTAGCTTGGTATCAAATGCACCTAACATTTACAGTATACCATTTTTCTATGATCGGATCTGCTACGATTACAAAAACATATTACTAAAATATGAACTTTTTATTATTTATTATTATTATTATCTTCTAATATGCCTATCACCCCATTTCTTTCCGATTAAAAGAATCCGTCCATTTCATGAAAACCCACTCCATTCTTTTGTTTACCGAATAATGATCTCTAGCGAGGCCTAG +>Transcript_18 len=2971 CDS=1285-2971 exon=0-2971 five_prime_UTR=0-1285 gene=0-2971 mRNA=0-2971 hmm_matches=CwfJ_C_1:2290-2692,CwfJ_C_2:2731-2968 +GAGGAATGCTTAAAACTGAACTATTAGATACTGCAGTACGCAATAGCAATTTGTTTATGATAATTCAGAGAAATTTCTGTACTGTATATATATACACACATACTTGATAAATGAATCATTATAGATGTCTCAAATAAAATTATTTTTATGCGTCTATATTACACTATTTATAGACGACTAAACAAGTTGAGCATCACAATTGCTCAGAGTTCGGCGATTGGTAGAAACAAAGCATGAACAGAGAACAAAGATTGTTTTTTTTTGTGTTTTTGCTCTTGTTTTCCCCCATATCAAAATATCTTCTAGCAGAAAAGACGATGGAGAATTGATGAAATTAAATATTTTGACACACTGAACCATGGCTTTAAGTTAACAGCAGTACCTGCGTATACTTAGCTCGCTAAAGAAGCAGAAATGCTCTTGAAAACAAAGTCTAGCATTGTTTTTATATAAAGAAGTTAACAAATTTCAACTCGCAATCTCTCCACATTCCATAGCCCAGCACTTGCTAAAAGACAATTTTTTCTAAACAACAACGAAAACATTATCGGGTTACGGCAAAGACTAAAAAAAGGATGCCAATTTTCTCAAATTATTTTTTTTGAAGGGTTCTGCTAGATCAAGAGCATACAACAGAGGTGGATTAAAACAGTTTACCAAACACCACAGTGAAAGCAATACACATATGTTTGAAGCGTAGTGCTCAGTAATTCATATGAAGTATAATTTTAATTCAGACTATGTTTGTCATAAGATCAGCGATATAAATAGAAGAAGTGATAAAAATGTCTATATGAAGAAACCATAATCGTCAATAAATCAAGTATTGAAAAAAGAAATCGACGTTCTCACACAATTTACATGCAAAAATCAATACTTGAAAAAATGTCAACATTCTACGCTAAGCGTTTACTTAAGAAAATTTGCAACTCATAATAGCTCATTAAATAAAGGAAAGGAACTGCTTTTGTTGTAGTGAGAATGTCACTTTGGTTCCAAATACATCATGGATTGTTGTCATTCATTATGAAATCCCCACTGACATATGTAACTGATTAGATGAAAATCTCACATTTGTTTTGTCTTGCGATTTACCACCATCTTCTAAGACACTCCTTTCTTTGAAGCAGCGTGGTTTCAGCAAACGAAGGCTTCAACTAAACCCTTGTTTGCTTACTTTTTTATCGTTTACGTTTGGTTGTGGAGGTTACTATCAGGCTACACCAAGGTACTCTTGACTTGAGCAGAATTAAATATATACGCCAACCGCCGAGATTTTCTAAATATGATTTTTTATGACAAACTGAAACCGGCTGATGTGCTGGTTATTGGGTCTGCTGATGGGCGAGTTATTGAAGCTATCGAGTATATTGCTGATCTTCACAAACAGCATGGTTTTAAATTTGCTATTTGTCTTGGCAATTTGTTTTCCCACAAGCGTACAACTAGTGCGGACGTTGTTAAACTAAAAAATGAAAAAGTAAAGGTTCCTATACCAGTCTATTTCGGGGTTGGTACTGCTGGTTTGCCAGAGTCCATTATTTCGCATATGGCCATGTATGGACCAGAGGTAGCACCTAACTTGTTTTGTATGGGTATTTGTGGGTTTATGAAAACTTTTTACAAGTTTACAATTGCTCAACTTGGTGGATCTTATAATGAGGAGAAATACTACCAACCTCCCGAAAAATTTGAGCAAAGCTTAAATGAAAAGTGTTTTCATCGAAGTGATGTACAAAAGTTGTCTAAACGTTGTGACATTTTGTTCAGCTCTGAATGGCCGGAGGACGTACAAGAAAACTCTACTCTCCCTGAGAGAAAGTTGCCTAAAGGTTGTATGCCGTTAGCTGCACTAGCTGCTAATTGTATGCCGCAGTACTTTTTTGTTCCTGGGCCAGTTTACTACGAACGTGAACCCTACAAAAACTCTGCCGCTATTAATGTTAACACTGGTACTGTCACTCATTTCGTGGCTTTGGCCCCTTTCAAAAACTCCAAAAATGAGAAGTTTTCATACGCTTTTACTCTCTACCCCTTGACAACTGAGTACATGCAGCCAGCTCCTCCTAACTGTACTGCTTCTCCATTTGAGCATAGGCCAATTCCCTTAAAGCGTGCTTCAGAAGATCAAATTATTCCCCAGCAAACAAATAAATTCCATAAATCTAAATCAAGCACTGCTCTCTTTAAATCTAAAAAAGATTCTAGCTCGTCCCTCAACAAAATGCACAAGTCAGAGTCACATAGTGCACTCAATAATTTGCACAAGTCCGAATCAGGCACTTCGCTCAATAATAGACGGTCTAAAGTTGGACCCGGGTCATGCTTCTTTTGTTTGAGTAATCCAAATGTTGCACTTCACTTAATAGTCGCTATTGGTAACGAAGCTTACATGGCGTTGCCCAAAGGCCCTCTTACTACCACGGCATCGAATACCCCAGCTTTAGCTTCCTCTGGTCATGTTTTGATTATACCAATTGCGCATGCTTCTGCTTTAAGTACTTTGTCGGACACCTCATATGAGAAAACTTTAAATGAAATGAATCGATTTCGTAAAGCTGTAACTGATATGTACAATGCTTGTGATTCCGATGCTTTAGTATATGAAATTAGTAGAGCTAACGGAGTTCATTTGCATTGGCAAATGATTCCCATCCCCAAGATTTCCTCACATCGTATTGAATCAGTCTTCCTTGAAATGGCAAAGGAAGCTGGTTACGACTTTGAGGAAAGGGATGTAGAACCTCATGAGCTGAACTATTTCCGTGTATTTCTACCCTCTGGAAAAATCTTAATTCATCGATTACAACTAAGAGAACGATTTGATTTACAGTTTGGGCGACGTGCTGCTGCAAAAATTTTGGGTCTTGAGGATAGGGTTGATTGGAGAAAATGCGTTCAGACAGAAGATGAAGAAAAAGCTGAGAGTGAAGCTTTCAAAATGTGTTTCAAACCTTACGACTTTACATAA +>Transcript_19 len=4533 CDS=119-2408,2471-3098,3210-4020 exon=0-4533,0-4533,0-4533 five_prime_UTR=0-119,3098-4533,4020-4533 gene=0-4533,0-4533,0-4533 mRNA=0-4533,0-4533,0-4533 hmm_matches=CwfJ_C_1:2522-2819,CwfJ_C_2:2858-3095,CwfJ_C_1:3017-3077,Peptidase_M3:938-2366 three_prime_UTR=0-2471,0-3210,2408-4533 +TTTATATGTATACTATTCATGCGGATACTTTTTGTGGTTGGTATTTCAAGTAAACCCTCCTGGAAATATATACCATTCATATAGCCTGTACATGTACCAAAAATTTGTCGCATATTACGATGCAAGTAAGAACTTTGCTTACATTGGGAAAAAAAAAAGTAATTGGAAATAGGCAGTGCATTCTTAGTCTTTATCGAAAATATTCTAATGTTCAAAGTCGCAAAGCGGAAGACCAATTGTTGCGTCAAATTTTTGATGATCAGAATATAGCTGTGAACCAGATAACGAAAAGAAATGGAATTCAGGGAGTAGGATTGTTTCGTAATCACTTCCTTTCCGACAAAGATACCGGCTTCCTAAGGCTCGCGGAAACTGCATCTGAAAAATGTAAGGCCGTGATTGAGGATCTTTTGCTCGAGGATACTGAAGACGGGTCAATTGTAGTCAGCAAATTTGACAGGATTTCTAACTTACTATGCAGTGTCATTGACCTTTTTGAGTTTGTGCGCTGCGCCCATCCTGACAAGATGGTGGTAATGAAAGCAGAAGAAGCTTACAGTTATCTATTTGAGCTGATGAACACTTTAAACACTCATCAAGGTCTTTACGAAAAATTAAAGTGTTCTTTACAACAGACTCCTACGTTGAAAGATACAGATCCTGAAGCATATACTGTTGGAAGAGTATTCCTCCAAGATTTTGAAAAATCGGGCGTAAATTTAGAGAGCTCGAAAAGAAACTCCTTTGTTAAAAAGTCCTCTGAATCTGCAACTCTTGGAAGAGCATTTTTTAATAATAGCATGAATCGTCCTCAGCGTTATTTAACTATTTCTAAGCAACGTCTGGCTGGTTCGGACCCATATTTTGTACGCTCACTCTCTAAGAATGACAAAAACTTTATTATGATTCCAACTGTTGGATACGAAGGTACACAGGCCTTGATTAGTGTAGCAAATCCCGACGTCAGGAAAGAAATTTACATGGAAGGTCATAAAGGAACAGTTGAAGAAGTCGAATTGCTAAATTCCTATTTGAGGTCTAAAGCGGAAGTTGCGAAACTAGTGGGAAAAAGTAGTTTTGCAGATTTACAACTTATAGATAAAATGGCTAATGCTCCTAAACATGTTGTTGAATTTTTAGAGAACTTATCATTAAAAAATTCTTCCGTGTTAAAAAAGATTTTAAACAATCTCGCGTTAATGAAGAAAAAAGAGTTAAACTTGAATTTTCTTCCATCATTTGATGTTTGGGACAGGGAATATTATACTGCTCGCTATAAACAATCTCTTATAAATCAAAAGCCTTCTTTAAACCCTTCTATAACGAATTATCGGCGTTTTTTTTCTGTTGGTACAGTTATTCAAGGTCTATCTAGACTATTTAGTTCTTTATATGGGCTTCGTTTTGTTCCAGCGGACATTTCCCCTGGTGAGGTATGGCATCCTGATGTAAATAAGGTCAATGTTTACAATGAAAATGATCATGTAATGGGTGTAATTTATTTCGATCTATTTGCTCGAACAGGAAAAACAGATGGAGCTGCTCATTTTACAATTCGTTCTTCTCGGGAATTAGACTTGACAAGCTTTGACGATTCTATAAGTCTTGGATTTGATGATGCTACTAATATAAGGGTCAAGGATAACAAACGGTATCAAATACCTGTCATTTCGTTATTGTGTAATTTCGTACGTTCTAGTGGAATGGATCCTACCTTTTTAGATTTGTGGGATGTGAAAACACTTTTTCACGAGATGGGGCATGCCATGCATTCCATTCTAGGTCATACTAAATATCAGAACTTAGCCGGAACTCGTTGTGCAACCGACTTTGTTGAACTTCCTTCAATTATTATGGAGTTTTTTATGTCAAATCCAGCCGTATTACCGCTTTATGCTCGCTACGAAGGAACTGAGATTCCATTACCTGTACAAGTTTTGAACCATCATAACATGGTTGAAAATAGTTCAGCACCCTTAGATTTACAATCTCAAATTTGTATGGCTATGGTGGATCAATTGTTTCACTCGAAGGTTGTCTTAGATCCGTCATTTAATTCTATCGATGAAGTTACTAATGTAACCAGAAAGTTCAGTGGGTTTGAGTCTGCTCCACCTGCTGCTTGGTATCTTCAGTTTAGTCATCTTTATGGATATAGCGCTACTTATTATTCATACATTTTTGATACGGTATTGGCTTCGCTAATCTTTAGTAAACTTTTTGCTGGAAATCCATTAAGCCGTGAGGCTGGTGAGAAATTTCGTAAAGCCATCCTACGATGGGGTGGCAGTAGAAGCCCATGGGAATGTGTTGCAGAAGCCCTTGAACAACCTATATTAGCAACGGGCGGCGAAGAGGCCATGCGTCGAATAGGAAGTGAAGGTATTAAAGCGACGTCCACCTTTTAATGGAATGATGTTCCAGTTATGAATTTAAATAATTTATTTATGAATTATAATGAAATACTAAATTTATGTAAAGTCGTAAGGTTTGAAACACATTTTGAAAGCTTCACTCTCAGCTTTTTCTTCATCTTCTGTCTGAACGCATTTTCTCCAATCAACCCTATCCTCAAGACCCAAAATTTTTGCAGCAGCACGTCGCCCAAACTGTAAATCAAATCGTTCTCTTAGTTGTAATCGATGAATTAAGATTTTTCCAGAGGGTAGAAATACACGGAAATAGTTCAGCTCATGAGGTTCTACATCCCTTTCCTCAAAGTCGTAACCAGCTTCCTTTGCCATTTCAAGGAAGACTGATTCAATACGATGTGAGGAAATCTTGGGGATGGGAATCATTTGCCAATGCAAATGAACTCCGTTAGCTCTACTAATTTCATATACTAAAGCATCGGAATCACAAGCATTGTACATATCAGTTACAGCTTTACGAAATCGATTCATTTCATTTAAAGTTTTCTCATATGAGGTGTCCGACAAAGTACTTAAAGCAGAAGCATGCGCAATTGGTATAATCAAAACATGACCAGAGGAAGCTAAAGCTGGGGTATTCGATGCCGTGGTAGTAAGAGGGCCTTTGGGCAACGCTGAGTCGTTAGTATAAAAAAGAGTAAAATTTAAACAGCGTGTCGCAAACATTGGAGTGTATAAACGTACCCATGTAAGCTTCGTTACCAATAGCGACTATTAAGTGAAGTGCAACATTTGGATTACTCAAACAAAAGAAGCATGACCCGGCTGAGAAAAGAAGTTAGTGACGGTGGAAAAAACGCAGAGATAAGAAGCGGAACTCACGTCCAACTTTAGACCGTCTATTATTGAGCGAAGTGCCTGATTCGGACTTGTGCAAATTATTGAGTGCACTATGTGACTCTGACTTGTGCATTTTGTTGAGGGACGAGCTAGAATCTTTTTTAGATTTAAAGAGAGCAGTGCTTGATTTAGATTTATGGAATTTATTTGTTTGCTGGGGAATAATTTGATCTTCTGAAGCACGCTTTAAGGGAATTGGCCTATGCTCAAATGGAGAAGCAGTACAGTTAGGAGGAGCTGGCTGCATGTACTCAGTTGTCAAGGGGTAGAGAGTAAAAGCGTATGAAAACTTCTCATTTTTGGAGTTTTTGAAAGGGGCCAAAGCCACGAAATGAGTGACAGTACCAGTGTTAACATTAATAGCGGCAGAGTTTTTGTAGGGTTCACGTTCGTAGTAAACTGGCCCAGGAACAAAAAAGTACTGCGGCATACAATTAGCAGCTAGTGCAGCTAACGGCATACAACCTTTAGGCAACTTTCTCTCAGGGAGAGTAGAGTTTTCTTGTACGTCCTCCGGCCATTCAGAGCTGAACAAAATGTCACAACGTTTAGACAACTTTTGTACATCACTTCGATGAAAACACTTTTCATTTAAGCTTTGCTCAAATTTTTCGGGAGGTTGGTAGTATTTCTCCTCATTATAAGATCCACCAAGTTGAGCAATTGTAAACTTGTAAAAAGTTTTCATAAACCCACAAATACCCATACAAAACAAGTTAGGTGCTACCTCTGGTCCATACATGGCCATATGCGAAATAATGGACTCTGGCAAACCAGCAGTACCAACCCCGAAATAGACTGGTATAGGAACTACAGCTCAGGTTAGCAACAAGAATGAATAAGAAGAAAGATTTATCAATCGTGATTAAAGCATTAAAGAAAAGAATTTCTCGTTCGATAAAACCGGCCATTCAAAATCATACCCTTTACTTTTTCATTTTTTAGTTTAACAACGTCCGCACTAGTTGTACGCTTGTGGGAAAACAAATTGCCAAGACAAATAGCAAATTTAAAACCATGCTGTTTGTGAAGATCAGCAATATACTCGATAGCTTCAATAACTCGCCCATCAGCAGACCCAATAACCAGCCTATTCGAATCTATGTTAGCGAGTTGCAAGACGTACTGAAAATTTTTCAATCTCGTTCACAAACTGAGTTGAAGTAGTTAAATATATGTATACTTACACATCAGCCGGTTTCAGTTTGTCATAAAAAATCATATTTAGAAAATCTCGGCGGTTGGCGTATATATTTAATTC +>Transcript_20 len=1876 CDS=1448-1769,0-771,994-1345 exon=0-1876,0-1876,0-1876 five_prime_UTR=1345-1876,1769-1876 gene=0-1876,0-1876,0-1876 mRNA=0-1876,0-1876,0-1876 hmm_matches=GRASP55_65:1451-1634,Hep_59:207-285,Hep_59:315-606,Hep_59:654-687 three_prime_UTR=0-1448,0-994,771-1876 +ATCCGCATGAATAGTATACATATAAAAAAGAAAAGCAATCGATCGTTCAGAAGAAGAAAAGTTTTTGGAAATGAAAAAGAATTTGATTTAGAAGAATTAGATGATAATGATATTCGTCTACGGCAAGCTTTGGAAGCTACTAAGAGGCGAAAAATTAGAAATTCGATTATCGGGATAAATGCTGAAAAGTTATTAAATCAAGAAACAAAAAAAGAGAAACAATTGAACACTGCTAATGAGCCTCATGAAGCTAATGATCAGACCTCAGCTCAATCGTCGAAACTTATAGAGGCGCAACTTCCAACCGTCGAAGATAGGTTTGCTAAACAAACAAACGAGGTTGACATCAACACGCATTTATTAAACTTTGTTGAAAAAAAACTGAAACAGGAAAGGTTGGCCCAAAACTACTCAGAAAATGGAGAGACTAATGCACTTAATACAAAAAATGAATCGACGGTACAAAACATAAAAAATTCCTTACATCCAAATGAACATTCATTTATTAGAGATGCAGCTGCTCTTGGTGCTATACGTGAAGTAGATTTAGGGATTATTAGTACCGACGTTGATAATTTGAAAAATGGTCGGAAACGACAAAAAAAAAGAGCAAGAATGAAAGAAAAACTAGACTCGAAGGCTCTTCGCACCTCTGAGGACGCTGCTCGGGATGAATTTATTGAAAAAATGTTAAAACCGATATCCCAAGATGAAGAAAGTAAGGGAATCTACAGGCGTTTTCGCGTTTACAAGGATGGAACTCAGGATTAACGATAATAAAAAAGAAGCAACAGTTTGGCAAGGTTCATTAATTCAAATTATTTATTACATTTTTTGAGTAATCAATTCGGATAAAGAGGTTTGTTTGTGTTTTATAAAATCCTTACTCAAAACCTCAAATGTTTATTTATCAAAAATATAGTTTTGTAACTTTTAATCATTATGGGCATTAAAAAGAGGGCTTTTGCTAGAAAAGACGAGCTTAACTAAATAACTAATTTTTCACAAGTTCTTCATTTTGAGGCGCTGATTCATCGTTTGTTGAATTAACAGCGACAGGAGGAGGAGGAGGCAAAGGAGTTGTTTGGGAATCGTTAGTAGAAGAAGCGTCTTTGGTTTTATGATCCAATTCTCTGCTTAGTTTTTCTTCTTCATCTAAATATGATTGAATAGAAGAATCTTGGATAGCGCCTTTATGAGACTTCTTATGTCTTTGATAGTGCGGGATAGATATTTCATTGCTAGATCCAGCATTAGCAGAAGCGATTTTAGGTGGTTCTGGAGTAGGCAAAAAGTTTTCAGTTTCACTGGGCTGAGACACTTTATGATCTGGACCCCCCAGCATGGGATTTGAAAACACAATGTCCCCAGGTTGTGGAGGAGGTCCTGACAAAGGAGCGGGTAAGCGATGCAAGACGCCATGTCCAACACCACATCCAATAGCTCCATTACCTCCCCAATGACGATTTGGGACAATGGTAACTTGACGAGTGGAGTCGCGATAATGATTGTAGATATACAGGCGTAAGGGTCTGTTGAGATGCTGTTAAATTGTTAGTCAAATAATTTATCTTAGCACATAATTTACATACAGACTCAATTAGGTCTGAAAGCGCTTTTTCTCCTGTCATCATTCCTTCAGGAGTTCCGACGATATAATCTTCATACGGAACAAGGCTAGCTCGTGCAACAGGAGAATCGTCTATAACATTCAAAATATGCCAAATGGCATCCACGGCAGGAGCGATTGATGCCCACTGTAAAACCATGCCAATTTTTTCTGTAGTCGTTAGAAAATTTATTTGTATTCAATAAGCGTTCATAAAAATACATCCAAAAAAGATATAAGAATCGTTAACCGCAGCTAGAAACTTAC diff --git a/dammit/tests/test-data/pom.20.udbs.dammit.gff3 b/dammit/tests/test-data/pom.20.udbs.dammit.gff3 index 74dcf108..060b93d5 100644 --- a/dammit/tests/test-data/pom.20.udbs.dammit.gff3 +++ b/dammit/tests/test-data/pom.20.udbs.dammit.gff3 @@ -1,153 +1,216 @@ ##gff-version 3.2.1 -Transcript_0 BUSCO BUSCO_ortholog 1 5662 8.400000e+01 . . ID=busco:c175e99ae828326adaedd0e8e20181c562f2cc2a;Name=367596at33208a;length=154;status=Fragmented -Transcript_0 HMMER protein_hmm_match 3604 4089 2.100000e-10 . . ID=homology:84650fc4aa4df19d561278cef53cd46b3c22f7a4;Name=DEAD;Target=DEAD 10 174 +;accuracy=0.75;env_coords=3580 4092;Dbxref="Pfam-A:PF00270.25";Note=DEAD/DEAH box helicase -Transcript_0 HMMER protein_hmm_match 4207 4548 3.200000e-18 . . ID=homology:ee81caa0c6870a9a9014dd352cc1c65031b1a930;Name=Helicase_C;Target=Helicase_C 8 105 +;accuracy=0.87;env_coords=4186 4548;Dbxref="Pfam-A:PF00271.27";Note=Helicase conserved C-terminal domain -Transcript_0 HMMER protein_hmm_match 5218 5274 1.100000e+04 . . ID=homology:f97b334d076a68dd960fa2da62071da10c0973b1;Name=Helicase_C;Target=Helicase_C 16 34 +;accuracy=0.78;env_coords=5203 5307;Dbxref="Pfam-A:PF00271.27";Note=Helicase conserved C-terminal domain -Transcript_0 shmlast.LAST conditional_reciprocal_best_LAST 1 1887 0.000000e+00 + . ID=homology:94a770b951c0d15c4b3d0d2b57d07c3851565147;Name=SPAC212.11|tlh1|I|RecQ type DNA helicase;Target=SPAC212.11|tlh1|I|RecQ type DNA helicase 1 1887 +;database=pep.fa -Transcript_0 transdecoder CDS 1 5661 . + 0 ID=cds.Transcript_0.p1;Parent=Transcript_0.p1 -Transcript_0 transdecoder exon 1 5662 . + . ID=Transcript_0.p1.exon1;Parent=Transcript_0.p1 -Transcript_0 transdecoder gene 1 5662 . + . ID=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3A3prime_partial%20len%3A1888%20%28%2B%29%2Cscore%3D464.77%2CHelicase_C%7CPF00271.27%7C3.2e-18%2CHelicase_C%7CPF00271.27%7C1.1e%2B04%2CDEAD%7CPF00270.25%7C2.1e-10 -Transcript_0 transdecoder mRNA 1 5662 . + . ID=Transcript_0.p1;Parent=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3A3prime_partial%20len%3A1888%20%28%2B%29%2Cscore%3D464.77%2CHelicase_C%7CPF00271.27%7C3.2e-18%2CHelicase_C%7CPF00271.27%7C1.1e%2B04%2CDEAD%7CPF00270.25%7C2.1e-10 -Transcript_10 HMMER protein_hmm_match 200 340 1.300000e-10 . . ID=homology:360d91ea72c98f8edd46f422390080235e870699;Name=Pombe_5TM;Target=Pombe_5TM 1 52 +;accuracy=0.95;env_coords=200 352;Dbxref="Pfam-A:PF09437.6";Note=Pombe specific 5TM protein -Transcript_10 HMMER protein_hmm_match 356 598 5.100000e-26 . . ID=homology:79cc2e997715c97105ac3dff1b1fd643258a1218;Name=Pombe_5TM;Target=Pombe_5TM 118 220 +;accuracy=0.93;env_coords=341 634;Dbxref="Pfam-A:PF09437.6";Note=Pombe specific 5TM protein -Transcript_10 shmlast.LAST conditional_reciprocal_best_LAST 66 211 3.300000e-103 + . ID=homology:5bddc141f52e14a4e285ddcb7c87aea1cbd54ce4;Name=SPAC977.02|SPAC977.02|I|S. pombe specific 5Tm protein family;Target=SPAC977.02|SPAC977.02|I|S. pombe specific 5Tm protein family 1 146 +;database=pep.fa -Transcript_10 transdecoder CDS 197 637 . + 0 ID=cds.Transcript_10.p1;Parent=Transcript_10.p1 -Transcript_10 transdecoder exon 1 979 . + . ID=Transcript_10.p1.exon1;Parent=Transcript_10.p1 -Transcript_10 transdecoder five_prime_UTR 1 196 . + . ID=Transcript_10.p1.utr5p1;Parent=Transcript_10.p1 -Transcript_10 transdecoder gene 1 979 . + . ID=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A147%20%28%2B%29%2Cscore%3D82.86%2CPombe_5TM%7CPF09437.6%7C1.3e-10%2CPombe_5TM%7CPF09437.6%7C5.1e-26 -Transcript_10 transdecoder mRNA 1 979 . + . ID=Transcript_10.p1;Parent=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A147%20%28%2B%29%2Cscore%3D82.86%2CPombe_5TM%7CPF09437.6%7C1.3e-10%2CPombe_5TM%7CPF09437.6%7C5.1e-26 -Transcript_10 transdecoder three_prime_UTR 638 979 . + . ID=Transcript_10.p1.utr3p1;Parent=Transcript_10.p1 -Transcript_11 HMMER protein_hmm_match 22 342 1.400000e-11 . . ID=homology:720816922e5720ad3a3b08c8ec4dcec41f989599;Name=Methyltransf_23;Target=Methyltransf_23 21 120 +;accuracy=0.79;env_coords=1 420;Dbxref="Pfam-A:PF13489.2";Note=Methyltransferase domain -Transcript_11 HMMER protein_hmm_match 28 252 7.500000e-06 . . ID=homology:fef38a04a9928995794ff4003df57fb2dc428ba4;Name=TPMT;Target=TPMT 38 126 +;accuracy=0.66;env_coords=7 360;Dbxref="Pfam-A:PF05724.7";Note=Thiopurine S-methyltransferase (TPMT) -Transcript_11 HMMER protein_hmm_match 31 258 6.100000e-10 . . ID=homology:efdb8560b80a01eed3e13b9b49d21ffc75e6459a;Name=Methyltransf_31;Target=Methyltransf_31 5 85 +;accuracy=0.84;env_coords=22 387;Dbxref="Pfam-A:PF13847.2";Note=Methyltransferase domain -Transcript_11 HMMER protein_hmm_match 31 276 5.400000e-09 . . ID=homology:b83291ea939d431142fac383446959f9dc24253b;Name=Methyltransf_18;Target=Methyltransf_18 3 87 +;accuracy=0.8;env_coords=28 345;Dbxref="Pfam-A:PF12847.3";Note=Methyltransferase domain -Transcript_11 HMMER protein_hmm_match 37 267 8.600000e-09 . . ID=homology:15a224e5b577b0264be925afd2a9fa31e69e462e;Name=Methyltransf_25;Target=Methyltransf_25 1 82 +;accuracy=0.88;env_coords=37 354;Dbxref="Pfam-A:PF13649.2";Note=Methyltransferase domain -Transcript_11 HMMER protein_hmm_match 40 279 1.800000e-09 . . ID=homology:78d115e66b6c61c97055fab1b8a6265814cea958;Name=Methyltransf_12;Target=Methyltransf_12 1 80 +;accuracy=0.74;env_coords=40 315;Dbxref="Pfam-A:PF08242.8";Note=Methyltransferase domain -Transcript_11 HMMER protein_hmm_match 40 279 7.900000e-10 . . ID=homology:e61b3cf4766a563d73c1f0590712ce9a66d146d5;Name=Methyltransf_11;Target=Methyltransf_11 1 77 +;accuracy=0.85;env_coords=40 333;Dbxref="Pfam-A:PF08241.8";Note=Methyltransferase domain -Transcript_11 shmlast.LAST conditional_reciprocal_best_LAST 1 145 4.300000e-109 + . ID=homology:a69c6cd647c5cc147e84d4553dbeab70cff38442;Name=SPAC977.03|SPAC977.03|I|methyltransferase (predicted);Target=SPAC977.03|SPAC977.03|I|methyltransferase (predicted) 1 145 +;database=pep.fa -Transcript_11 transdecoder CDS 1 438 . + 0 ID=cds.Transcript_11.p1;Parent=Transcript_11.p1 -Transcript_11 transdecoder exon 1 438 . + . ID=Transcript_11.p1.exon1;Parent=Transcript_11.p1 -Transcript_11 transdecoder gene 1 438 . + . ID=GENE.Transcript_11~~Transcript_11.p1;Name=ORF%20type%3Acomplete%20len%3A146%20%28%2B%29%2Cscore%3D85.63%2CMethyltransf_23%7CPF13489.2%7C1.4e-11%2CMethyltransf_31%7CPF13847.2%7C6.1e-10%2CMethyltransf_11%7CPF08241.8%7C7.9e-10%2CMethyltransf_12%7CPF08242.8%7C1.8e-09%2CMethyltransf_18%7CPF12847.3%7C5.4e-09%2CMethyltransf_25%7CPF13649.2%7C8.6e-09%2CTPMT%7CPF05724.7%7C7.5e-06 -Transcript_11 transdecoder mRNA 1 438 . + . ID=Transcript_11.p1;Parent=GENE.Transcript_11~~Transcript_11.p1;Name=ORF%20type%3Acomplete%20len%3A146%20%28%2B%29%2Cscore%3D85.63%2CMethyltransf_23%7CPF13489.2%7C1.4e-11%2CMethyltransf_31%7CPF13847.2%7C6.1e-10%2CMethyltransf_11%7CPF08241.8%7C7.9e-10%2CMethyltransf_12%7CPF08242.8%7C1.8e-09%2CMethyltransf_18%7CPF12847.3%7C5.4e-09%2CMethyltransf_25%7CPF13649.2%7C8.6e-09%2CTPMT%7CPF05724.7%7C7.5e-06 -Transcript_12 shmlast.LAST conditional_reciprocal_best_LAST 18 172 1.200000e-116 + . ID=homology:c435df18cff450cb65b1c8a55bc27e28a97c9f50;Name=SPAC977.04|SPAC977.04|I|truncated C terminal region of membrane transporter;Target=SPAC977.04|SPAC977.04|I|truncated C terminal region of membrane transporter 1 155 +;database=pep.fa -Transcript_12 transdecoder CDS 1 519 . + 0 ID=cds.Transcript_12.p1;Parent=Transcript_12.p1 -Transcript_12 transdecoder exon 1 681 . + . ID=Transcript_12.p1.exon1;Parent=Transcript_12.p1 -Transcript_12 transdecoder gene 1 681 . + . ID=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A173%20%28%2B%29%2Cscore%3D104.11 -Transcript_12 transdecoder mRNA 1 681 . + . ID=Transcript_12.p1;Parent=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A173%20%28%2B%29%2Cscore%3D104.11 -Transcript_12 transdecoder three_prime_UTR 520 681 . + . ID=Transcript_12.p1.utr3p1;Parent=Transcript_12.p1 -Transcript_13 HMMER protein_hmm_match 31 612 6.700000e-107 . . ID=homology:25e04c02da322c661bcb7e475a4f11af32c0eebf;Name=Vel1p;Target=Vel1p 8 201 +;accuracy=0.97;env_coords=7 612;Dbxref="Pfam-A:PF10339.5";Note=Yeast-specific zinc responsive -Transcript_13 shmlast.LAST conditional_reciprocal_best_LAST 1 204 2.700000e-155 + . ID=homology:3c4185a4986c931924c0b92956b14295ccf302f1;Name=SPAC977.05c|SPAC977.05c|I|conserved fungal family;Target=SPAC977.05c|SPAC977.05c|I|conserved fungal family 1 204 +;database=pep.fa -Transcript_13 transdecoder CDS 1 615 . + 0 ID=cds.Transcript_13.p1;Parent=Transcript_13.p1 -Transcript_13 transdecoder exon 1 615 . + . ID=Transcript_13.p1.exon1;Parent=Transcript_13.p1 -Transcript_13 transdecoder gene 1 615 . + . ID=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A205%20%28%2B%29%2Cscore%3D126.49%2CVel1p%7CPF10339.5%7C6.7e-107 -Transcript_13 transdecoder mRNA 1 615 . + . ID=Transcript_13.p1;Parent=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A205%20%28%2B%29%2Cscore%3D126.49%2CVel1p%7CPF10339.5%7C6.7e-107 -Transcript_14 HMMER protein_hmm_match 16 432 6.000000e-78 . . ID=homology:85b21689c5e713d50ca92d35457e5f9171d04c9b;Name=DUF999;Target=DUF999 1 143 +;accuracy=0.99;env_coords=16 432;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) -Transcript_14 HMMER protein_hmm_match 481 510 1.100000e+04 . . ID=homology:6b21eda2b5258ab5cc4805527e762b2f128a3f29;Name=DUF999;Target=DUF999 92 101 +;accuracy=0.55;env_coords=460 555;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) -Transcript_14 shmlast.LAST conditional_reciprocal_best_LAST 6 194 2.900000e-143 + . ID=homology:bbbbb2217ab55d406588836a15266f0f6ec3bcd4;Name=SPAC977.06|SPAC977.06|I|S. pombe specific DUF999 family protein 3;Target=SPAC977.06|SPAC977.06|I|S. pombe specific DUF999 family protein 3 1 189 +;database=pep.fa -Transcript_14 transdecoder CDS 1 585 . + 0 ID=cds.Transcript_14.p1;Parent=Transcript_14.p1 -Transcript_14 transdecoder exon 1 607 . + . ID=Transcript_14.p1.exon1;Parent=Transcript_14.p1 -Transcript_14 transdecoder gene 1 607 . + . ID=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3A5prime_partial%20len%3A195%20%28%2B%29%2Cscore%3D142.29%2CDUF999%7CPF06198.7%7C6e-78%2CDUF999%7CPF06198.7%7C1.1e%2B04 -Transcript_14 transdecoder mRNA 1 607 . + . ID=Transcript_14.p1;Parent=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3A5prime_partial%20len%3A195%20%28%2B%29%2Cscore%3D142.29%2CDUF999%7CPF06198.7%7C6e-78%2CDUF999%7CPF06198.7%7C1.1e%2B04 -Transcript_14 transdecoder three_prime_UTR 586 607 . + . ID=Transcript_14.p1.utr3p1;Parent=Transcript_14.p1 -Transcript_15 HMMER protein_hmm_match 178 180 4.700000e+03 . . ID=homology:127ef42ed898b79cc422bc7af762afb849b3f09a;Name=PA14_2;Target=PA14_2 97 97 +;accuracy=0.59;env_coords=55 291;Dbxref="Pfam-A:PF10528.5";Note=GLEYA domain -Transcript_15 HMMER protein_hmm_match 385 477 6.000000e+03 . . ID=homology:fda972fb3251c2815dc721d0473f7fbcc188c7b3;Name=PA14_2;Target=PA14_2 64 95 +;accuracy=0.48;env_coords=334 540;Dbxref="Pfam-A:PF10528.5";Note=GLEYA domain -Transcript_15 HMMER protein_hmm_match 832 1182 1.200000e-49 . . ID=homology:c2cfea5e0e1bbb10b9f093eb39a99a91da879316;Name=PA14_2;Target=PA14_2 1 115 +;accuracy=0.98;env_coords=832 1185;Dbxref="Pfam-A:PF10528.5";Note=GLEYA domain -Transcript_15 shmlast.LAST conditional_reciprocal_best_LAST 1 416 1.976263e-323 + . ID=homology:3f9fd792943afae5b71c19f6a6348e97e0f632b2;Name=SPAC977.07c|pfl6|I|cell surface glycoprotein, adhesion molecule (predicted);Target=SPAC977.07c|pfl6|I|cell surface glycoprotein, adhesion molecule (predicted) 1 416 +;database=pep.fa -Transcript_15 transdecoder CDS 1 1251 . + 0 ID=cds.Transcript_15.p1;Parent=Transcript_15.p1 -Transcript_15 transdecoder exon 1 1251 . + . ID=Transcript_15.p1.exon1;Parent=Transcript_15.p1 -Transcript_15 transdecoder gene 1 1251 . + . ID=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3Acomplete%20len%3A417%20%28%2B%29%2Cscore%3D268.06%2CPA14_2%7CPF10528.5%7C4.7e%2B03%2CPA14_2%7CPF10528.5%7C6e%2B03%2CPA14_2%7CPF10528.5%7C1.2e-49 -Transcript_15 transdecoder mRNA 1 1251 . + . ID=Transcript_15.p1;Parent=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3Acomplete%20len%3A417%20%28%2B%29%2Cscore%3D268.06%2CPA14_2%7CPF10528.5%7C4.7e%2B03%2CPA14_2%7CPF10528.5%7C6e%2B03%2CPA14_2%7CPF10528.5%7C1.2e-49 -Transcript_16 HMMER protein_hmm_match 106 510 2.000000e-12 . . ID=homology:00e3681c9f0dafa06b5dc3ea643852510d9b2be2;Name=adh_short_C2;Target=adh_short_C2 46 184 +;accuracy=0.83;env_coords=64 669;Dbxref="Pfam-A:PF13561.2";Note=Enoyl-(Acyl carrier protein) reductase -Transcript_16 HMMER protein_hmm_match 76 528 9.100000e-36 . . ID=homology:f379157a96e8158f5aa86dbb6a941c1fb466bb44;Name=adh_short;Target=adh_short 37 191 +;accuracy=0.94;env_coords=61 540;Dbxref="Pfam-A:PF00106.21";Note=short chain dehydrogenase -Transcript_16 shmlast.LAST conditional_reciprocal_best_LAST 21 256 6.300000e-174 + . ID=homology:669a1dd29f2b40aa7db12d129b95ccef21219987;Name=SPAC977.08|SPAC977.08|I|short chain dehydrogenase (predicted);Target=SPAC977.08|SPAC977.08|I|short chain dehydrogenase (predicted) 1 236 +;database=pep.fa -Transcript_16 transdecoder CDS 61 771 . + 0 ID=cds.Transcript_16.p1;Parent=Transcript_16.p1 -Transcript_16 transdecoder exon 1 825 . + . ID=Transcript_16.p1.exon1;Parent=Transcript_16.p1 -Transcript_16 transdecoder five_prime_UTR 1 60 . + . ID=Transcript_16.p1.utr5p1;Parent=Transcript_16.p1 -Transcript_16 transdecoder gene 1 825 . + . ID=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A237%20%28%2B%29%2Cscore%3D135.27%2Cadh_short%7CPF00106.21%7C9.1e-36%2Cadh_short_C2%7CPF13561.2%7C2e-12 -Transcript_16 transdecoder mRNA 1 825 . + . ID=Transcript_16.p1;Parent=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A237%20%28%2B%29%2Cscore%3D135.27%2Cadh_short%7CPF00106.21%7C9.1e-36%2Cadh_short_C2%7CPF13561.2%7C2e-12 -Transcript_16 transdecoder three_prime_UTR 772 825 . + . ID=Transcript_16.p1.utr3p1;Parent=Transcript_16.p1 -Transcript_17 HMMER protein_hmm_match 633 2081 7.100000e-204 . . ID=homology:58260bb20cdcf6a0926f9eefe737aa0793fb66b0;Name=PLA2_B;Target=PLA2_B 1 490 +;accuracy=0.99;env_coords=633 2084;Dbxref="Pfam-A:PF01735.14";Note=Lysophospholipase catalytic domain -Transcript_17 shmlast.LAST conditional_reciprocal_best_LAST 80 752 0.000000e+00 + . ID=homology:02b94f4c02b2a78881d6e3cdddea00d4f99be7db;Name=SPAC977.09c|SPAC977.09c|I|phospholipase (predicted);Target=SPAC977.09c|SPAC977.09c|I|phospholipase (predicted) 1 673 +;database=pep.fa -Transcript_17 transdecoder CDS 240 2261 . + 0 ID=cds.Transcript_17.p1;Parent=Transcript_17.p1 -Transcript_17 transdecoder exon 1 2461 . + . ID=Transcript_17.p1.exon1;Parent=Transcript_17.p1 -Transcript_17 transdecoder five_prime_UTR 1 239 . + . ID=Transcript_17.p1.utr5p1;Parent=Transcript_17.p1 -Transcript_17 transdecoder gene 1 2461 . + . ID=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A674%20%28%2B%29%2Cscore%3D453.37%2CPLA2_B%7CPF01735.14%7C7.1e-204 -Transcript_17 transdecoder mRNA 1 2461 . + . ID=Transcript_17.p1;Parent=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A674%20%28%2B%29%2Cscore%3D453.37%2CPLA2_B%7CPF01735.14%7C7.1e-204 -Transcript_17 transdecoder three_prime_UTR 2262 2461 . + . ID=Transcript_17.p1.utr3p1;Parent=Transcript_17.p1 -Transcript_18 HMMER protein_hmm_match 1217 2473 2.600000e-76 . . ID=homology:7f7ee6423af5bd40affac6b99d664045c24586c2;Name=Na_H_Exchanger;Target=Na_H_Exchanger 1 381 +;accuracy=0.95;env_coords=1217 2473;Dbxref="Pfam-A:PF00999.17";Note=Sodium/hydrogen exchanger family -Transcript_18 shmlast.LAST conditional_reciprocal_best_LAST 391 858 0.000000e+00 + . ID=homology:e135e2e2099cb1a8d9495f2345471292a4e72722;Name=SPAC977.10|sod2|I|plasma membrane sodium ion/proton antiporter Sod2;Target=SPAC977.10|sod2|I|plasma membrane sodium ion/proton antiporter Sod2 1 468 +;database=pep.fa -Transcript_18 transdecoder CDS 947 2578 . + 0 ID=cds.Transcript_18.p1;Parent=Transcript_18.p1 -Transcript_18 transdecoder exon 1 2836 . + . ID=Transcript_18.p1.exon1;Parent=Transcript_18.p1 -Transcript_18 transdecoder five_prime_UTR 1 946 . + . ID=Transcript_18.p1.utr5p1;Parent=Transcript_18.p1 -Transcript_18 transdecoder gene 1 2836 . + . ID=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A544%20%28%2B%29%2Cscore%3D299.04%2CNa_H_Exchanger%7CPF00999.17%7C2.6e-76 -Transcript_18 transdecoder mRNA 1 2836 . + . ID=Transcript_18.p1;Parent=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A544%20%28%2B%29%2Cscore%3D299.04%2CNa_H_Exchanger%7CPF00999.17%7C2.6e-76 -Transcript_18 transdecoder three_prime_UTR 2579 2836 . + . ID=Transcript_18.p1.utr3p1;Parent=Transcript_18.p1 -Transcript_19 HMMER protein_hmm_match 237 566 2.000000e-15 . . ID=homology:b6cb34c1b8f6eadcf119b1691749637deb800e2b;Name=CRCB;Target=CRCB 3 88 +;accuracy=0.84;env_coords=231 599;Dbxref="Pfam-A:PF02537.11";Note=CrcB-like protein, Camphor Resistance (CrcB) -Transcript_19 HMMER protein_hmm_match 711 755 5.000000e+03 . . ID=homology:178a4a4d3e4a362935e0526cd6e6cbe10215ce59;Name=CRCB;Target=CRCB 41 53 +;accuracy=0.58;env_coords=651 764;Dbxref="Pfam-A:PF02537.11";Note=CrcB-like protein, Camphor Resistance (CrcB) -Transcript_19 HMMER protein_hmm_match 783 1103 9.100000e-15 . . ID=homology:60f5430d270abb5f9692f9610750150cdca521d9;Name=CRCB;Target=CRCB 3 90 +;accuracy=0.84;env_coords=777 1130;Dbxref="Pfam-A:PF02537.11";Note=CrcB-like protein, Camphor Resistance (CrcB) -Transcript_19 shmlast.LAST conditional_reciprocal_best_LAST 72 382 5.700000e-237 + . ID=homology:c7170753b69543028628218cfc2957aaca46be84;Name=SPAC977.11|SPAC977.11|I|CRCB domain protein;Target=SPAC977.11|SPAC977.11|I|CRCB domain protein 1 311 +;database=pep.fa -Transcript_19 transdecoder CDS 216 1151 . + 0 ID=cds.Transcript_19.p1;Parent=Transcript_19.p1 -Transcript_19 transdecoder exon 1 1250 . + . ID=Transcript_19.p1.exon1;Parent=Transcript_19.p1 -Transcript_19 transdecoder five_prime_UTR 1 215 . + . ID=Transcript_19.p1.utr5p1;Parent=Transcript_19.p1 -Transcript_19 transdecoder gene 1 1250 . + . ID=GENE.Transcript_19~~Transcript_19.p1;Name=ORF%20type%3Acomplete%20len%3A312%20%28%2B%29%2Cscore%3D203.47%2CCRCB%7CPF02537.11%7C2e-15%2CCRCB%7CPF02537.11%7C5e%2B03%2CCRCB%7CPF02537.11%7C9.1e-15 -Transcript_19 transdecoder mRNA 1 1250 . + . ID=Transcript_19.p1;Parent=GENE.Transcript_19~~Transcript_19.p1;Name=ORF%20type%3Acomplete%20len%3A312%20%28%2B%29%2Cscore%3D203.47%2CCRCB%7CPF02537.11%7C2e-15%2CCRCB%7CPF02537.11%7C5e%2B03%2CCRCB%7CPF02537.11%7C9.1e-15 -Transcript_19 transdecoder three_prime_UTR 1152 1250 . + . ID=Transcript_19.p1.utr3p1;Parent=Transcript_19.p1 -Transcript_1 shmlast.LAST conditional_reciprocal_best_LAST 125 402 3.000000e-216 + . ID=homology:89e3c799b148e94ed8dca8df7bfd9b8c4b2de625;Name=SPAC212.08c|SPAC212.08c|I|S. pombe specific GPI anchored protein family 1;Target=SPAC212.08c|SPAC212.08c|I|S. pombe specific GPI anchored protein family 1 1 278 +;database=pep.fa -Transcript_1 transdecoder CDS 375 1211 . + 0 ID=cds.Transcript_1.p1;Parent=Transcript_1.p1 -Transcript_1 transdecoder exon 1 1211 . + . ID=Transcript_1.p1.exon1;Parent=Transcript_1.p1 -Transcript_1 transdecoder five_prime_UTR 1 374 . + . ID=Transcript_1.p1.utr5p1;Parent=Transcript_1.p1 -Transcript_1 transdecoder gene 1 1211 . + . ID=GENE.Transcript_1~~Transcript_1.p1;Name=ORF%20type%3Acomplete%20len%3A279%20%28%2B%29%2Cscore%3D220.14 -Transcript_1 transdecoder mRNA 1 1211 . + . ID=Transcript_1.p1;Parent=GENE.Transcript_1~~Transcript_1.p1;Name=ORF%20type%3Acomplete%20len%3A279%20%28%2B%29%2Cscore%3D220.14 -Transcript_2 shmlast.LAST conditional_reciprocal_best_LAST 1 123 7.000000e-90 + . ID=homology:962be10307d04a237970c81641eb8f829cd0955e;Name=SPAC212.12|SPAC212.12|I|S. pombe specific GPI anchored protein family 1;Target=SPAC212.12|SPAC212.12|I|S. pombe specific GPI anchored protein family 1 1 123 +;database=pep.fa -Transcript_2 transdecoder CDS 1 372 . + 0 ID=cds.Transcript_2.p1;Parent=Transcript_2.p1 -Transcript_2 transdecoder exon 1 372 . + . ID=Transcript_2.p1.exon1;Parent=Transcript_2.p1 -Transcript_2 transdecoder gene 1 372 . + . ID=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A124%20%28%2B%29%2Cscore%3D125.11 -Transcript_2 transdecoder mRNA 1 372 . + . ID=Transcript_2.p1;Parent=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A124%20%28%2B%29%2Cscore%3D125.11 -Transcript_3 HMMER protein_hmm_match 10 117 1.000000e-05 . . ID=homology:36ca0ce448e8e97f949864c071d7740c44fd2ab6;Name=Helicase_C;Target=Helicase_C 70 105 +;accuracy=0.93;env_coords=1 117;Dbxref="Pfam-A:PF00271.27";Note=Helicase conserved C-terminal domain -Transcript_3 shmlast.LAST conditional_reciprocal_best_LAST 11 157 4.900000e-106 + . ID=homology:90a3fa8c08141359b39bce4833db5842fde36a7d;Name=SPAC212.06c|SPAC212.06c|I|DNA helicase in rearranged telomeric region, truncated;Target=SPAC212.06c|SPAC212.06c|I|DNA helicase in rearranged telomeric region, truncated 1 147 +;database=pep.fa -Transcript_3 transdecoder CDS 1 474 . + 0 ID=cds.Transcript_3.p1;Parent=Transcript_3.p1 -Transcript_3 transdecoder exon 1 891 . + . ID=Transcript_3.p1.exon1;Parent=Transcript_3.p1 -Transcript_3 transdecoder gene 1 891 . + . ID=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3A5prime_partial%20len%3A158%20%28%2B%29%2Cscore%3D108.17%2CHelicase_C%7CPF00271.27%7C1e-05 -Transcript_3 transdecoder mRNA 1 891 . + . ID=Transcript_3.p1;Parent=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3A5prime_partial%20len%3A158%20%28%2B%29%2Cscore%3D108.17%2CHelicase_C%7CPF00271.27%7C1e-05 -Transcript_3 transdecoder three_prime_UTR 475 891 . + . ID=Transcript_3.p1.utr3p1;Parent=Transcript_3.p1 -Transcript_4 HMMER protein_hmm_match 267 695 2.600000e-88 . . ID=homology:8695dd6363bf6c920301bb2269d5e7b83660b27e;Name=DUF999;Target=DUF999 1 143 +;accuracy=0.99;env_coords=267 695;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) -Transcript_4 shmlast.LAST conditional_reciprocal_best_LAST 69 356 8.700000e-207 + . ID=homology:245ebc80e8bb87a88ca8462b3ede0ac3ea3d7978;Name=SPAC212.04c|SPAC212.04c|I|S. pombe specific DUF999 family protein 1;Target=SPAC212.04c|SPAC212.04c|I|S. pombe specific DUF999 family protein 1 1 288 +;database=pep.fa -Transcript_4 transdecoder CDS 207 1073 . + 0 ID=cds.Transcript_4.p1;Parent=Transcript_4.p1 -Transcript_4 transdecoder exon 1 1615 . + . ID=Transcript_4.p1.exon1;Parent=Transcript_4.p1 -Transcript_4 transdecoder five_prime_UTR 1 206 . + . ID=Transcript_4.p1.utr5p1;Parent=Transcript_4.p1 -Transcript_4 transdecoder gene 1 1615 . + . ID=GENE.Transcript_4~~Transcript_4.p1;Name=ORF%20type%3Acomplete%20len%3A289%20%28%2B%29%2Cscore%3D286.81%2CDUF999%7CPF06198.7%7C2.6e-88 -Transcript_4 transdecoder mRNA 1 1615 . + . ID=Transcript_4.p1;Parent=GENE.Transcript_4~~Transcript_4.p1;Name=ORF%20type%3Acomplete%20len%3A289%20%28%2B%29%2Cscore%3D286.81%2CDUF999%7CPF06198.7%7C2.6e-88 -Transcript_4 transdecoder three_prime_UTR 1074 1615 . + . ID=Transcript_4.p1.utr3p1;Parent=Transcript_4.p1 -Transcript_5 shmlast.LAST conditional_reciprocal_best_LAST 26 154 1.200000e-100 + . ID=homology:02257bb29738d9df3cd8a6b10606b67a92664d3b;Name=SPAC212.03|SPAC212.03|I|hypothetical protein;Target=SPAC212.03|SPAC212.03|I|hypothetical protein 1 129 +;database=pep.fa -Transcript_5 transdecoder CDS 77 466 . + 0 ID=cds.Transcript_5.p1;Parent=Transcript_5.p1 -Transcript_5 transdecoder exon 1 466 . + . ID=Transcript_5.p1.exon1;Parent=Transcript_5.p1 -Transcript_5 transdecoder five_prime_UTR 1 76 . + . ID=Transcript_5.p1.utr5p1;Parent=Transcript_5.p1 -Transcript_5 transdecoder gene 1 466 . + . ID=GENE.Transcript_5~~Transcript_5.p1;Name=ORF%20type%3Acomplete%20len%3A130%20%28%2B%29%2Cscore%3D68.44 -Transcript_5 transdecoder mRNA 1 466 . + . ID=Transcript_5.p1;Parent=GENE.Transcript_5~~Transcript_5.p1;Name=ORF%20type%3Acomplete%20len%3A130%20%28%2B%29%2Cscore%3D68.44 -Transcript_6 shmlast.LAST conditional_reciprocal_best_LAST 1 136 9.400000e-103 + . ID=homology:aa2030cc9fa44f795e7308c594832186506cc04f;Name=SPAC212.02|SPAC212.02|I|Schizosaccharomyces pombe specific protein;Target=SPAC212.02|SPAC212.02|I|Schizosaccharomyces pombe specific protein 1 136 +;database=pep.fa -Transcript_6 transdecoder CDS 1 411 . + 0 ID=cds.Transcript_6.p1;Parent=Transcript_6.p1 -Transcript_6 transdecoder exon 1 411 . + . ID=Transcript_6.p1.exon1;Parent=Transcript_6.p1 -Transcript_6 transdecoder gene 1 411 . + . ID=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A137%20%28%2B%29%2Cscore%3D91.01 -Transcript_6 transdecoder mRNA 1 411 . + . ID=Transcript_6.p1;Parent=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A137%20%28%2B%29%2Cscore%3D91.01 -Transcript_7 HMMER protein_hmm_match 61 489 1.900000e-91 . . ID=homology:ea6004d5f415a306a2af53323a1e758539c76184;Name=DUF999;Target=DUF999 1 143 +;accuracy=0.99;env_coords=61 489;Dbxref="Pfam-A:PF06198.7";Note=Protein of unknown function (DUF999) -Transcript_7 shmlast.LAST conditional_reciprocal_best_LAST 1 280 8.400000e-209 + . ID=homology:c6aff8c4d38d12fb8cbc360f91d42eb384e58ebd;Name=SPAC212.01c|SPAC212.01c|I|S. pombe specific DUF999 family protein 2;Target=SPAC212.01c|SPAC212.01c|I|S. pombe specific DUF999 family protein 2 1 280 +;database=pep.fa -Transcript_7 transdecoder CDS 1 843 . + 0 ID=cds.Transcript_7.p1;Parent=Transcript_7.p1 -Transcript_7 transdecoder exon 1 862 . + . ID=Transcript_7.p1.exon1;Parent=Transcript_7.p1 -Transcript_7 transdecoder gene 1 862 . + . ID=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A281%20%28%2B%29%2Cscore%3D279.01%2CDUF999%7CPF06198.7%7C1.9e-91 -Transcript_7 transdecoder mRNA 1 862 . + . ID=Transcript_7.p1;Parent=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A281%20%28%2B%29%2Cscore%3D279.01%2CDUF999%7CPF06198.7%7C1.9e-91 -Transcript_7 transdecoder three_prime_UTR 844 862 . + . ID=Transcript_7.p1.utr3p1;Parent=Transcript_7.p1 -Transcript_8 HMMER protein_hmm_match 243 812 1.300000e-05 . . ID=homology:f887979d6a8989dadbd2d76738268fe9d5ed34a6;Name=Lung_7-TM_R;Target=Lung_7-TM_R 60 258 +;accuracy=0.83;env_coords=78 851;Dbxref="Pfam-A:PF06814.9";Note=Lung seven transmembrane receptor -Transcript_8 HMMER protein_hmm_match 3 728 1.600000e-155 . . ID=homology:c6eb24225496d1bc09fdea5c094961ed877d2054;Name=Pombe_5TM;Target=Pombe_5TM 15 256 +;accuracy=1.0;env_coords=3 728;Dbxref="Pfam-A:PF09437.6";Note=Pombe specific 5TM protein -Transcript_8 shmlast.LAST conditional_reciprocal_best_LAST 1 316 8.700000e-241 + . ID=homology:4b1595941d7f979b3c480239a7fb19274ab1fcda;Name=SPAC977.01|SPAC977.01|I|S. pombe specific 5Tm protein family;Target=SPAC977.01|SPAC977.01|I|S. pombe specific 5Tm protein family 1 316 +;database=pep.fa -Transcript_8 transdecoder CDS 3 953 . + 0 ID=cds.Transcript_8.p1;Parent=Transcript_8.p1 -Transcript_8 transdecoder exon 1 1306 . + . ID=Transcript_8.p1.exon1;Parent=Transcript_8.p1 -Transcript_8 transdecoder gene 1 1306 . + . ID=GENE.Transcript_8~~Transcript_8.p1;Name=ORF%20type%3A5prime_partial%20len%3A317%20%28%2B%29%2Cscore%3D163.63%2CPombe_5TM%7CPF09437.6%7C1.6e-155%2CLung_7-TM_R%7CPF06814.9%7C1.3e-05 -Transcript_8 transdecoder mRNA 1 1306 . + . ID=Transcript_8.p1;Parent=GENE.Transcript_8~~Transcript_8.p1;Name=ORF%20type%3A5prime_partial%20len%3A317%20%28%2B%29%2Cscore%3D163.63%2CPombe_5TM%7CPF09437.6%7C1.6e-155%2CLung_7-TM_R%7CPF06814.9%7C1.3e-05 -Transcript_8 transdecoder three_prime_UTR 954 1306 . + . ID=Transcript_8.p1.utr3p1;Parent=Transcript_8.p1 -Transcript_9 shmlast.LAST conditional_reciprocal_best_LAST 53 185 4.400000e-95 + . ID=homology:e26c123afd68729a1a3c67041d92510505a2fd93;Name=SPAC977.18|SPAC977.18|I|conserved fungal protein;Target=SPAC977.18|SPAC977.18|I|conserved fungal protein 1 133 +;database=pep.fa -Transcript_9 transdecoder CDS 159 560 . + 0 ID=cds.Transcript_9.p1;Parent=Transcript_9.p1 -Transcript_9 transdecoder exon 1 747 . + . ID=Transcript_9.p1.exon1;Parent=Transcript_9.p1 -Transcript_9 transdecoder five_prime_UTR 1 158 . + . ID=Transcript_9.p1.utr5p1;Parent=Transcript_9.p1 -Transcript_9 transdecoder gene 1 747 . + . ID=GENE.Transcript_9~~Transcript_9.p1;Name=ORF%20type%3Acomplete%20len%3A134%20%28%2B%29%2Cscore%3D88.84 -Transcript_9 transdecoder mRNA 1 747 . + . ID=Transcript_9.p1;Parent=GENE.Transcript_9~~Transcript_9.p1;Name=ORF%20type%3Acomplete%20len%3A134%20%28%2B%29%2Cscore%3D88.84 -Transcript_9 transdecoder three_prime_UTR 561 747 . + . ID=Transcript_9.p1.utr3p1;Parent=Transcript_9.p1 +Transcript_0 HMMER protein_hmm_match 1455 1787 8.800000e-15 . . ID=homology:9e7debe20d5864489389385196e8ce1f582ce080;Name=TPP_enzyme_C;Target=TPP_enzyme_C 15 120 +;accuracy=0.73;env_coords=1416 1880;Dbxref="Pfam-A:PF02775.17";Note=Thiamine pyrophosphate enzyme, C-terminal TPP binding domain +Transcript_0 HMMER protein_hmm_match 261 773 4.900000e-34 . . ID=homology:b7bd2085166d404acba13f1d98b5b89a6b788034;Name=TPP_enzyme_N;Target=TPP_enzyme_N 3 166 +;accuracy=0.94;env_coords=255 788;Dbxref="Pfam-A:PF02776.14";Note=Thiamine pyrophosphate enzyme, N-terminal TPP binding domain +Transcript_0 HMMER protein_hmm_match 630 746 8.100000e+02 . . ID=homology:499fcc76f5ace0dfdce5ebafbac99fc062ed7041;Name=TPP_enzyme_C;Target=TPP_enzyme_C 112 151 +;accuracy=0.62;env_coords=540 752;Dbxref="Pfam-A:PF02775.17";Note=Thiamine pyrophosphate enzyme, C-terminal TPP binding domain +Transcript_0 HMMER protein_hmm_match 633 740 6.300000e+03 . . ID=homology:8c5e9814c89cad321361a9e17a1b0a517062eb26;Name=TPP_enzyme_M;Target=TPP_enzyme_M 7 42 +;accuracy=0.6;env_coords=624 815;Dbxref="Pfam-A:PF00205.18";Note=Thiamine pyrophosphate enzyme, central domain +Transcript_0 HMMER protein_hmm_match 852 1244 4.800000e-28 . . ID=homology:aafc5146615c383024816cc864a986c311a1f373;Name=TPP_enzyme_M;Target=TPP_enzyme_M 1 131 +;accuracy=0.9;env_coords=852 1262;Dbxref="Pfam-A:PF00205.18";Note=Thiamine pyrophosphate enzyme, central domain +Transcript_0 shmlast.LAST conditional_reciprocal_best_LAST 87 567 3.700000e-71 + . ID=homology:88c9e45badc71a505ce01827215455d619156432;Name=SPAC1F8.07c|SPAC1F8.07c|I|pyruvate decarboxylase (predicted);Target=SPAC1F8.07c|SPAC1F8.07c|I|pyruvate decarboxylase (predicted) 11 483 +;database=pep.fa +Transcript_0 transdecoder CDS 243 1958 . + 0 ID=cds.Transcript_0.p1;Parent=Transcript_0.p1 +Transcript_0 transdecoder exon 1 2141 . + . ID=Transcript_0.p1.exon1;Parent=Transcript_0.p1 +Transcript_0 transdecoder five_prime_UTR 1 242 . + . ID=Transcript_0.p1.utr5p1;Parent=Transcript_0.p1 +Transcript_0 transdecoder gene 1 2141 . + . ID=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3Acomplete%20len%3A572%20%28%2B%29%2Cscore%3D269.50%2CTPP_enzyme_N%7CPF02776.14%7C4.9e-34%2CTPP_enzyme_M%7CPF00205.18%7C6.3e%2B03%2CTPP_enzyme_M%7CPF00205.18%7C4.8e-28%2CTPP_enzyme_C%7CPF02775.17%7C8.1e%2B02%2CTPP_enzyme_C%7CPF02775.17%7C8.8e-15 +Transcript_0 transdecoder mRNA 1 2141 . + . ID=Transcript_0.p1;Parent=GENE.Transcript_0~~Transcript_0.p1;Name=ORF%20type%3Acomplete%20len%3A572%20%28%2B%29%2Cscore%3D269.50%2CTPP_enzyme_N%7CPF02776.14%7C4.9e-34%2CTPP_enzyme_M%7CPF00205.18%7C6.3e%2B03%2CTPP_enzyme_M%7CPF00205.18%7C4.8e-28%2CTPP_enzyme_C%7CPF02775.17%7C8.1e%2B02%2CTPP_enzyme_C%7CPF02775.17%7C8.8e-15 +Transcript_0 transdecoder three_prime_UTR 1959 2141 . + . ID=Transcript_0.p1.utr3p1;Parent=Transcript_0.p1 +Transcript_10 BUSCO BUSCO_ortholog 57 2374 456.5 . . ID=busco:5c4a5d982ea687d0838f35937e5e0570a5cb4b90;Name=6427at4891;length=481;status=Complete +Transcript_10 HMMER protein_hmm_match 1380 1580 1.700000e-13 . . ID=homology:b020baac38cd37de1fd51d6859a5c32336dfe271;Name=HRDC;Target=HRDC 2 68 +;accuracy=0.96;env_coords=1377 1580;Dbxref="Pfam-A:PF00570.19";Note=HRDC domain +Transcript_10 HMMER protein_hmm_match 1647 1745 5.700000e+03 . . ID=homology:188c7429a0a925d6fd5f579c8d96520691c0571f;Name=DNA_pol_A_exo1;Target=DNA_pol_A_exo1 18 52 +;accuracy=0.58;env_coords=1614 1793;Dbxref="Pfam-A:PF01612.16";Note=3'-5' exonuclease +Transcript_10 HMMER protein_hmm_match 699 1199 2.000000e-54 . . ID=homology:f714fc1ee0347dbbc4535677efa4aee167256505;Name=DNA_pol_A_exo1;Target=DNA_pol_A_exo1 2 174 +;accuracy=0.99;env_coords=696 1202;Dbxref="Pfam-A:PF01612.16";Note=3'-5' exonuclease +Transcript_10 HMMER protein_hmm_match 78 338 5.200000e-18 . . ID=homology:1b730598f53ff015ca7cf48bcec1622baef9fe2a;Name=PMC2NT;Target=PMC2NT 2 92 +;accuracy=0.95;env_coords=75 338;Dbxref="Pfam-A:PF08066.8";Note=PMC2NT (NUC016) domain +Transcript_10 HMMER protein_hmm_match 84 164 1.600000e+03 . . ID=homology:3d7e4051ac420f137deb02902cb54c2a443a4bcf;Name=DNA_pol_A_exo1;Target=DNA_pol_A_exo1 11 34 +;accuracy=0.76;env_coords=66 212;Dbxref="Pfam-A:PF01612.16";Note=3'-5' exonuclease +Transcript_10 transdecoder CDS 45 2378 . + 0 ID=cds.Transcript_10.p1;Parent=Transcript_10.p1 +Transcript_10 transdecoder exon 1 2439 . + . ID=Transcript_10.p1.exon1;Parent=Transcript_10.p1 +Transcript_10 transdecoder five_prime_UTR 1 44 . + . ID=Transcript_10.p1.utr5p1;Parent=Transcript_10.p1 +Transcript_10 transdecoder gene 1 2439 . + . ID=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A778%20%28%2B%29%2Cscore%3D359.02%2CDNA_pol_A_exo1%7CPF01612.16%7C1.6e%2B03%2CDNA_pol_A_exo1%7CPF01612.16%7C2e-54%2CDNA_pol_A_exo1%7CPF01612.16%7C5.7e%2B03%2CPMC2NT%7CPF08066.8%7C5.2e-18%2CHRDC%7CPF00570.19%7C1.7e-13 +Transcript_10 transdecoder mRNA 1 2439 . + . ID=Transcript_10.p1;Parent=GENE.Transcript_10~~Transcript_10.p1;Name=ORF%20type%3Acomplete%20len%3A778%20%28%2B%29%2Cscore%3D359.02%2CDNA_pol_A_exo1%7CPF01612.16%7C1.6e%2B03%2CDNA_pol_A_exo1%7CPF01612.16%7C2e-54%2CDNA_pol_A_exo1%7CPF01612.16%7C5.7e%2B03%2CPMC2NT%7CPF08066.8%7C5.2e-18%2CHRDC%7CPF00570.19%7C1.7e-13 +Transcript_10 transdecoder three_prime_UTR 2379 2439 . + . ID=Transcript_10.p1.utr3p1;Parent=Transcript_10.p1 +Transcript_11 BUSCO BUSCO_ortholog 1365 3808 479.8 . . ID=busco:16b84e701e7c0883803b1b04812c3558ee2a6339;Name=1979at4891;length=341;status=Complete +Transcript_11 HMMER protein_hmm_match 2955 3758 5.500000e-67 . . ID=homology:0b09435b720b4ffcc7879d1d397b8be194ee0d5e;Name=Pkinase;Target=Pkinase 3 262 +;accuracy=0.9;env_coords=2949 3758;Dbxref="Pfam-A:PF00069.21";Note=Protein kinase domain +Transcript_11 HMMER protein_hmm_match 2958 3746 2.300000e-42 . . ID=homology:ec435277ea6b3f81a5e6d8f14e78760424cfcb33;Name=Pkinase_Tyr;Target=Pkinase_Tyr 4 258 +;accuracy=0.84;env_coords=2952 3749;Dbxref="Pfam-A:PF07714.13";Note=Protein tyrosine kinase +Transcript_11 shmlast.LAST conditional_reciprocal_best_LAST 989 1252 8.800000e-38 + . ID=homology:13f9f267f09234f37e26ced5faf6cecc938fa3f9;Name=SPAC1F5.09c|shk2|I|PAK-related kinase Shk2;Target=SPAC1F5.09c|shk2|I|PAK-related kinase Shk2 315 566 +;database=pep.fa +Transcript_11 transdecoder CDS 477 3827 . + 0 ID=cds.Transcript_11.p1;Parent=Transcript_11.p1 +Transcript_11 transdecoder exon 1 3956 . + . ID=Transcript_11.p1.exon1;Parent=Transcript_11.p1 +Transcript_11 transdecoder five_prime_UTR 1 476 . + . ID=Transcript_11.p1.utr5p1;Parent=Transcript_11.p1 +Transcript_11 transdecoder gene 1 3956 . + . ID=GENE.Transcript_11~~Transcript_11.p1;Name=ORF%20type%3Acomplete%20len%3A1117%20%28%2B%29%2Cscore%3D521.04%2CPkinase%7CPF00069.21%7C5.5e-67%2CPkinase_Tyr%7CPF07714.13%7C2.3e-42 +Transcript_11 transdecoder mRNA 1 3956 . + . ID=Transcript_11.p1;Parent=GENE.Transcript_11~~Transcript_11.p1;Name=ORF%20type%3Acomplete%20len%3A1117%20%28%2B%29%2Cscore%3D521.04%2CPkinase%7CPF00069.21%7C5.5e-67%2CPkinase_Tyr%7CPF07714.13%7C2.3e-42 +Transcript_11 transdecoder three_prime_UTR 3828 3956 . + . ID=Transcript_11.p1.utr3p1;Parent=Transcript_11.p1 +Transcript_12 BUSCO BUSCO_ortholog 3455 4273 250.0 . . ID=busco:8eea87d684deb7dee6ce84c85522565efef64511;Name=23784at4891;length=163;status=Duplicated +Transcript_12 HMMER protein_hmm_match 1604 2725 8.400000e-109 . . ID=homology:a815fc767027eef954c09ea846b01bc323897a15;Name=Lgl_C;Target=Lgl_C 3 393 +;accuracy=0.98;env_coords=1598 2725;Dbxref="Pfam-A:PF08596.6";Note=Lethal giant larvae(Lgl) like, C-terminal +Transcript_12 HMMER protein_hmm_match 3236 3388 1.200000e-13 . . ID=homology:dda9a4d07523e1267b7d56ab96c05f479c80a786;Name=DUF367;Target=DUF367 77 127 +;accuracy=0.98;env_coords=3236 3388;Dbxref="Pfam-A:PF04034.9";Note=Domain of unknown function (DUF367) +Transcript_12 transdecoder CDS 2 3043 . + 0 ID=cds.Transcript_12.p1;Parent=Transcript_12.p1 +Transcript_12 transdecoder CDS 3236 3682 . - 0 ID=cds.Transcript_12.p2;Parent=Transcript_12.p2 +Transcript_12 transdecoder exon 1 4750 . + . ID=Transcript_12.p1.exon1;Parent=Transcript_12.p1 +Transcript_12 transdecoder exon 1 4750 . - . ID=Transcript_12.p2.exon1;Parent=Transcript_12.p2 +Transcript_12 transdecoder five_prime_UTR 3683 4750 . - . ID=Transcript_12.p2.utr5p1;Parent=Transcript_12.p2 +Transcript_12 transdecoder gene 1 4750 . + . ID=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A1014%20%28%2B%29%2Cscore%3D458.23%2CLgl_C%7CPF08596.6%7C8.4e-109 +Transcript_12 transdecoder gene 1 4750 . - . ID=GENE.Transcript_12~~Transcript_12.p2;Name=ORF%20type%3Acomplete%20len%3A149%20%28-%29%2Cscore%3D69.62%2CDUF367%7CPF04034.9%7C1.2e-13 +Transcript_12 transdecoder mRNA 1 4750 . + . ID=Transcript_12.p1;Parent=GENE.Transcript_12~~Transcript_12.p1;Name=ORF%20type%3A5prime_partial%20len%3A1014%20%28%2B%29%2Cscore%3D458.23%2CLgl_C%7CPF08596.6%7C8.4e-109 +Transcript_12 transdecoder mRNA 1 4750 . - . ID=Transcript_12.p2;Parent=GENE.Transcript_12~~Transcript_12.p2;Name=ORF%20type%3Acomplete%20len%3A149%20%28-%29%2Cscore%3D69.62%2CDUF367%7CPF04034.9%7C1.2e-13 +Transcript_12 transdecoder three_prime_UTR 1 3235 . - . ID=Transcript_12.p2.utr3p1;Parent=Transcript_12.p2 +Transcript_12 transdecoder three_prime_UTR 3044 4750 . + . ID=Transcript_12.p1.utr3p1;Parent=Transcript_12.p1 +Transcript_13 BUSCO BUSCO_ortholog 41 723 250.0 . . ID=busco:53c2a8991213423793113d9948183cfffcc1eead;Name=23784at4891;length=163;status=Duplicated +Transcript_13 HMMER protein_hmm_match 158 259 1.100000e-12 . . ID=homology:6c397a2e5a78e97b252b4eb6e1d94c9867a0ef8f;Name=RLI;Target=RLI 2 35 +;accuracy=0.97;env_coords=155 259;Dbxref="Pfam-A:PF04068.11";Note=Possible Fer4-like domain in RNase L inhibitor, RLI +Transcript_13 HMMER protein_hmm_match 269 649 1.700000e-50 . . ID=homology:d09eb69832fcbf800ca9b38ce7afe7bc063a79d2;Name=DUF367;Target=DUF367 1 127 +;accuracy=0.99;env_coords=269 649;Dbxref="Pfam-A:PF04034.9";Note=Domain of unknown function (DUF367) +Transcript_13 transdecoder CDS 77 943 . + 0 ID=cds.Transcript_13.p1;Parent=Transcript_13.p1 +Transcript_13 transdecoder exon 1 1078 . + . ID=Transcript_13.p1.exon1;Parent=Transcript_13.p1 +Transcript_13 transdecoder five_prime_UTR 1 76 . + . ID=Transcript_13.p1.utr5p1;Parent=Transcript_13.p1 +Transcript_13 transdecoder gene 1 1078 . + . ID=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A289%20%28%2B%29%2Cscore%3D133.35%2CDUF367%7CPF04034.9%7C1.7e-50%2CRLI%7CPF04068.11%7C1.1e-12 +Transcript_13 transdecoder mRNA 1 1078 . + . ID=Transcript_13.p1;Parent=GENE.Transcript_13~~Transcript_13.p1;Name=ORF%20type%3Acomplete%20len%3A289%20%28%2B%29%2Cscore%3D133.35%2CDUF367%7CPF04034.9%7C1.7e-50%2CRLI%7CPF04068.11%7C1.1e-12 +Transcript_13 transdecoder three_prime_UTR 944 1078 . + . ID=Transcript_13.p1.utr3p1;Parent=Transcript_13.p1 +Transcript_14 HMMER protein_hmm_match 1241 1294 7.600000e+03 . . ID=homology:9dc8dedfa6d018182b6b6b8e3926509303f4f2b7;Name=Alpha_adaptinC2;Target=Alpha_adaptinC2 48 65 +;accuracy=0.59;env_coords=1229 1354;Dbxref="Pfam-A:PF02883.16";Note=Adaptin C-terminal domain +Transcript_14 HMMER protein_hmm_match 1370 1681 3.800000e-14 . . ID=homology:8e1531261aab8b0133bff537d87955d711f5b8ac;Name=Alpha_adaptinC2;Target=Alpha_adaptinC2 4 100 +;accuracy=0.9;env_coords=1361 1708;Dbxref="Pfam-A:PF02883.16";Note=Adaptin C-terminal domain +Transcript_14 HMMER protein_hmm_match 188 619 2.400000e-49 . . ID=homology:4363a3b3309490ef4dea834fd6914603af269f1d;Name=VHS;Target=VHS 3 141 +;accuracy=0.98;env_coords=182 619;Dbxref="Pfam-A:PF00790.15";Note=VHS domain +Transcript_14 transdecoder CDS 182 1714 . + 0 ID=cds.Transcript_14.p1;Parent=Transcript_14.p1 +Transcript_14 transdecoder exon 1 2035 . + . ID=Transcript_14.p1.exon1;Parent=Transcript_14.p1 +Transcript_14 transdecoder five_prime_UTR 1 181 . + . ID=Transcript_14.p1.utr5p1;Parent=Transcript_14.p1 +Transcript_14 transdecoder gene 1 2035 . + . ID=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3Acomplete%20len%3A511%20%28%2B%29%2Cscore%3D242.08%2CVHS%7CPF00790.15%7C2.4e-49%2CAlpha_adaptinC2%7CPF02883.16%7C7.6e%2B03%2CAlpha_adaptinC2%7CPF02883.16%7C3.8e-14 +Transcript_14 transdecoder mRNA 1 2035 . + . ID=Transcript_14.p1;Parent=GENE.Transcript_14~~Transcript_14.p1;Name=ORF%20type%3Acomplete%20len%3A511%20%28%2B%29%2Cscore%3D242.08%2CVHS%7CPF00790.15%7C2.4e-49%2CAlpha_adaptinC2%7CPF02883.16%7C7.6e%2B03%2CAlpha_adaptinC2%7CPF02883.16%7C3.8e-14 +Transcript_14 transdecoder three_prime_UTR 1715 2035 . + . ID=Transcript_14.p1.utr3p1;Parent=Transcript_14.p1 +Transcript_15 transdecoder CDS 3 5972 . + 0 ID=cds.Transcript_15.p1;Parent=Transcript_15.p1 +Transcript_15 transdecoder exon 1 6229 . + . ID=Transcript_15.p1.exon1;Parent=Transcript_15.p1 +Transcript_15 transdecoder gene 1 6229 . + . ID=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3A5prime_partial%20len%3A1990%20%28%2B%29%2Cscore%3D255.50 +Transcript_15 transdecoder mRNA 1 6229 . + . ID=Transcript_15.p1;Parent=GENE.Transcript_15~~Transcript_15.p1;Name=ORF%20type%3A5prime_partial%20len%3A1990%20%28%2B%29%2Cscore%3D255.50 +Transcript_15 transdecoder three_prime_UTR 5973 6229 . + . ID=Transcript_15.p1.utr3p1;Parent=Transcript_15.p1 +Transcript_16 transdecoder CDS 262 1473 . + 0 ID=cds.Transcript_16.p1;Parent=Transcript_16.p1 +Transcript_16 transdecoder exon 1 1518 . + . ID=Transcript_16.p1.exon1;Parent=Transcript_16.p1 +Transcript_16 transdecoder five_prime_UTR 1 261 . + . ID=Transcript_16.p1.utr5p1;Parent=Transcript_16.p1 +Transcript_16 transdecoder gene 1 1518 . + . ID=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A404%20%28%2B%29%2Cscore%3D190.13 +Transcript_16 transdecoder mRNA 1 1518 . + . ID=Transcript_16.p1;Parent=GENE.Transcript_16~~Transcript_16.p1;Name=ORF%20type%3Acomplete%20len%3A404%20%28%2B%29%2Cscore%3D190.13 +Transcript_16 transdecoder three_prime_UTR 1474 1518 . + . ID=Transcript_16.p1.utr3p1;Parent=Transcript_16.p1 +Transcript_17 transdecoder CDS 1 327 . + 0 ID=cds.Transcript_17.p1;Parent=Transcript_17.p1 +Transcript_17 transdecoder exon 1 327 . + . ID=Transcript_17.p1.exon1;Parent=Transcript_17.p1 +Transcript_17 transdecoder gene 1 327 . + . ID=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A109%20%28%2B%29%2Cscore%3D31.04 +Transcript_17 transdecoder mRNA 1 327 . + . ID=Transcript_17.p1;Parent=GENE.Transcript_17~~Transcript_17.p1;Name=ORF%20type%3Acomplete%20len%3A109%20%28%2B%29%2Cscore%3D31.04 +Transcript_18 HMMER protein_hmm_match 2291 2692 1.000000e-45 . . ID=homology:934ed21ee6c0774d7bcc3843a3b0696aed6b82ba;Name=CwfJ_C_1;Target=CwfJ_C_1 3 121 +;accuracy=0.98;env_coords=2285 2695;Dbxref="Pfam-A:PF04677.11";Note=Protein similar to CwfJ C-terminus 1 +Transcript_18 HMMER protein_hmm_match 2732 2968 3.300000e-15 . . ID=homology:b5659e0755e432d0f60f315b3dacca8f80ee4741;Name=CwfJ_C_2;Target=CwfJ_C_2 18 98 +;accuracy=0.88;env_coords=2693 2968;Dbxref="Pfam-A:PF04676.10";Note=Protein similar to CwfJ C-terminus 2 +Transcript_18 transdecoder CDS 1286 2971 . + 0 ID=cds.Transcript_18.p1;Parent=Transcript_18.p1 +Transcript_18 transdecoder exon 1 2971 . + . ID=Transcript_18.p1.exon1;Parent=Transcript_18.p1 +Transcript_18 transdecoder five_prime_UTR 1 1285 . + . ID=Transcript_18.p1.utr5p1;Parent=Transcript_18.p1 +Transcript_18 transdecoder gene 1 2971 . + . ID=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A562%20%28%2B%29%2Cscore%3D261.47%2CCwfJ_C_1%7CPF04677.11%7C1e-45%2CCwfJ_C_2%7CPF04676.10%7C3.3e-15 +Transcript_18 transdecoder mRNA 1 2971 . + . ID=Transcript_18.p1;Parent=GENE.Transcript_18~~Transcript_18.p1;Name=ORF%20type%3Acomplete%20len%3A562%20%28%2B%29%2Cscore%3D261.47%2CCwfJ_C_1%7CPF04677.11%7C1e-45%2CCwfJ_C_2%7CPF04676.10%7C3.3e-15 +Transcript_19 BUSCO BUSCO_ortholog 228 2377 453.7 . . ID=busco:862fcc3b055d4cb6d781a7531e12b3ead301d634;Name=5324at4891;length=552;status=Complete +Transcript_19 HMMER protein_hmm_match 2523 2819 2.100000e-28 . . ID=homology:3cb5651c5d8e58d5671869394015acce27cf7bed;Name=CwfJ_C_1;Target=CwfJ_C_1 38 121 +;accuracy=0.96;env_coords=2505 2822;Dbxref="Pfam-A:PF04677.11";Note=Protein similar to CwfJ C-terminus 1 +Transcript_19 HMMER protein_hmm_match 2859 3095 5.400000e-16 . . ID=homology:2293e85f820ee0c563a66e85728b2605ae5e41f0;Name=CwfJ_C_2;Target=CwfJ_C_2 18 98 +;accuracy=0.88;env_coords=2814 3095;Dbxref="Pfam-A:PF04676.10";Note=Protein similar to CwfJ C-terminus 2 +Transcript_19 HMMER protein_hmm_match 3018 3077 2.900000e+03 . . ID=homology:0038ca219f656a247cc2c9b56345d4848a5ec4fb;Name=CwfJ_C_1;Target=CwfJ_C_1 59 78 +;accuracy=0.78;env_coords=3012 3083;Dbxref="Pfam-A:PF04677.11";Note=Protein similar to CwfJ C-terminus 1 +Transcript_19 HMMER protein_hmm_match 939 2366 2.800000e-153 . . ID=homology:1b945fcc2102b1ac3eb5228e6af692bfc5484003;Name=Peptidase_M3;Target=Peptidase_M3 2 457 +;accuracy=0.97;env_coords=936 2369;Dbxref="Pfam-A:PF01432.16";Note=Peptidase family M3 +Transcript_19 transdecoder CDS 120 2408 . + 0 ID=cds.Transcript_19.p1;Parent=Transcript_19.p1 +Transcript_19 transdecoder CDS 2472 3098 . - 0 ID=cds.Transcript_19.p3;Parent=Transcript_19.p3 +Transcript_19 transdecoder CDS 3211 4020 . - 0 ID=cds.Transcript_19.p2;Parent=Transcript_19.p2 +Transcript_19 transdecoder exon 1 4533 . + . ID=Transcript_19.p1.exon1;Parent=Transcript_19.p1 +Transcript_19 transdecoder exon 1 4533 . - . ID=Transcript_19.p2.exon1;Parent=Transcript_19.p2 +Transcript_19 transdecoder exon 1 4533 . - . ID=Transcript_19.p3.exon1;Parent=Transcript_19.p3 +Transcript_19 transdecoder five_prime_UTR 1 119 . + . ID=Transcript_19.p1.utr5p1;Parent=Transcript_19.p1 +Transcript_19 transdecoder five_prime_UTR 3099 4533 . - . ID=Transcript_19.p3.utr5p1;Parent=Transcript_19.p3 +Transcript_19 transdecoder five_prime_UTR 4021 4533 . - . ID=Transcript_19.p2.utr5p1;Parent=Transcript_19.p2 +Transcript_19 transdecoder gene 1 4533 . + . ID=GENE.Transcript_19~~Transcript_19.p1;Name=ORF%20type%3Acomplete%20len%3A763%20%28%2B%29%2Cscore%3D329.09%2CPeptidase_M3%7CPF01432.16%7C2.8e-153 +Transcript_19 transdecoder gene 1 4533 . - . ID=GENE.Transcript_19~~Transcript_19.p2;Name=ORF%20type%3Acomplete%20len%3A270%20%28-%29%2Cscore%3D125.18 +Transcript_19 transdecoder gene 1 4533 . - . ID=GENE.Transcript_19~~Transcript_19.p3;Name=ORF%20type%3Acomplete%20len%3A209%20%28-%29%2Cscore%3D88.03%2CCwfJ_C_1%7CPF04677.11%7C2.1e-28%2CCwfJ_C_1%7CPF04677.11%7C2.9e%2B03%2CCwfJ_C_2%7CPF04676.10%7C5.4e-16 +Transcript_19 transdecoder mRNA 1 4533 . + . ID=Transcript_19.p1;Parent=GENE.Transcript_19~~Transcript_19.p1;Name=ORF%20type%3Acomplete%20len%3A763%20%28%2B%29%2Cscore%3D329.09%2CPeptidase_M3%7CPF01432.16%7C2.8e-153 +Transcript_19 transdecoder mRNA 1 4533 . - . ID=Transcript_19.p2;Parent=GENE.Transcript_19~~Transcript_19.p2;Name=ORF%20type%3Acomplete%20len%3A270%20%28-%29%2Cscore%3D125.18 +Transcript_19 transdecoder mRNA 1 4533 . - . ID=Transcript_19.p3;Parent=GENE.Transcript_19~~Transcript_19.p3;Name=ORF%20type%3Acomplete%20len%3A209%20%28-%29%2Cscore%3D88.03%2CCwfJ_C_1%7CPF04677.11%7C2.1e-28%2CCwfJ_C_1%7CPF04677.11%7C2.9e%2B03%2CCwfJ_C_2%7CPF04676.10%7C5.4e-16 +Transcript_19 transdecoder three_prime_UTR 1 2471 . - . ID=Transcript_19.p3.utr3p1;Parent=Transcript_19.p3 +Transcript_19 transdecoder three_prime_UTR 1 3210 . - . ID=Transcript_19.p2.utr3p1;Parent=Transcript_19.p2 +Transcript_19 transdecoder three_prime_UTR 2409 4533 . + . ID=Transcript_19.p1.utr3p1;Parent=Transcript_19.p1 +Transcript_1 HMMER protein_hmm_match 1580 1597 1.600000e+04 . . ID=homology:1cc2277983d54d82f2a0060ca1becc0ccaa035ab;Name=CRAL_TRIO_N;Target=CRAL_TRIO_N 39 44 +;accuracy=0.92;env_coords=1580 1597;Dbxref="Pfam-A:PF03765.11";Note=CRAL/TRIO, N-terminal domain +Transcript_1 HMMER protein_hmm_match 512 541 9.900000e+03 . . ID=homology:6eb530dcf9d8478c3be94de9840c7340daf9f354;Name=CRAL_TRIO_N;Target=CRAL_TRIO_N 5 14 +;accuracy=0.7;env_coords=509 601;Dbxref="Pfam-A:PF03765.11";Note=CRAL/TRIO, N-terminal domain +Transcript_1 HMMER protein_hmm_match 686 820 3.400000e-10 . . ID=homology:635a9561ea0c863d59f4c8a8fff83d5fb43adb41;Name=CRAL_TRIO_N;Target=CRAL_TRIO_N 9 56 +;accuracy=0.78;env_coords=638 823;Dbxref="Pfam-A:PF03765.11";Note=CRAL/TRIO, N-terminal domain +Transcript_1 HMMER protein_hmm_match 689 823 1.800000e+02 . . ID=homology:e323ac8fb83a0afaf6d29c7de07fe5c51f01fcd3;Name=CRAL_TRIO;Target=CRAL_TRIO 12 56 +;accuracy=0.83;env_coords=665 880;Dbxref="Pfam-A:PF00650.16";Note=CRAL/TRIO domain +Transcript_1 HMMER protein_hmm_match 917 1354 7.500000e-46 . . ID=homology:a26520ea6fec002f7f82e136b61e724e791e0fb5;Name=CRAL_TRIO;Target=CRAL_TRIO 5 158 +;accuracy=0.96;env_coords=908 1357;Dbxref="Pfam-A:PF00650.16";Note=CRAL/TRIO domain +Transcript_1 HMMER protein_hmm_match 959 1354 1.700000e-09 . . ID=homology:08122f28fecb8eca2ac447687657c01cb6fd386b;Name=CRAL_TRIO_2;Target=CRAL_TRIO_2 2 131 +;accuracy=0.91;env_coords=956 1387;Dbxref="Pfam-A:PF13716.2";Note=Divergent CRAL/TRIO domain +Transcript_1 transdecoder CDS 383 1717 . + 0 ID=cds.Transcript_1.p1;Parent=Transcript_1.p1 +Transcript_1 transdecoder exon 1 2209 . + . ID=Transcript_1.p1.exon1;Parent=Transcript_1.p1 +Transcript_1 transdecoder five_prime_UTR 1 382 . + . ID=Transcript_1.p1.utr5p1;Parent=Transcript_1.p1 +Transcript_1 transdecoder gene 1 2209 . + . ID=GENE.Transcript_1~~Transcript_1.p1;Name=ORF%20type%3Acomplete%20len%3A445%20%28%2B%29%2Cscore%3D227.45%2CCRAL_TRIO%7CPF00650.16%7C1.8e%2B02%2CCRAL_TRIO%7CPF00650.16%7C7.5e-46%2CCRAL_TRIO_N%7CPF03765.11%7C9.9e%2B03%2CCRAL_TRIO_N%7CPF03765.11%7C3.4e-10%2CCRAL_TRIO_N%7CPF03765.11%7C1.6e%2B04%2CCRAL_TRIO_2%7CPF13716.2%7C1.7e-09 +Transcript_1 transdecoder mRNA 1 2209 . + . ID=Transcript_1.p1;Parent=GENE.Transcript_1~~Transcript_1.p1;Name=ORF%20type%3Acomplete%20len%3A445%20%28%2B%29%2Cscore%3D227.45%2CCRAL_TRIO%7CPF00650.16%7C1.8e%2B02%2CCRAL_TRIO%7CPF00650.16%7C7.5e-46%2CCRAL_TRIO_N%7CPF03765.11%7C9.9e%2B03%2CCRAL_TRIO_N%7CPF03765.11%7C3.4e-10%2CCRAL_TRIO_N%7CPF03765.11%7C1.6e%2B04%2CCRAL_TRIO_2%7CPF13716.2%7C1.7e-09 +Transcript_1 transdecoder three_prime_UTR 1718 2209 . + . ID=Transcript_1.p1.utr3p1;Parent=Transcript_1.p1 +Transcript_20 HMMER protein_hmm_match 1452 1634 2.900000e-17 . . ID=homology:61ee16af95a60ab49b3add5135ae770036a44b59;Name=GRASP55_65;Target=GRASP55_65 31 91 +;accuracy=0.89;env_coords=1449 1727;Dbxref="Pfam-A:PF04495.10";Note=GRASP55/65 PDZ-like domain +Transcript_20 HMMER protein_hmm_match 208 285 3.500000e+02 . . ID=homology:016a59379fa90966017ed18a235adca6dc7f9760;Name=Hep_59;Target=Hep_59 24 82 +;accuracy=0.5;env_coords=88 315;Dbxref="Pfam-A:PF07052.7";Note=Hepatocellular carcinoma-associated antigen 59 +Transcript_20 HMMER protein_hmm_match 316 606 3.300000e-10 . . ID=homology:5791e915229df3d67385263f0fda658b534e6339;Name=Hep_59;Target=Hep_59 1 102 +;accuracy=0.68;env_coords=316 618;Dbxref="Pfam-A:PF07052.7";Note=Hepatocellular carcinoma-associated antigen 59 +Transcript_20 HMMER protein_hmm_match 655 687 9.800000e+02 . . ID=homology:a0ad3b8401d6602feacf550d3611aaa7129e31e7;Name=Hep_59;Target=Hep_59 11 21 +;accuracy=0.37;env_coords=571 729;Dbxref="Pfam-A:PF07052.7";Note=Hepatocellular carcinoma-associated antigen 59 +Transcript_20 transdecoder CDS 1449 1769 . - 0 ID=cds.Transcript_20.p3;Parent=Transcript_20.p3 +Transcript_20 transdecoder CDS 1 771 . + 0 ID=cds.Transcript_20.p1;Parent=Transcript_20.p1 +Transcript_20 transdecoder CDS 995 1345 . - 0 ID=cds.Transcript_20.p2;Parent=Transcript_20.p2 +Transcript_20 transdecoder exon 1 1876 . + . ID=Transcript_20.p1.exon1;Parent=Transcript_20.p1 +Transcript_20 transdecoder exon 1 1876 . - . ID=Transcript_20.p2.exon1;Parent=Transcript_20.p2 +Transcript_20 transdecoder exon 1 1876 . - . ID=Transcript_20.p3.exon1;Parent=Transcript_20.p3 +Transcript_20 transdecoder five_prime_UTR 1346 1876 . - . ID=Transcript_20.p2.utr5p1;Parent=Transcript_20.p2 +Transcript_20 transdecoder five_prime_UTR 1770 1876 . - . ID=Transcript_20.p3.utr5p1;Parent=Transcript_20.p3 +Transcript_20 transdecoder gene 1 1876 . + . ID=GENE.Transcript_20~~Transcript_20.p1;Name=ORF%20type%3A5prime_partial%20len%3A257%20%28%2B%29%2Cscore%3D121.42%2CHep_59%7CPF07052.7%7C3.5e%2B02%2CHep_59%7CPF07052.7%7C3.3e-10%2CHep_59%7CPF07052.7%7C9.8e%2B02 +Transcript_20 transdecoder gene 1 1876 . - . ID=GENE.Transcript_20~~Transcript_20.p2;Name=ORF%20type%3Acomplete%20len%3A117%20%28-%29%2Cscore%3D66.67 +Transcript_20 transdecoder gene 1 1876 . - . ID=GENE.Transcript_20~~Transcript_20.p3;Name=ORF%20type%3Acomplete%20len%3A107%20%28-%29%2Cscore%3D40.74%2CGRASP55_65%7CPF04495.10%7C2.9e-17 +Transcript_20 transdecoder mRNA 1 1876 . + . ID=Transcript_20.p1;Parent=GENE.Transcript_20~~Transcript_20.p1;Name=ORF%20type%3A5prime_partial%20len%3A257%20%28%2B%29%2Cscore%3D121.42%2CHep_59%7CPF07052.7%7C3.5e%2B02%2CHep_59%7CPF07052.7%7C3.3e-10%2CHep_59%7CPF07052.7%7C9.8e%2B02 +Transcript_20 transdecoder mRNA 1 1876 . - . ID=Transcript_20.p2;Parent=GENE.Transcript_20~~Transcript_20.p2;Name=ORF%20type%3Acomplete%20len%3A117%20%28-%29%2Cscore%3D66.67 +Transcript_20 transdecoder mRNA 1 1876 . - . ID=Transcript_20.p3;Parent=GENE.Transcript_20~~Transcript_20.p3;Name=ORF%20type%3Acomplete%20len%3A107%20%28-%29%2Cscore%3D40.74%2CGRASP55_65%7CPF04495.10%7C2.9e-17 +Transcript_20 transdecoder three_prime_UTR 1 1448 . - . ID=Transcript_20.p3.utr3p1;Parent=Transcript_20.p3 +Transcript_20 transdecoder three_prime_UTR 1 994 . - . ID=Transcript_20.p2.utr3p1;Parent=Transcript_20.p2 +Transcript_20 transdecoder three_prime_UTR 772 1876 . + . ID=Transcript_20.p1.utr3p1;Parent=Transcript_20.p1 +Transcript_2 HMMER protein_hmm_match 443 691 5.500000e-26 . . ID=homology:8027aa3561b005abd390af35437e65d32710c453;Name=Img2;Target=Img2 1 80 +;accuracy=0.96;env_coords=443 691;Dbxref="Pfam-A:PF05046.10";Note=Mitochondrial large subunit ribosomal protein (Img2) +Transcript_2 transdecoder CDS 377 694 . + 0 ID=cds.Transcript_2.p1;Parent=Transcript_2.p1 +Transcript_2 transdecoder exon 1 1291 . + . ID=Transcript_2.p1.exon1;Parent=Transcript_2.p1 +Transcript_2 transdecoder five_prime_UTR 1 376 . + . ID=Transcript_2.p1.utr5p1;Parent=Transcript_2.p1 +Transcript_2 transdecoder gene 1 1291 . + . ID=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A106%20%28%2B%29%2Cscore%3D49.61%2CImg2%7CPF05046.10%7C5.5e-26 +Transcript_2 transdecoder mRNA 1 1291 . + . ID=Transcript_2.p1;Parent=GENE.Transcript_2~~Transcript_2.p1;Name=ORF%20type%3Acomplete%20len%3A106%20%28%2B%29%2Cscore%3D49.61%2CImg2%7CPF05046.10%7C5.5e-26 +Transcript_2 transdecoder three_prime_UTR 695 1291 . + . ID=Transcript_2.p1.utr3p1;Parent=Transcript_2.p1 +Transcript_3 HMMER protein_hmm_match 1265 1330 1.600000e+04 . . ID=homology:405effda0997113b71052e55260260847cf87b7d;Name=DUF4210;Target=DUF4210 24 45 +;accuracy=0.7;env_coords=1250 1336;Dbxref="Pfam-A:PF13915.2";Note=Domain of unknown function (DUF4210) +Transcript_3 HMMER protein_hmm_match 1376 1468 9.300000e-05 . . ID=homology:79d75d2f91cfcc272a185fce04ab274483d55801;Name=Chromosome_seg;Target=Chromosome_seg 2 32 +;accuracy=0.92;env_coords=1373 1510;Dbxref="Pfam-A:PF13889.2";Note=Chromosome segregation during meiosis +Transcript_3 HMMER protein_hmm_match 569 604 3.300000e+02 . . ID=homology:033ae3bfd0f6fdd32e19b729f9ef607d814e8d3f;Name=Chromosome_seg;Target=Chromosome_seg 20 31 +;accuracy=0.83;env_coords=545 664;Dbxref="Pfam-A:PF13889.2";Note=Chromosome segregation during meiosis +Transcript_3 HMMER protein_hmm_match 932 1132 1.200000e-21 . . ID=homology:4914682cff851ca629a650cc56be4e54b6b3f6c4;Name=DUF4210;Target=DUF4210 1 68 +;accuracy=0.97;env_coords=932 1132;Dbxref="Pfam-A:PF13915.2";Note=Domain of unknown function (DUF4210) +Transcript_3 transdecoder CDS 518 1534 . + 0 ID=cds.Transcript_3.p1;Parent=Transcript_3.p1 +Transcript_3 transdecoder exon 1 1681 . + . ID=Transcript_3.p1.exon1;Parent=Transcript_3.p1 +Transcript_3 transdecoder five_prime_UTR 1 517 . + . ID=Transcript_3.p1.utr5p1;Parent=Transcript_3.p1 +Transcript_3 transdecoder gene 1 1681 . + . ID=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3Acomplete%20len%3A339%20%28%2B%29%2Cscore%3D133.40%2CDUF4210%7CPF13915.2%7C1.2e-21%2CDUF4210%7CPF13915.2%7C1.6e%2B04%2CChromosome_seg%7CPF13889.2%7C3.3e%2B02%2CChromosome_seg%7CPF13889.2%7C9.3e-05 +Transcript_3 transdecoder mRNA 1 1681 . + . ID=Transcript_3.p1;Parent=GENE.Transcript_3~~Transcript_3.p1;Name=ORF%20type%3Acomplete%20len%3A339%20%28%2B%29%2Cscore%3D133.40%2CDUF4210%7CPF13915.2%7C1.2e-21%2CDUF4210%7CPF13915.2%7C1.6e%2B04%2CChromosome_seg%7CPF13889.2%7C3.3e%2B02%2CChromosome_seg%7CPF13889.2%7C9.3e-05 +Transcript_3 transdecoder three_prime_UTR 1535 1681 . + . ID=Transcript_3.p1.utr3p1;Parent=Transcript_3.p1 +Transcript_4 HMMER protein_hmm_match 2743 3480 1.600000e-17 . . ID=homology:b6e8a0814ddda2c9716ec2479f1d30788e72164b;Name=CPSF_A;Target=CPSF_A 20 267 +;accuracy=0.85;env_coords=2719 3513;Dbxref="Pfam-A:PF03178.11";Note=CPSF A subunit region +Transcript_4 HMMER protein_hmm_match 2854 3009 1.200000e+03 . . ID=homology:85a47debd66613bff63e95e1239a3316e2e749ee;Name=MMS1_N;Target=MMS1_N 8 56 +;accuracy=0.52;env_coords=2848 3027;Dbxref="Pfam-A:PF10433.5";Note=Mono-functional DNA-alkylating methyl methanesulfonate N-term +Transcript_4 HMMER protein_hmm_match 547 1872 9.600000e-45 . . ID=homology:66e2d0aed267e0ca7e828d91ce2b290ae65eaab0;Name=MMS1_N;Target=MMS1_N 3 437 +;accuracy=0.8;env_coords=544 2007;Dbxref="Pfam-A:PF10433.5";Note=Mono-functional DNA-alkylating methyl methanesulfonate N-term +Transcript_4 transdecoder CDS 310 3531 . + 0 ID=cds.Transcript_4.p1;Parent=Transcript_4.p1 +Transcript_4 transdecoder exon 1 3607 . + . ID=Transcript_4.p1.exon1;Parent=Transcript_4.p1 +Transcript_4 transdecoder five_prime_UTR 1 309 . + . ID=Transcript_4.p1.utr5p1;Parent=Transcript_4.p1 +Transcript_4 transdecoder gene 1 3607 . + . ID=GENE.Transcript_4~~Transcript_4.p1;Name=ORF%20type%3Acomplete%20len%3A1074%20%28%2B%29%2Cscore%3D410.74%2CMMS1_N%7CPF10433.5%7C9.6e-45%2CMMS1_N%7CPF10433.5%7C1.2e%2B03%2CCPSF_A%7CPF03178.11%7C1.6e-17 +Transcript_4 transdecoder mRNA 1 3607 . + . ID=Transcript_4.p1;Parent=GENE.Transcript_4~~Transcript_4.p1;Name=ORF%20type%3Acomplete%20len%3A1074%20%28%2B%29%2Cscore%3D410.74%2CMMS1_N%7CPF10433.5%7C9.6e-45%2CMMS1_N%7CPF10433.5%7C1.2e%2B03%2CCPSF_A%7CPF03178.11%7C1.6e-17 +Transcript_4 transdecoder three_prime_UTR 3532 3607 . + . ID=Transcript_4.p1.utr3p1;Parent=Transcript_4.p1 +Transcript_5 HMMER protein_hmm_match 1167 1391 2.100000e-08 . . ID=homology:20a5ae526b4cf232341f7fb53a2e6cdf1c18fbaa;Name=PAP2;Target=PAP2 49 130 +;accuracy=0.86;env_coords=1047 1403;Dbxref="Pfam-A:PF01569.17";Note=PAP2 superfamily +Transcript_5 HMMER protein_hmm_match 657 749 1.300000e+03 . . ID=homology:bcee78517648aabec1a971bc103d6bc350c0f7bf;Name=PAP2;Target=PAP2 64 98 +;accuracy=0.54;env_coords=651 773;Dbxref="Pfam-A:PF01569.17";Note=PAP2 superfamily +Transcript_5 HMMER protein_hmm_match 738 956 2.700000e+03 . . ID=homology:a67a8122b8c9c6cc5a801a2620e063e175d9afdf;Name=PAP2;Target=PAP2 12 91 +;accuracy=0.52;env_coords=705 1025;Dbxref="Pfam-A:PF01569.17";Note=PAP2 superfamily +Transcript_5 HMMER protein_hmm_match 870 1373 2.800000e-08 . . ID=homology:6d9fe1a422b4169e2543b0250ebf118f3997bba0;Name=PAP2_3;Target=PAP2_3 28 189 +;accuracy=0.75;env_coords=828 1379;Dbxref="Pfam-A:PF14378.2";Note=PAP2 superfamily +Transcript_5 transdecoder CDS 444 1712 . + 0 ID=cds.Transcript_5.p1;Parent=Transcript_5.p1 +Transcript_5 transdecoder exon 1 2333 . + . ID=Transcript_5.p1.exon1;Parent=Transcript_5.p1 +Transcript_5 transdecoder five_prime_UTR 1 443 . + . ID=Transcript_5.p1.utr5p1;Parent=Transcript_5.p1 +Transcript_5 transdecoder gene 1 2333 . + . ID=GENE.Transcript_5~~Transcript_5.p1;Name=ORF%20type%3Acomplete%20len%3A423%20%28%2B%29%2Cscore%3D222.07%2CPAP2_3%7CPF14378.2%7C2.8e-08%2CPAP2%7CPF01569.17%7C1.3e%2B03%2CPAP2%7CPF01569.17%7C2.7e%2B03%2CPAP2%7CPF01569.17%7C2.1e-08 +Transcript_5 transdecoder mRNA 1 2333 . + . ID=Transcript_5.p1;Parent=GENE.Transcript_5~~Transcript_5.p1;Name=ORF%20type%3Acomplete%20len%3A423%20%28%2B%29%2Cscore%3D222.07%2CPAP2_3%7CPF14378.2%7C2.8e-08%2CPAP2%7CPF01569.17%7C1.3e%2B03%2CPAP2%7CPF01569.17%7C2.7e%2B03%2CPAP2%7CPF01569.17%7C2.1e-08 +Transcript_5 transdecoder three_prime_UTR 1713 2333 . + . ID=Transcript_5.p1.utr3p1;Parent=Transcript_5.p1 +Transcript_6 BUSCO BUSCO_ortholog 262 758 118.3 . . ID=busco:967309dd9b02edfb5177002d21836fa2c192b1f0;Name=33875at4891;length=122;status=Complete +Transcript_6 HMMER protein_hmm_match 328 372 1.900000e+03 . . ID=homology:208eced63426fa4c6b7f35d04502d6597002cb0c;Name=Prefoldin;Target=Prefoldin 86 100 +;accuracy=0.54;env_coords=313 378;Dbxref="Pfam-A:PF02996.13";Note=Prefoldin subunit +Transcript_6 HMMER protein_hmm_match 379 738 8.000000e-34 . . ID=homology:334cf02a2fc1b5a8d7a966933dd4300623fc6ed4;Name=Prefoldin;Target=Prefoldin 1 119 +;accuracy=0.99;env_coords=379 741;Dbxref="Pfam-A:PF02996.13";Note=Prefoldin subunit +Transcript_6 transdecoder CDS 265 774 . + 0 ID=cds.Transcript_6.p1;Parent=Transcript_6.p1 +Transcript_6 transdecoder exon 1 831 . + . ID=Transcript_6.p1.exon1;Parent=Transcript_6.p1 +Transcript_6 transdecoder five_prime_UTR 1 264 . + . ID=Transcript_6.p1.utr5p1;Parent=Transcript_6.p1 +Transcript_6 transdecoder gene 1 831 . + . ID=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A170%20%28%2B%29%2Cscore%3D79.50%2CPrefoldin%7CPF02996.13%7C1.9e%2B03%2CPrefoldin%7CPF02996.13%7C8e-34 +Transcript_6 transdecoder mRNA 1 831 . + . ID=Transcript_6.p1;Parent=GENE.Transcript_6~~Transcript_6.p1;Name=ORF%20type%3Acomplete%20len%3A170%20%28%2B%29%2Cscore%3D79.50%2CPrefoldin%7CPF02996.13%7C1.9e%2B03%2CPrefoldin%7CPF02996.13%7C8e-34 +Transcript_6 transdecoder three_prime_UTR 775 831 . + . ID=Transcript_6.p1.utr3p1;Parent=Transcript_6.p1 +Transcript_7 HMMER protein_hmm_match 1137 1163 3.500000e+03 . . ID=homology:f3b12c38f78f5c9265ac782078efeb5fbafa0c6e;Name=Zn_clus;Target=Zn_clus 23 31 +;accuracy=0.8;env_coords=1131 1178;Dbxref="Pfam-A:PF00172.14";Note=Fungal Zn(2)-Cys(6) binuclear cluster domain +Transcript_7 HMMER protein_hmm_match 1551 1565 3.700000e+03 . . ID=homology:73143411567bf289f89f82a13804244b04e21a7f;Name=Zn_clus;Target=Zn_clus 2 6 +;accuracy=0.59;env_coords=1548 1574;Dbxref="Pfam-A:PF00172.14";Note=Fungal Zn(2)-Cys(6) binuclear cluster domain +Transcript_7 HMMER protein_hmm_match 291 389 2.800000e-09 . . ID=homology:cdbabccc6cb0203e07f7b47162d44b4835e4257c;Name=Zn_clus;Target=Zn_clus 1 34 +;accuracy=0.9;env_coords=291 404;Dbxref="Pfam-A:PF00172.14";Note=Fungal Zn(2)-Cys(6) binuclear cluster domain +Transcript_7 shmlast.LAST conditional_reciprocal_best_LAST 98 129 3.700000e-09 + . ID=homology:ad12dc2e8fab5c38092b97327c8d890796d1ec6b;Name=SPAC11D3.11c|SPAC11D3.11c|I|zn(2)-C6 fungal-type DNA-binding transcription factor, truncated;Target=SPAC11D3.11c|SPAC11D3.11c|I|zn(2)-C6 fungal-type DNA-binding transcription factor, truncated 5 36 +;database=pep.fa +Transcript_7 transdecoder CDS 243 1934 . + 0 ID=cds.Transcript_7.p1;Parent=Transcript_7.p1 +Transcript_7 transdecoder exon 1 2146 . + . ID=Transcript_7.p1.exon1;Parent=Transcript_7.p1 +Transcript_7 transdecoder five_prime_UTR 1 242 . + . ID=Transcript_7.p1.utr5p1;Parent=Transcript_7.p1 +Transcript_7 transdecoder gene 1 2146 . + . ID=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A564%20%28%2B%29%2Cscore%3D237.95%2CZn_clus%7CPF00172.14%7C2.8e-09%2CZn_clus%7CPF00172.14%7C3.5e%2B03%2CZn_clus%7CPF00172.14%7C3.7e%2B03 +Transcript_7 transdecoder mRNA 1 2146 . + . ID=Transcript_7.p1;Parent=GENE.Transcript_7~~Transcript_7.p1;Name=ORF%20type%3Acomplete%20len%3A564%20%28%2B%29%2Cscore%3D237.95%2CZn_clus%7CPF00172.14%7C2.8e-09%2CZn_clus%7CPF00172.14%7C3.5e%2B03%2CZn_clus%7CPF00172.14%7C3.7e%2B03 +Transcript_7 transdecoder three_prime_UTR 1935 2146 . + . ID=Transcript_7.p1.utr3p1;Parent=Transcript_7.p1 +Transcript_8 HMMER protein_hmm_match 1986 2177 1.400000e-07 . . ID=homology:6c81497c9c07c85cc5bccde19b64231ca9ad48cd;Name=RRM_1;Target=RRM_1 1 70 +;accuracy=0.91;env_coords=1986 2177;Dbxref="Pfam-A:PF00076.18";Note=RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) +Transcript_8 HMMER protein_hmm_match 2031 2189 2.900000e-06 . . ID=homology:be0f5c69dc309638c4bc7ee3730bb103e640689e;Name=RRM_5;Target=RRM_5 1 56 +;accuracy=0.97;env_coords=2031 2189;Dbxref="Pfam-A:PF13893.2";Note=RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) +Transcript_8 HMMER protein_hmm_match 2271 2303 3.100000e+03 . . ID=homology:a2caa8f0087a7738a3dd31164691b16f25c2cda4;Name=RRM_1;Target=RRM_1 2 12 +;accuracy=0.82;env_coords=2271 2309;Dbxref="Pfam-A:PF00076.18";Note=RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) +Transcript_8 transdecoder CDS 894 3110 . + 0 ID=cds.Transcript_8.p1;Parent=Transcript_8.p1 +Transcript_8 transdecoder exon 1 3294 . + . ID=Transcript_8.p1.exon1;Parent=Transcript_8.p1 +Transcript_8 transdecoder five_prime_UTR 1 893 . + . ID=Transcript_8.p1.utr5p1;Parent=Transcript_8.p1 +Transcript_8 transdecoder gene 1 3294 . + . ID=GENE.Transcript_8~~Transcript_8.p1;Name=ORF%20type%3Acomplete%20len%3A739%20%28%2B%29%2Cscore%3D320.56%2CRRM_1%7CPF00076.18%7C1.4e-07%2CRRM_1%7CPF00076.18%7C3.1e%2B03%2CRRM_5%7CPF13893.2%7C2.9e-06 +Transcript_8 transdecoder mRNA 1 3294 . + . ID=Transcript_8.p1;Parent=GENE.Transcript_8~~Transcript_8.p1;Name=ORF%20type%3Acomplete%20len%3A739%20%28%2B%29%2Cscore%3D320.56%2CRRM_1%7CPF00076.18%7C1.4e-07%2CRRM_1%7CPF00076.18%7C3.1e%2B03%2CRRM_5%7CPF13893.2%7C2.9e-06 +Transcript_8 transdecoder three_prime_UTR 3111 3294 . + . ID=Transcript_8.p1.utr3p1;Parent=Transcript_8.p1 +Transcript_9 HMMER protein_hmm_match 238 315 4.300000e-08 . . ID=homology:a3544f04ba5833a2e0b422d7a57aeb66f7de2fb7;Name=CRAL_TRIO_N;Target=CRAL_TRIO_N 31 56 +;accuracy=0.74;env_coords=163 318;Dbxref="Pfam-A:PF03765.11";Note=CRAL/TRIO, N-terminal domain +Transcript_9 HMMER protein_hmm_match 391 885 1.500000e-38 . . ID=homology:c13857aaa94eca562afbb6b807e95894cd8a3e2e;Name=CRAL_TRIO;Target=CRAL_TRIO 3 159 +;accuracy=0.94;env_coords=385 885;Dbxref="Pfam-A:PF00650.16";Note=CRAL/TRIO domain +Transcript_9 transdecoder CDS 1 960 . + 0 ID=cds.Transcript_9.p1;Parent=Transcript_9.p1 +Transcript_9 transdecoder exon 1 1504 . + . ID=Transcript_9.p1.exon1;Parent=Transcript_9.p1 +Transcript_9 transdecoder gene 1 1504 . + . ID=GENE.Transcript_9~~Transcript_9.p1;Name=ORF%20type%3A5prime_partial%20len%3A320%20%28%2B%29%2Cscore%3D147.90%2CCRAL_TRIO%7CPF00650.16%7C1.5e-38%2CCRAL_TRIO_N%7CPF03765.11%7C4.3e-08 +Transcript_9 transdecoder mRNA 1 1504 . + . ID=Transcript_9.p1;Parent=GENE.Transcript_9~~Transcript_9.p1;Name=ORF%20type%3A5prime_partial%20len%3A320%20%28%2B%29%2Cscore%3D147.90%2CCRAL_TRIO%7CPF00650.16%7C1.5e-38%2CCRAL_TRIO_N%7CPF03765.11%7C4.3e-08 +Transcript_9 transdecoder three_prime_UTR 961 1504 . + . ID=Transcript_9.p1.utr3p1;Parent=Transcript_9.p1 diff --git a/generate-test-data.sh b/generate-test-data.sh index 8f910e3e..fdc64420 100644 --- a/generate-test-data.sh +++ b/generate-test-data.sh @@ -21,6 +21,9 @@ dammit run --busco-group saccharomycetes_odb10 --n-threads 4 annotate --global # Passing a user database dammit run --busco-group saccharomycetes_odb10 --n-threads 4 --pipeline quick annotate $DATA_DIR/$TEST_FILE --user-database $DATA_DIR/$TEST_PEP -o $TEST_NAME.dammit.udb +# multiple user databases +dammit run --n-threads 4 --busco-group saccharomycetes_odb10 --pipeline quick annotate --user-database $DATA_DIR/pep.fa --user-database $DATA_DIR/odb_subset.fa $DATA_DIR/$TEST_FILE -o $TEST_NAME.dammit.multi-udb + # Passing multiple musco groups dammit run --n-threads 4 --pipeline quick --busco-group bacteria_odb10 --busco-group saccharomycetes_odb10 annotate -o pom.256.dammit.busco-multi $DATA_DIR/pom.256.fa @@ -30,6 +33,7 @@ dammit run --busco-group saccharomycetes_odb10 --pipeline quick annotate --regex # Rename with backmapping #dammit run annotate $DATA_DIR/$TEST_FILE --no-rename -o $TEST_FILE.dammit.norename + # # Copy the data # From ca270e354a3f3abb4b2bc17fc89974bd8fe6a997 Mon Sep 17 00:00:00 2001 From: Camille Scott Date: Wed, 26 May 2021 14:12:07 -0700 Subject: [PATCH 11/13] Uncomment multi user database test --- dammit/tests/test_annotate.py | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index 85d80e2b..ef95bce9 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -43,7 +43,8 @@ def test_default(self, tmpdir, datadir, n_threads): exp_gff3 = datadir('pom.20.dammit.gff3') exp_fasta = datadir('pom.20.dammit.fasta') - args = ['run', '--busco-group', 'saccharomycetes_odb10', '--n-threads', str(n_threads), 'annotate', transcripts] + args = ['run', '--busco-group', 'saccharomycetes_odb10', + '--n-threads', str(n_threads), 'annotate', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' @@ -66,7 +67,8 @@ def test_evalue(self, tmpdir, datadir): exp_gff3 = datadir('pom.20.dammit.evalue10.gff3') exp_fasta = datadir('pom.20.dammit.evalue10.fasta') - args = ['run', '--busco-group', 'saccharomycetes_odb10', 'annotate', transcripts, '--global-evalue', '10.0'] + args = ['run', '--busco-group', 'saccharomycetes_odb10', + 'annotate', transcripts, '--global-evalue', '10.0'] status, out, err = run(*args) outdir = 'pom.20.dammit' @@ -87,7 +89,8 @@ def test_user_database(self, tmpdir, datadir, n_threads): exp_gff3 = datadir('pom.20.udb.dammit.gff3') exp_fasta = datadir('pom.20.udb.dammit.fasta') - args = ['run', '--busco-group', 'saccharomycetes_odb10', '--n-threads', str(n_threads), '--pipeline', 'quick', 'annotate', + args = ['run', '--busco-group', 'saccharomycetes_odb10', + '--n-threads', str(n_threads), '--pipeline', 'quick', 'annotate', transcripts, '--user-database', pep] status, out, err = run(*args) @@ -101,7 +104,6 @@ def test_user_database(self, tmpdir, datadir, n_threads): assert compare_gff(gff3_fn, exp_gff3) assert open(fasta_fn).read() == open(exp_fasta).read() - """ @pytest.mark.parametrize('n_threads', (1,4)) def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): '''--pipeline quick annotate --user-database [PEP1.fa] --user-database [PEP2.fa] [INPUT.fa] @@ -129,7 +131,7 @@ def test_annotate_multiple_user_databases(self, tmpdir, datadir, n_threads): assert status == 0 assert compare_gff(gff3_fn, exp_gff3) assert open(fasta_fn).read() == open(exp_fasta).read() - """ + def test_annotate_basename(self, tmpdir, datadir): '''Test annotate --pipeline quick annotate --base-name [NAME] [INPUT.fa] ''' @@ -227,7 +229,8 @@ def test_annotate_dbdir(self, tmpdir, datadir): transcripts = datadir('pom.20.fa') database_dir = os.environ['DAMMIT_DB_DIR'] - args = ['run', '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', '--database-dir', database_dir, 'annotate', '--dry-run', transcripts] + args = ['run', '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', + '--database-dir', database_dir, 'annotate', '--dry-run', transcripts] status, out, err = run(*args) assert status == 0 @@ -252,7 +255,8 @@ def test_max_threads_per_task(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') - args = ['run', '--max-threads-per-task', 1, '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] + args = ['run', '--max-threads-per-task', 1, '--busco-group', 'saccharomycetes_odb10', + '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' @@ -267,7 +271,8 @@ def test_config_file(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') conf = datadir('test-conf.yml') - args = ['--config-file', conf, 'run', '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] + args = ['--config-file', conf, 'run', '--busco-group', 'saccharomycetes_odb10', + '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' @@ -287,7 +292,8 @@ def test_busco_config_file(self, tmpdir, datadir): with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') busco_conf = os.path.join(__path__, 'busco.default.ini') - args = ['run', '--busco-config-file', busco_conf, '--busco-group', 'saccharomycetes_odb10', '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] + args = ['run', '--busco-config-file', busco_conf, '--busco-group', 'saccharomycetes_odb10', + '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' From 400e2d03ca055585a46babc48e1ede9449c122cc Mon Sep 17 00:00:00 2001 From: Camille Scott Date: Wed, 26 May 2021 14:55:45 -0700 Subject: [PATCH 12/13] Fix --max-threads-per-tasp CLI and config interplay --- dammit/components/run.py | 3 ++- dammit/config.yml | 2 +- dammit/tests/{ => test-data}/test-conf.yml | 0 3 files changed, 3 insertions(+), 2 deletions(-) rename dammit/tests/{ => test-data}/test-conf.yml (100%) diff --git a/dammit/components/run.py b/dammit/components/run.py index c4cc282c..c898ed56 100644 --- a/dammit/components/run.py +++ b/dammit/components/run.py @@ -111,7 +111,8 @@ def run_group(config, config.core['n_threads'] = n_threads if not max_threads_per_task: - config.core['max_threads_per_task'] = config.core['n_threads'] + config.core['max_threads_per_task'] = config.core['n_threads'] if config.core['max_threads_per_task'] == 0 \ + else min(config.core['n_threads'], config.core['max_threads_per_task']) else: config.core['max_threads_per_task'] = min(config.core['n_threads'], max_threads_per_task) diff --git a/dammit/config.yml b/dammit/config.yml index 46b5d301..85cd0533 100644 --- a/dammit/config.yml +++ b/dammit/config.yml @@ -15,7 +15,7 @@ regex_rename: null # n_threads: total threads to pass to snakemake -j n_threads: 0 # max threads to use on a single job -max_threads_per_task: 1 +max_threads_per_task: 0 verbosity: 0 diff --git a/dammit/tests/test-conf.yml b/dammit/tests/test-data/test-conf.yml similarity index 100% rename from dammit/tests/test-conf.yml rename to dammit/tests/test-data/test-conf.yml From 09b4b4081549741bdd9a87309beefd4943f5baff Mon Sep 17 00:00:00 2001 From: Camille Scott Date: Wed, 26 May 2021 14:56:14 -0700 Subject: [PATCH 13/13] Update test for user supplied config file --- dammit/tests/test-data/test-conf.yml | 6 ++++-- dammit/tests/test_annotate.py | 11 ++++++----- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/dammit/tests/test-data/test-conf.yml b/dammit/tests/test-data/test-conf.yml index 3ed1ed1c..25bfb57f 100644 --- a/dammit/tests/test-data/test-conf.yml +++ b/dammit/tests/test-data/test-conf.yml @@ -1,7 +1,9 @@ -basename: Transcript +basename: Splat busco: configfile: busco.default.ini params: extra: '' +global_evalue: 1.0 busco_groups: -- bacteria_odb10 +- saccharomycetes_odb10 +max_threads_per_task: 1 diff --git a/dammit/tests/test_annotate.py b/dammit/tests/test_annotate.py index ef95bce9..1e0e048f 100644 --- a/dammit/tests/test_annotate.py +++ b/dammit/tests/test_annotate.py @@ -264,25 +264,26 @@ def test_max_threads_per_task(self, tmpdir, datadir): assert "Threads (per-task): 1" in err - def test_config_file(self, tmpdir, datadir): + def test_user_config_file(self, tmpdir, datadir): '''Test that --config-file works. ''' with tmpdir.as_cwd(): transcripts = datadir('pom.20.fa') conf = datadir('test-conf.yml') - args = ['--config-file', conf, 'run', '--busco-group', 'saccharomycetes_odb10', + args = ['--config-file', conf, 'run', '--n-threads', '2', '--pipeline', 'quick', 'annotate', '--dry-run', transcripts] status, out, err = run(*args) outdir = 'pom.20.dammit' + print(out, err) + assert status == 0 assert "BUSCO groups: saccharomycetes_odb10" in err assert "E-value Cutoff (global): 1.0" in err assert "Pipeline: quick" in err - # these two are failing - # assert "Threads (per-task): 1" in err - # assert "Threads (total): 2" in err + assert "Threads (per-task): 1" in err + assert "Threads (total): 2" in err def test_busco_config_file(self, tmpdir, datadir):