new data for cram test (#29)

Add a two haplotype test
cbg-ethz · Feb 10, 2017 · 2542ed7 · 2542ed7
1 parent e6c35df
commit 2542ed7
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Showing 8 changed files with 12 additions and 9,182 deletions.
diff --git a/circle.yml b/circle.yml
@@ -22,4 +22,4 @@ dependencies:
 ## Customize test
 test:
   override:
-    - cd build; make check
+    - cd build; make check
diff --git a/test/cram/arabis_large_500_01.t b/test/cram/arabis_large_500_01.t
@@ -0,0 +1,4 @@
+## This script performs an end to end test on haploclique project. The test input data arabis_large_500_01/reads.bam is a simulated dataset generated from Arabis mosaic virus large satellite RNA reference sequence using Simseq simulator. The expected output is presented in arabis_large_500_01/quasispecies.fasta.fasta and is compared to actual output quasispecies.fasta.fasta.
+
+  $ $__HC_EXE --edge_quasi_cutoff_cliques=0.85 --edge_quasi_cutoff_mixed=0.85 --edge_quasi_cutoff_single=0.8 --min_overlap_cliques=0.6 --min_overlap_single=0.5 --no_singletons --significance=4 --noProb0 $TESTDIR/../data/simulation/arabis_large_500_01/reads.bam > /dev/null;
+  $ diff quasispecies.fasta.fasta ${TESTDIR}/../data/simulation/arabis_large_500_01/quasispecies.fasta.fasta
diff --git a/test/data/simulation/arabis_large_500_01/haplo.fasta b/test/data/simulation/arabis_large_500_01/haplo.fasta
@@ -0,0 +1 @@
+>gi|20066014|ref|NC_003523.1|TATGAAAAATTTCTATGGATTCCCATATTAACGCGAATACATTTTTTTCCTCTCCCAGAGCCTCAGTTAAGATTTTGGTCCCAAACAAGTACGCGAAACTGTTTACCCTTAAACAGCTCGCTCGCATGCGTGTATTGCCGTGTAGGCTCCGTGCACGGCAAGCCGCTAGCCCGGTAAGCAAACGGTCCTTCCGAGATCGCGATGGGAGTAAAATAATGGGTCAGGGTCATCCTGCTGTTGGCCGTCTAGTGTCGAAGGGACACAAACAGTAGTCTGACGGAGGGGCGAGCCTAGCCCCAGTGAAGTTTAAGCGCGCAGTACGTCGTGAAAAGCGACGCTGCCGCAAAAAAGGCGCAACCAAGGCCGGGACTACACCCGTATAAAAAGTCGGGCATTGTGTCCACGCCTCGAAGGTGCAGAAGCAGGCGACTTATCTGTCTAGCTTCCTTTCCAATCCTTGTGGGGCAAAATCCAGAATGGGGCCTGTGAGCATGCGCCCCCAATCAAAAAATGCTCCCGACGCCAGCAAGGATGTTTTCACCCTTACTGCAATCTCTCCTGCTGAGTGCCGGAATGAAACCGCGCGCAGGTGTCACGCTATAACTGGTACCTGCAAGGATGCCCCTGGGTTTTGCACGCTGGCCCGCGAGGGTTGTGGCGTCTGTGCAGCTTGTGAAGCCAAGCTTGCACAGCTGGGTTTCGACCGCAGTTTCGACTCGATTGTTACTTCACGTGTCATCCGTGTCGGTTCAATGAAGGAAGAAACTTCTGATGAAATGGCTAGTCCTAGTGCAACAGAGCCTGTTGAGTTCTTGGCTCCTGCTGAAAAGCAGGCACCTCGTTGGGGGGGACAGCCCATATAAAGGTGCGATGTGGTGGCACTCGCACGCGCGACGCCGGTTCTCCGGGTGTTGCGTAAGGTTGATCCCACTTTTGTGGACAACCGGCTAGTATGGGAAGCTGCGCACTCAGCCAGTTTTTCCTCGGCGCAGGTTCGTATCCCTTTGGTTGCTTTGGGGACTCGGGGTAGGGAAGACTGCTGCGGTACAGCGTTTGCTCATAGACTGACGCAAGTTGGGATTTTTGTTGCTCTTTAGTCAACTC
diff --git a/test/data/simulation/arabis_large_500_01/quasispecies.fasta.fasta b/test/data/simulation/arabis_large_500_01/quasispecies.fasta.fasta
@@ -0,0 +1,4 @@
+>Clique_489|ht_freq:0.50000|start1:1|end1:1104|#reads:552
+TATGAAAAATTTCTATGGATTCCCATATTAACGCGAATACATTTTTTTCCTCTCCCAGAGCCTCAGTTAAGATTTTGGTCCCAAACAAGTACGCGAAACTGTTTACCCTTAAACAGCTCGCTCGCATGCGTGTATTGCCGTGTAGGCTCCGTGCACGGCAAGCCGCTAGCCCGGTAAGCAAACGGTCCTTCCGAGATCGCGATGGGAGTAAAATAATGGGTCAGGGTCATCCTGCTGTTGGCCGTCTAGTGTCGAAGGGACACAAACAGTAGTCTGACGGAGGGGCGAGCCTAGCCCCAGTGAAGTTTAAGCGCGCAGTACGTCGTGAAAAGCGACGCTGCCGCAAAAAAGGCGCAACCAAGGCCGGGACTACACCCGTATAAAAAGTCGGGCATTGTGTCCACGCCTCGAAGGTGCAGAAGCAGGCGACTTATCTGTCTAGCTTCCTTTCCAATCCTTGTGGGGCAAAATCCAGAATGGGGCCTGTGAGCATGCGCCCCCAATCAAAAAATGCTCCCGACGCCAGCAAGGATGTTTTCACCCTTACTGCAATCTCTCCTGCTGAGTGCCGGAATGAAACCGCGCGCAGGTGTCACGCTATAACTGGTACCTGCAAGGATGCCCCTGGGTTTTGCACGCTGGCCCGCGAGGGTTGTGGCGTCTGTGCAGCTTGTGAAGCCAAGCTTGCACAGCTGGGTTTCGACCGCAGTTTCGACTCGATTGTTACTTCACGTGTCATCCGTGTCGGTTCAATGAAGGAAGAAACTTCTGATGAAATGGCTAGTCCTAGTGCAACAGAGCCTGTTGAGTTCTTGGCTCCTGCTGAAAAGCAGGCACCTCGTTGGGGGGGACAGCCCATATAAAGGTGCGATGTGGTGGCACTCGCACGCGCGACGCCGGTTCTCCGGGTGTTGCGTAAGGTTGATCCCACTTTTGTGGACAACCGGCTAGTATGGGAAGCTGCGCACTCAGCCAGTTTTTCCTCGGCGCAGGTTCGTATCCCTTTGGTTGCTTTGGGGACTCGGGGTAGGGAAGACTGCTGCGGTACAGCGTTTGCTCATAGACTGACGCAAGTTGGGATTTTTGTTGCTCTTTAGTCAACTC
+>Clique_490|ht_freq:0.50000|start1:1|end1:1103|#reads:552
+TATGAAAAATTTCTATGGATTCCCATATTAACGCGAATACATCTTTTTCCTCTCCCAGAGTCTCAGTTGAGATTCTGGTCCCAACCAAGTACGCGAAACTGTTTACCCTTAAACAGCTCACTCGCATGCTTGTATTGTCGTGTAAGCACCGTGCACGGCAAGCCGCTAACCCGGTAAGCAAACGGACCTCCCGAGATCGAGATGGGAGTAAAATAATGGGTCAGGGACCTCCTGCTGTGGGCCCGCGAGTGTCGAAGGGACACAAACAGCAGTCTGACGGAGGGGCGAGCCTAGCCCCTGTGAAGTCTAAGCGCGCAGTACGTCGTGAAAAGCGTCGCTGCCGCAAAAAAGGCGCAACCAAGGCCGGGACTACACCCGTACAAAAAGGTGGGCATTGTGTCCACGCCTCGAAGGGGCAGAAGCAGGCGACTTATTTGTCTAGCTTGCTTTCCAATCCTTCTGGGGCAAAATCCAGAATGGGGGCTGTGAGCAAGCCCCCCCAAACAAAAAATGCTCCCGACGCCAGCAAGGGTGGTTTCACCCTTACTGCTATCTCACCGGCTGAGTGCCGGAAGGAAACCGCGCGCAGGTTTCACCCTATAACTGGTACCTTCAAGGGTGCCCCTGGGTTTTGCACGCGGTCCCGAGAGGGTTGTGGCGTCTGTGCAGCTTGTGAAGCCAAGCTTGCACAGCTTGGTTTCGACCGGAGTTTCGACTCGATTGGCACTTCACGTGTCATCCGTGTCGATTCAATGAAGGAAGAAACTTCTGATGACATGGCTAGTCCTAGTGCTACAGAGCCTGTTGGGTTCTGGGCTCCTGCTGAAAAGCAGGCCCCTCGTTGGGAGGGACAGCCCATAAAAAGGTGCGATGTGGTGACACTCGCACGCGTGACGCCGGTTCTCCGGATGTTGCGTAAGGTTGATCCCACTTTTGTGGACAACCGGCTATTATGGGAAGCTGCGCACTCAGACAGTTTTTCCTCAGCGCAAGTGCGTATCCCTTTGGTTGCTTTGGCGACTCGGGGTAGGGAAGACTGTTGCGGGACATCGTTTGTTTATAGTCTGACGCAAGTTGGGATTTTGGTTGCTCTTTAGTCAACT
diff --git a/test/data/simulation/arabis_large_500_01/reads.bam b/test/data/simulation/arabis_large_500_01/reads.bam
diff --git a/test/data/simulation/arabis_large_500_01/ref.fasta b/test/data/simulation/arabis_large_500_01/ref.fasta
@@ -0,0 +1,2 @@
+>gi|20066014|ref|NC_003523.1| Arabis mosaic virus large satellite RNA, complete genome
+TATGAAAAATTTCTATGGATTCCCATATTAACGCGAATACATCTTTTTCCTCTCCCAGAGTCTCAGTTGAGATTCTGGTCCCAACCAAGTACGCGAAACTGTTTACCCTTAAACAGCTCACTCGCATGCTTGTATTGTCGTGTAAGCACCGTGCACGGCAAGCCGCTAACCCGGTAAGCAAACGGACCTCCCGAGATCGAGATGGGAGTAAAATAATGGGTCAGGGACCTCCTGCTGTGGGCCCGCGAGTGTCGAAGGGACACAAACAGCAGTCTGACGGAGGGGCGAGCCTAGCCCCTGTGAAGTCTAAGCGCGCAGTACGTCGTGAAAAGCGTCGCTGCCGCAAAAAAGGCGCAACCAAGGCCGGGACTACACCCGTACAAAAAGGTGGGCATTGTGTCCACGCCTCGAAGGGGCAGAAGCAGGCGACTTATTTGTCTAGCTTGCTTTCCAATCCTTCTGGGGCAAAATCCAGAATGGGGGCTGTGAGCAAGCCCCCCCAAACAAAAAATGCTCCCGACGCCAGCAAGGGTGGTTTCACCCTTACTGCTATCTCACCGGCTGAGTGCCGGAAGGAAACCGCGCGCAGGTTTCACCCTATAACTGGTACCTTCAAGGGTGCCCCTGGGTTTTGCACGCGGTCCCGAGAGGGTTGTGGCGTCTGTGCAGCTTGTGAAGCCAAGCTTGCACAGCTTGGTTTCGACCGGAGTTTCGACTCGATTGGCACTTCACGTGTCATCCGTGTCGATTCAATGAAGGAAGAAACTTCTGATGACATGGCTAGTCCTAGTGCTACAGAGCCTGTTGGGTTCTGGGCTCCTGCTGAAAAGCAGGCCCCTCGTTGGGAGGGACAGCCCATAAAAAGGTGCGATGTGGTGACACTCGCACGCGTGACGCCGGTTCTCCGGATGTTGCGTAAGGTTGATCCCACTTTTGTGGACAACCGGCTATTATGGGAAGCTGCGCACTCAGACAGTTTTTCCTCAGCGCAAGTGCGTATCCCTTTGGTTGCTTTGGCGACTCGGGGTAGGGAAGACTGTTGCGGGACATCGTTTGTTTATAGTCTGACGCAAGTTGGGATTTTGGTTGCTCTTTAGTCAACTC
diff --git a/test/data/simulation/reads_arabis_mosaic_virus_25_01.bam b/test/data/simulation/reads_arabis_mosaic_virus_25_01.bam
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		@@ -0,0 +1 @@
		>gi\|20066014\|ref\|NC_003523.1\|TATGAAAAATTTCTATGGATTCCCATATTAACGCGAATACATTTTTTTCCTCTCCCAGAGCCTCAGTTAAGATTTTGGTCCCAAACAAGTACGCGAAACTGTTTACCCTTAAACAGCTCGCTCGCATGCGTGTATTGCCGTGTAGGCTCCGTGCACGGCAAGCCGCTAGCCCGGTAAGCAAACGGTCCTTCCGAGATCGCGATGGGAGTAAAATAATGGGTCAGGGTCATCCTGCTGTTGGCCGTCTAGTGTCGAAGGGACACAAACAGTAGTCTGACGGAGGGGCGAGCCTAGCCCCAGTGAAGTTTAAGCGCGCAGTACGTCGTGAAAAGCGACGCTGCCGCAAAAAAGGCGCAACCAAGGCCGGGACTACACCCGTATAAAAAGTCGGGCATTGTGTCCACGCCTCGAAGGTGCAGAAGCAGGCGACTTATCTGTCTAGCTTCCTTTCCAATCCTTGTGGGGCAAAATCCAGAATGGGGCCTGTGAGCATGCGCCCCCAATCAAAAAATGCTCCCGACGCCAGCAAGGATGTTTTCACCCTTACTGCAATCTCTCCTGCTGAGTGCCGGAATGAAACCGCGCGCAGGTGTCACGCTATAACTGGTACCTGCAAGGATGCCCCTGGGTTTTGCACGCTGGCCCGCGAGGGTTGTGGCGTCTGTGCAGCTTGTGAAGCCAAGCTTGCACAGCTGGGTTTCGACCGCAGTTTCGACTCGATTGTTACTTCACGTGTCATCCGTGTCGGTTCAATGAAGGAAGAAACTTCTGATGAAATGGCTAGTCCTAGTGCAACAGAGCCTGTTGAGTTCTTGGCTCCTGCTGAAAAGCAGGCACCTCGTTGGGGGGGACAGCCCATATAAAGGTGCGATGTGGTGGCACTCGCACGCGCGACGCCGGTTCTCCGGGTGTTGCGTAAGGTTGATCCCACTTTTGTGGACAACCGGCTAGTATGGGAAGCTGCGCACTCAGCCAGTTTTTCCTCGGCGCAGGTTCGTATCCCTTTGGTTGCTTTGGGGACTCGGGGTAGGGAAGACTGCTGCGGTACAGCGTTTGCTCATAGACTGACGCAAGTTGGGATTTTTGTTGCTCTTTAGTCAACTC
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		@@ -0,0 +1,2 @@
		>gi\|20066014\|ref\|NC_003523.1\| Arabis mosaic virus large satellite RNA, complete genome
		TATGAAAAATTTCTATGGATTCCCATATTAACGCGAATACATCTTTTTCCTCTCCCAGAGTCTCAGTTGAGATTCTGGTCCCAACCAAGTACGCGAAACTGTTTACCCTTAAACAGCTCACTCGCATGCTTGTATTGTCGTGTAAGCACCGTGCACGGCAAGCCGCTAACCCGGTAAGCAAACGGACCTCCCGAGATCGAGATGGGAGTAAAATAATGGGTCAGGGACCTCCTGCTGTGGGCCCGCGAGTGTCGAAGGGACACAAACAGCAGTCTGACGGAGGGGCGAGCCTAGCCCCTGTGAAGTCTAAGCGCGCAGTACGTCGTGAAAAGCGTCGCTGCCGCAAAAAAGGCGCAACCAAGGCCGGGACTACACCCGTACAAAAAGGTGGGCATTGTGTCCACGCCTCGAAGGGGCAGAAGCAGGCGACTTATTTGTCTAGCTTGCTTTCCAATCCTTCTGGGGCAAAATCCAGAATGGGGGCTGTGAGCAAGCCCCCCCAAACAAAAAATGCTCCCGACGCCAGCAAGGGTGGTTTCACCCTTACTGCTATCTCACCGGCTGAGTGCCGGAAGGAAACCGCGCGCAGGTTTCACCCTATAACTGGTACCTTCAAGGGTGCCCCTGGGTTTTGCACGCGGTCCCGAGAGGGTTGTGGCGTCTGTGCAGCTTGTGAAGCCAAGCTTGCACAGCTTGGTTTCGACCGGAGTTTCGACTCGATTGGCACTTCACGTGTCATCCGTGTCGATTCAATGAAGGAAGAAACTTCTGATGACATGGCTAGTCCTAGTGCTACAGAGCCTGTTGGGTTCTGGGCTCCTGCTGAAAAGCAGGCCCCTCGTTGGGAGGGACAGCCCATAAAAAGGTGCGATGTGGTGACACTCGCACGCGTGACGCCGGTTCTCCGGATGTTGCGTAAGGTTGATCCCACTTTTGTGGACAACCGGCTATTATGGGAAGCTGCGCACTCAGACAGTTTTTCCTCAGCGCAAGTGCGTATCCCTTTGGTTGCTTTGGCGACTCGGGGTAGGGAAGACTGTTGCGGGACATCGTTTGTTTATAGTCTGACGCAAGTTGGGATTTTGGTTGCTCTTTAGTCAACTC