Make trueCoverage executable and add references for other species

INNUca.py

@@ -11,7 +11,7 @@
 
 Copyright (C) 2017 Miguel Machado <[email protected]>
 
-Last modified: June 21, 2017
+Last modified: February 27, 2018
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -83,7 +83,7 @@ def include_rematch_dependencies_path(doNotUseProvidedSoftware):
 
 
 def main():
-    version = '3.1'
+    version = '3.2'
     args = utils.parseArguments(version)
 
     general_start_time = time.time()
@@ -386,7 +386,7 @@ def run_INNUca(sampleName, outdir, fastq_files, args, script_path, scheme, spade
         if args.skipEstimatedCoverage or (run_successfully_estimatedCoverage and not estimatedCoverage < args.estimatedMinimumCoverage):
             if not args.skipTrueCoverage and trueCoverage_config is not None:
                 # Run True Coverage
-                run_successfully_trueCoverage, pass_qc_trueCoverage, time_taken, failing = trueCoverage.runTrueCoverage(sampleName, fastq_files, trueCoverage_config['reference_file'], threads, outdir, trueCoverage_config['length_extra_seq'], trueCoverage_config['minimum_depth_presence'], trueCoverage_config['minimum_depth_call'], trueCoverage_config['minimum_depth_frequency_dominant_allele'], trueCoverage_config['minimum_gene_coverage'], False, False, 1, trueCoverage_config['minimum_gene_identity'], trueCoverage_config, rematch_script)
+                run_successfully_trueCoverage, pass_qc_trueCoverage, time_taken, failing = trueCoverage.runTrueCoverage(sampleName, fastq_files, trueCoverage_config['reference_file'], threads, outdir, trueCoverage_config['length_extra_seq'], trueCoverage_config['minimum_depth_presence'], trueCoverage_config['minimum_depth_call'], trueCoverage_config['minimum_depth_frequency_dominant_allele'], trueCoverage_config['minimum_gene_coverage'], False, trueCoverage_config['minimum_gene_identity'], trueCoverage_config, rematch_script)
                 runs['trueCoverage_ReMatCh'] = [run_successfully_trueCoverage, pass_qc_trueCoverage, time_taken, failing, {}]
             else:
                 print '\n' + '--skipTrueCoverage set. Skipping True coverage analysis'

README.md

@@ -306,6 +306,9 @@ In order to manually combine **INNUca** trueCoverage_ReMatCh module reports in r
 
 
 
+## Citation
+MP Machado, J Halkilahti, A Jaakkonen, DN Silva, I Mendes, Y Nalbantoglu, V Borges, M Ramirez, M Rossi, JA Carriço. _INNUca_ **GitHub** https://github.com/B-UMMI/INNUca
+
 Contact
 -------
 Miguel Machado

modules/trueCoverage_rematch/haemophilus_influenzae.config

@@ -0,0 +1,20 @@
+#reference_file (fasta file full path)
+/home/mpmachado/INNUca/modules/trueCoverage_rematch/haemophilus_influenzae.fasta
+#length_extra_seq (int)
+200
+#maximum_number_absent_genes (int)
+0
+#maximum_number_genes_multiple_alleles (int)
+1
+#minimum_read_coverage (x, int)
+25
+#minimum_depth_presence (x, int)
+5
+#minimum_depth_call (x, int)
+10
+#minimum_depth_frequency_dominant_allele (0-1, double)
+0.60
+#minimum_gene_coverage (0-100, int)
+80
+#minimum_gene_identity (0-100, int)
+70

modules/trueCoverage_rematch/haemophilus_influenzae.fasta

@@ -0,0 +1,84 @@
+>mdh
+CTAACACATAAGGAGTATTTATGAAAGTTGCTGTATTAGGTGCCGCAGGTGGTATTGGTCAAGCATTAGCGTTATTACTA
+AAACTTCAGTTGCCAGCAGGCTCAGATTTAGCATTATATGATATTGCCCCTGTTACCCCAGGTGTTGCAGTGGATGTGAG
+CCATATTCCAACTGCAGTGAATGTAAAAGGTTTTTCTGGTGAAGATCCAACTCCAGCACTTGAAGGTGCGGATGTTGTAT
+TAATTTCTGCTGGTGTTGCTCGTAAACCTGGTATGGATCGTTCAGATTTATTCAATATTAATGCAGGTATCGTGCGTGGT
+TTAATTGAAAAAGTCGCGGTTACTTGCCCGAAAGCCTGTGTTGGTATCATCACTAACCCAGTAAATACTACTGTTGCGAT
+TGCGGCTGAAGTGTTGAAAAAAGCAGGTGTTTACGACAAACGTAAATTATTTGGCGTGACAACTTTAGATGTGTTGCGTT
+CTGAAACCTTTGTGGCTGAATTAAAAGGTTTAAATGTTTCTCGTACGAGCGTTCCTGTTATTGGTGGTCACTCAGGTGTG
+ACTATTCTTCCATTACTTTCTCAAGTTCAATATGCAAAATGGAATGAAGATGAAATCGAACCATTAACAAAACGTATCCA
+AAATGCAGGTACAGAAGTGGTCAATGCAAAAGCGGGTGGCGGTTCTGCAACCCTTTCAATGGCGCAAGCTGCAGCACGTT
+TTGCGCGTTCTTTAGTGAAAGGATTAAGTGGCGAGACAGTGGTTGAATGTACTTATGTTGAAGGTGATGGCAAATATGCT
+CGTTT
+>pgi
+ATCGTTTTGACGATTATTCTTTAACATTCAATAACCAAATTCTTGTCGATTTTTCCAAAAATAACATCAATCAAACAACC
+CTTTCACTTCTTCGCCAACTTGCTCAAGAATGCGCACTTGATAGCGCAAAAGAAGCGATGTTTACTGGCGAAAAAATCAA
+TCGTACAGAAAATCGTGCCGTGCTACATACTGCACTTCGCAATCGCACTAATACGCCAGTGCTTGTTGATGGCAAAGATG
+TCATGCCTGAAGTCAATACTGTGCTAGCTAAAATGAAAGATTTCTGTCAGCGTATTATTTCTGGTGAATGGAAAGGCTAT
+ACAGGTAAAGCCATTACGGATGTCGTGAATATTGGTATTGGTGGCTCTGACTTAGGCCCTTATATGGTAACCGAAGCACT
+TCGCCCGTATAAAAATCATCTAAATATGCACTTTGTTTCAAATGTCGATGGTACACATATTGCGGAAACCTTAAAAAAAG
+TCAATCCAGAAACAACTCTTTTCTTAGTGGCATCGAAAACTTTTACAACTCAAGAAACCATGACAAATGCGCAAAGTGCG
+CGTGATTGGTTACTGAAAGCGGCGAAAGATGAAAGTGCAGTTGCAAAACATTTTGCAGCATTATCAACCAATGCTAAAGA
+TGTAGAAAAATTTGGTATTGATACCAATAACATGTTTGAATTTTGGGATTGGGTTGGCGGTCGTTACTCTTTATGGTCAG
+CTATTGGTCTTTCAATTGCACTATCAATTGGCTTTGAAAACTTTGAAGCGTTATTAAATGGCGCGCATGAAATGGATAAA
+CATTTCCACTCTACTCCAATTGAAAAAAATATTCCAACCACTTTAGCATTAGTTGGTTTATGGAATAC
+>recA
+TATTAATATAAATATTTTTCTTGACCTGTACATCAATACAGATATAATCATAAAAAATTGAACATTCAAACAGGATTTTA
+ATTATGGCAACTCAAGAAGAAAAACAAAAAGCACTAGCAGCTGCATTAGGGCAAATCGAAAAACAATTTGGTAAAGGCTC
+AATTATGAAATTAGGCGATACCAAAACGTTAGACGTAGAGTCTATTTCTACTGGATCACTTGGGTTAGATGTTGCGCTTG
+GGATTGGTGGTTTGCCTATGGGTCGAATTGTAGAAATTTTCGGGCCTGAATCATCGGGTAAAACAACATTAACTCTTTCC
+GTCATTGCTCAAGCGCAAAAAGCAGGAAAAACCTGTGCATTTATTGATGCAGAACACGCACTTGATCCTATTTATGCAGC
+AAAACTTGGTGTAGATGTAAAAGAACTTTTTGTTTCTCAACCAGATAATGGGGAACAGGCACTTGAAATCTGTGATGCAT
+TAGTTCGCTCAGGTGCAATTGATGTAATTATTGTGGACTCCGTTGCCGCACTGACACCAAAAGCCGAAATTGAAGGCGAT
+ATGGGCGATTCTCATATGGGTCTGCAAGCACGTTTAATGTCTCAAGCTTTGCGTAAACTCACAGGTCAAATTAAAAATGC
+AAACTGTCTAGTTGTGTTTATTAACCAAATCCGTATGAAAATAGGCGTGATGTTTGGTAATCCTGAAACCACCACAGGCG
+GTAATGCATTAAAATTCTATTCTTCTGTTCGCTTAGATATTCGCCGTACAGGTTCTGTAAAAGATGGCGAAAATATTATT
+GGAAATGAAACCCGCGTAAAAGTAGT
+>frdB
+AAATGGCTAATTCACCAGTAATGAATGTTGAAGTATTACGCTACAATCCTGAAATCGATCAAGAGCCACATTTAAGCACC
+TATCAAGTACCTTATGATAATCAAACTTCATTGCTTGATGCGTTAGGCTATATTAAGGATAAACTTGAACCCTCTCTTTC
+TTATCGTTGGTCTTGCCGTATGGCGATCTGCGGTTCTTGCGGGATGATGGTAAATAACAAACCAAAATTGGCTTGTAAAA
+CTTTCTTACGTGATTACAGCGGCCATATGCGTATCGAGCCATTAGCAAACTTCCCTATTGAACGCGATTTAGTGGTTGAT
+TTAAGCCACTTTATCGAAAGTTTAGAGGCAATTAAGCCTTATATTATTGGTAACGAAGCACCAGCATTAGATGGTAAACC
+ACATCCATCGAAAGAATTACAAGTAAGCCGTACTAAACAAACACCAGCACAGCTTGAGAAATATCGTCAATTCTCAATGT
+GTATCAACTGTGGTTTATGCTATGCCGCTTGCCCTCAATTTGGTTTAAATCCTGAATTCTTAGGTCCTGCAGCTATTACG
+ATGGCTCATCGTTATAATCTTGATAACCGTGACCATGGTAAAGCAAAACGTATGTCATTATTAAATGGTAAAAACGGGGT
+TTGGAGTTGTACTTTCGTTGGCTATTGCTCAGAAGTTTGTCCAAAACATGTGGATCCTGCTTCTGCAATTAACCAAGGCA
+AAGTGGAAAGCGCCAAAGATTATGTTATCTCTATGCTAAAACCAAAAGGCTAAGGGGGAAGGAATGTCAGTAACAGTGAG
+TAAACGTAAAAAATATGTTCGTCCAATGACAGCGACTTGGTGGCAAAAATTGGACTTCTACAAAGCTTATATGCTACGTG
+AAGCGACTT
+>adk
+AGACCAGCTCAGTATAAAAGTGCGGTAAAAATTATAAAAAATTTGACCGCACTATGCTTTATCAGTATCTTAATCACGTT
+TTGTATTAATGGAGATTTTTTATGAAAATTATTCTTTTAGGTGCACCGGGTGCAGGTAAAGGCACTCAAGCACAATTTAT
+TATGAACAAATTTGGTATCCCGCAAATTTCAACTGGTGATATGTTCCGTGCTGCAATCAAAGCGGGGACTGAACTTGGCA
+AACAAGCTAAAGCATTAATGGATGAAGGTAAATTAGTACCAGATGAATTAACCGTTGCTCTTGTAAAAGATCGTATTGCT
+CAAGCTGACTGTGCAAATGGTTTCTTGTTAGATGGTTTCCCTCGTACTATTCCACAAGCGGATGCACTGAAAGATTCAGG
+TGTTAAAATTGACTTTGTTTTAGAATTTGATGTGCCAGACGAAGTGATTGTTGAACGTATGAGTGGCCGTCGCGTACACC
+AAGCGTCTGGTCGTTCTTACCACATCGTTTATAATCCACCAAAAGTGGAAGGTAAAGATGATGTAACAGGCGAAGATTTA
+ATTATTCGTGCAGACGATAAACCAGAAACTGTATTAGATCGTTTAGCCGTATATCATAAACAAACTAGCCCATTAATTGA
+TTATTACCAAGCAGAAGCGAAAGCGGGGAATACTCAATATTTCCGTTTAGACGGTACACAAAAAGTAGAAGAAGTTAGCC
+AAGAGTTAGATAAAATCTTAGGCTAAAAATAATCTAAAAATTAACCGCACTTTAGAAAATATAATTAATCTGCACCTTAA
+AGGCTGAATAAATCAGCGAATTAAAGTGCAGATTTTTTTATAAACTACCCAAATTTATAATAGGCTGAAAAAAGTGC
+>fucK
+TAACCTCTTGTGCAACTCAAACCTTCAATCAATTAATGCAACAAGGTATTGATTTAAAAGATATTGTAGGAATATCTGTT
+ACCACTTTCGGCGTGGATGGCGCACCTTTTGATGAAAATGATCAACAACTTTATCCGATTATTTCATGGAAATGCCCACG
+AACCATACCAGTAATGGAAAATCTATCTAATCAATTAGATATCAAATATCTTTATCAACGTAACGGCATTGGTCAATACA
+GTTTTAATACTTTATTTAAATTACATTGGTTAAAAACACACAGGCCAGATGTTTTCCAAAAAATGGCTAAATTCGTTTTT
+ATTTCGTCAATGCTCACTCAACGCTTAACTGGTCAATTCACTACAGATCACACAATGGCGGGAACATCAATGATGACAAA
+CCTTACTAGCGGTAATTGGGATCCATCGATTTTAACATCGCTGGGTTTAAGTAATAACCATTTCCCTCCTATGCGTTATG
+CAGGTGAAAAAGTTGGAAAATTACGTACACCGTTAGCCCAGAAATGGGGATTAAATCCCGTACCTGTCATTTCTTGTGGA
+CATGATACTCAATTTGCTGTGTTTGGGTCTGGTGCAGGGCTAAATCAGCCTGTGTTAAGTTCTGGCACCTGGGAAATCTT
+AATGGCTAGAACCCAGCACGCAGAACCTAGATTTGAGTTTGTTTCTCAAGGCTTAACCACTGAATTTGATGCACAATCCA
+ATTGCTTTAATCCAGCGGTACAATG
+>atpG
+ATTCTAACCGTAATCACGCTGAATTTATGCAAGAGCTTAATAAAACCGGTAACTATAATGATGAAATCAAAGATACGTTA
+AAAAGTATTTTAGATGGTTTTAAAGCGAATAGTGCTTGGTAGTAACGGAGAGATAAGATGGCAGGTGCAAAAGAGATAAA
+AACCAAAATTGCCAGTGTACAAAGTACACAAAAAATCACTAAGGCAATGGAAATGGTGGCAACCTCGAAAATGCGTAAAA
+CGCAGGATCGTATGGCTGCATCTCGTCCGTATTCTGAAACTATCCGTAACGTTATTAGTCATGTGTCTAAGGCAAGTATC
+GGTTATAAACATCCGTTCTTAGTTGAGCGCGAAGTGAAGAAAATCGGTATCTTGGTTATTTCAACAGATCGTGGGATGTG
+TGGTGGGTTAAATGTTAATTTATTCAAAACCATACTTAACCAAATAAAAAATTGGAAAGAACAAAATATTTCTACAGATT
+TGGGCTTAATAGGTTCAAAAGGGATTAGTTTTTTCCGTTCCTTTGGATTTAATATCAAAGGTCAGCTTTCTGGTTTAGGC
+GATACGCCCGCTCTAGAAGAGTTAATTGGTGTGGCAAATACAATGTTTGATGCTTATCGTAATGGTGAAATTGATGCAAT
+TTATATTGCATACAATAAATTTGTTAATACGATGTCGCAAAAGCCTGTTGTACAACAATTAGTTCCTTTACCAGAATCTA
+AAGACGATCATTTAAATGAAAGACAACAGACTTGGGATTATCTTTATGAGCCAGAACCAAAAGTACTATTAGATAGCCTT
+TTAGTTCGTTATTTAGAATCCCAAATTTATCAAGCGGTTGTAGATAA

modules/trueCoverage_rematch/listeria_monocytogenes.config

@@ -0,0 +1,20 @@
+#reference_file (fasta file full path)
+/home/mpmachado/INNUca/modules/trueCoverage_rematch/listeria_monocytogenes.fasta
+#length_extra_seq (int)
+200
+#maximum_number_absent_genes (int)
+0
+#maximum_number_genes_multiple_alleles (int)
+1
+#minimum_read_coverage (x, int)
+25
+#minimum_depth_presence (x, int)
+5
+#minimum_depth_call (x, int)
+10
+#minimum_depth_frequency_dominant_allele (0-1, double)
+0.60
+#minimum_gene_coverage (0-100, int)
+80
+#minimum_gene_identity (0-100, int)
+70

modules/trueCoverage_rematch/listeria_monocytogenes.fasta

@@ -0,0 +1,85 @@
+>abcZ
+CGACATACCTTCAAGTAAAAGCACCACAATATATTGGTAACGCCGTTCAAGAACTTGGAGATTACGTGGTTAATTTAATG
+CAAACGGGTGTTGATGACAAGAGTGACTTCATCCATATCATTTGGATGCTGATTCTCTGCTACGTACTGCTCGCTGCTGC
+CACTTTTATCCAAAGTATCATTATGACAGGGGTAGCTGGTAAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGA
+TGGAAAAACTATCGATTCGTTTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGTCGTTTTACTAGTGACTTAGATAAT
+ATTTCCAATACACTAAACCAAGCATTGATCCAGGTGCTATCCAACGTCGCGCTAATGATTGGTGTTATCATCATGATGTT
+CCAACAAAACGTGGAACTAGCCTTCGTTACTTTAATATCTGCTCCATTTGCGATTATTATTGCAACAGTGATTATTCGAA
+AAGCACGTAAATTCGTTGATGTTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGACAA
+AAAATCATTATCACAAATGGTTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAACAATATCGTTAAAAACGCCAC
+TTATAAAGGGCAAGTTTACTCCGGTTTACTTTTCCCAATGATGCAAGGTATTTCACTATTAAATACAGCTATCGTTATCT
+TCTTCGGTGGATGGTTAGCTCTAAACGGCGACCTTGAACGCACAGCCGCTCTTGGTTTAATCGTTATGTTCGTTCAATAT
+TCACAACAATTCTATATGCCACTTACACAAATTTCGTCCCAGTACAGCTTGCTACAACTAGCAATCACTGGTGCGCGCCG
+TGTTAGTGAAGTATTTGCAGAGGAAGAAGAAGTAGAACGCGAAAACTTACAAACAAT
+>bglA
+TTTTAACTATAAATCGGAATGTTACCGACGTAAGCCGGGCATAACCAAATATTTTTCTAAGTACCATGTTTTTTTGCATG
+TATTTAGAAAAGTATTTGGTTTTTTTCATAGATACTTTAAAATGTAGAAAAGGAGTTTTTAACATGCATACAAATACAGG
+ATTTCCGGCCGACTTTTTATGGGGTGGAGCTGCTGCTGCAAACCAATTCGAAGGCGCTTACAACGTCGATGGAAAAGGAC
+TTTCCGTTCAAGATGTTACTCCAAAAGGCGGATTCGGTCACATTACTGACGGTCCAACACCAGATAACTTAAAATTAGAA
+GGAATCGACTTCTACCATCGCTACAAAGATGACGTGAAACTTTTTGCCGAAATGGGCTTCAAGGTTTTCCGTACTTCCAT
+CGCTTGGTCCCGTATCTTCCCAAATGGTGACGAAACAGAGCCAAACGAAGCAGGACTACAATTTTACGATGATTTATTCG
+ATGAACTTCTAGCACATAATATCGAACCACTGATTACTTTATCTCACTATGAAACACCACTTCACTTATCGAAAACTTAC
+GACGGATGGGTAAATAGAAAAATGATCGACTTCTATGAAAACTATGTCCGCACCGTATTTAATCGCTATAAAGGCAAAGT
+AAAATATTGGCTAACATTCAATGAAATCAACTCGATTTTACACGCACCATTCATGAGCGGCGGTATTTCTACAAGCCCAG
+ATAAATTATCACAAAAAGACCTATACCAAGCTGTCCACCACGAACTTGTGGCGAGCGCGCTGGCTACAAAAATTGGTCA
+>cat
+AAAATGATATAGAATTGTTATGGAGGTATATACATATGACAGATAGAAAAAATTTAACGACGAATCAAGGTGTGCCAGTT
+GGTGATAACCAAAATTCAATGACAGCGGGACGTAAAGGACCTACTTTGATAGAAGATTATGTGCTTATTGAGAAATTGGC
+GCATTTTGATAGAGAACGAGTTCCTGAGAGGGTTGTACATGCTCGTGGTGCTGGTGCGCACGGGAAATTTGTTACTAAAA
+AAAGCATGAAAAAATATACAATGGCTAAATTTTTGCAAGAAGAAGGAACGGAAACAGAGGTTTTTGCTCGTTTTTCAACA
+GTAATTCATGGGCAACATTCTCCAGAAACATTACGTGATCCACGCGGTTTCTCCGTTAAGTTTTATACGGAAGAGGGAAA
+TTATGACTTTGTCGGAAATAATTTGCCAGTATTTTTCATTCGTGATGCGATTAAGTTTCCAGATGTTATTCATTCCTTGA
+AGCCTGACCCGCGCACAAATATTCAAGATGGCAATCGTTACTGGGATTTCTTTAGCCTTACACCGGAAGCTACGACAATG
+ATTATGTACTTATTCAGTGATGAAGGAACGCCGGCTTCTTACCGCGAAGTCCGGGGCTCTAGTGTTCATGCGTTCAAATG
+GATTAACGAAGAAGGCAAAACAGTTTATGTAAAACTGCGCTGGGTTCCAAAAGCGGGAATAGTGAACCTTTCGACGGAGC
+AAGCTTCTCAAATTCAAGCAAAAGAATTTAACCATGCAAGTCGTGATTTGTACGAAGCAATTGAAAATGGAGACTATCCT
+GAATGGGATTTATATGTGCAAGTGTTGGATCCGAAAGACTTAGATAGCTTTGATTTCAATCCATTAGATGCTACAAAAGA
+TTGGTT
+>dapE
+TGTAAATCATGCAGAGACTAAGCCATTTTTTATTTGGTAATTATAAGAAGGAGTTTGCCTTTATAGAGAACGGGAAAACA
+TAGAGTGGAATTCATAGAAAGAGGGCGTGAAATATGGACCAACAAAAAAAGATTCAAATTTTAAAGGACTTGGTAAATAT
+TGATTCGACTAATGGGCATGAAGAACAAGTTGCGAACTATTTGCAAAAGTTGTTAGCTGAACATGGTATTGAGTCCGAAA
+AGGTACAATACGACCTAGACAGAGCTAGCCTAGTAAGCGAAATTGGTTCCAGTAACGAGAAGGTTTTGGCATTTTCAGGG
+CATATGGATGTAGTTGATGCGGGTGATGTATCTAAGTGGAAGTTCCCACCTTTTGAAGCGACAGAGCATGAAGGGAAACT
+ATACGGACGCGGCGCAACGGATATGAAGTCAGGTCTAGCGGCGATGGTTATTGCAATGATTGAACTTCATGAAGAAAAAC
+AAAAACTAAACGGCAAGATCAGATTATTAGCAACAGTTGGGGAAGAAATCGGTGAACTTGGAGCAGAACAACTAACACAA
+AAAGGTTACGCAGATGATTTAGATGGTTTAATCATCGGCGAACCGAGTGGACACAGAATCGTTTATGCGCATAAAGGTTC
+CATTAATTATACCGTTAAATCCACTGGTAAAAATGCCCATAGTTCGATGCCGGAATTTGGTGTGAATGCGATTGATAACT
+TGCTGCTATTTTATAATGAAGTAGAAAAATTCGTGAAATCAATTGATGCTACTAACGAAATATTAGGCGATTTTATTCAT
+AATGTCACCGTAATTGATGGTGGAAATCAAGTCAATAGTATCCCTGAAAAAGCACAACTGCA
+>dat
+ATAATTGAAAAAATTAACTGCTGCAAAGCTTAGTTTTGCGGCAGTTTCTTTGTTTCATTAAGTTTTTAGATAGTTCCAAA
+AATTAACTATGCAAGGAGAGACTCGAGATGAAAGTATTAGTAAATAACCATTTAGTTGAAAGAGAAGATGCCACAGTTGA
+CATTGAAGACCGCGGATATCAGTTTGGTGATGGTGTATATGAAGTAGTTCGTCTATATAATGGAAAATTCTTTACTTATA
+ATGAACACATTGATCGCTTATATGCTAGTGCAGCAAAAATTGACTTAGTTATTCCTTATTCCAAAGAAGAGCTACGTGAA
+TTACTTGAAAAATTAGTTGCCGAAAATAATATCAATACAGGGAATGTCTATTTACAAGTGACTCGTGGTGTTCAAAACCC
+ACGTAATCATGTAATCCCTGATGATTTCCCTCTAGAAGGCGTTTTAACAGCAGCAGCTCGTGAAGTACCTAGAAACGAGC
+GTCAATTCGTTGAAGGTGGAACGGCGATTACAGAAGAAGATGTGCGCTGGTTACGCTGTGATATTAAGAGCTTAAACCTT
+TTAGGAAATATTCTAGCAAAAAATAAAGCACATCAACAAAATGCTTTGGAAGCTATTTTACATCGCGGGGAACAAGTAAC
+GGAATGTTCTGCTTCAAACGTTTCTATTATTAAAGATGGTGTATTATGGACGCATGCGGCAGATAACTTAATCTTAAATG
+GTATCACTCGTCAAGTTATCATTGATGTTGCGAAAAAGAATGGCATTCCTGTTAAAGAAGCGGATTTCACTTTAACAGAC
+CTTCGTGAAGCGGATGAAGTGTTCATTTCAAGTACAACTATTGAAATTACACCTATTACGCATATTGACGG
+>ldh
+TCGAAATGAAAGATCATCAAAAAATTATTTTAGTTGGCGACGGAGCAGTTGGTTCTAGTTACGCATTTGCTTGTGTAAAT
+TTAAGCATTGGACAAGAATTCGGCATTATTGACATAGATAAAGACAGAACAATTGGGGATGCAATGGATTTAAGCCATGC
+CGTTCCATTTTCTACACCGAAGAAAATCTACTCAGCAAATTATAGCGACTGCCACGATGCGGACTTAGTTGTTGTAACTG
+CCGGTACTGCTCAAAAACCTGGTGAAACTCGTTTAGATCTAGTAAATCGTAATATCAAAATCATGAAAGGCATCGTGGAT
+GAAGTTATGGCAAGCGGATTTGATGGTATCTTCTTAATCGCTTCTAACCCAGTAGACATCTTAACTTACGCTACATGGAA
+ATTCTCAGGTCTTCCAAAAGAACGTGTTATCGGTTCTGGAACAAGCCTTGATACAGCACGTTTCCGTATGTCAATTGCTG
+ACTATCTAAAAGTAGATGCTCGTAACGTCCATGGTTACATCCTTGGCGAACACGGCGATACAGAATTCCCAGCATGGAGC
+CACACAACTGTCGGCGGCCTTCCAATTACTGAATGGATTAGCGAAGATGAACAAGGTGCAATGGATACTATTTTCGTAAG
+TGTTCGTGATGCAGCTTATGAAATTATTAATAAAAAAGGCGCTACATTCTACGGCGTTGCTGCAGCTCTTGCTCGTATTA
+CAAAAGCAATTCTAAATAACGAAAATGCGATTTTGCCACTTTCTGTTTATTTAGATGGCCATTACGGTATGAACGATATT
+TATATAGGTGCACCAGCAGTCGTTAACCGTCAAGGCGTTCGCCATATTGTTGA
+>lhkA
+GGGTGCTTGTCTCCCACTCATTAAAAGATTATTTTTACCAAAGCCAAGTAGATGACTTAACAAGTTATGGGCAAACGATT
+TCCAGGGATATTCGTTATTCGCCACAAGATGCAACGATGCAAGTTTTGAACACGTATCAGCGAATTTTAGATGTTAAAAA
+AATTCATTATACAATCAAGAATGCCAACGACGAAACCATTTATCCAACACAGATGAATCAGCCTTTACCTAAGGATTTCT
+CTATTTCTGCGGATGATAAGAAAAAGCTTGAAAGTGGTGAAACGGTTAGTAAGAAAATAGATAATCGCTTTAACAAAGAA
+ATGACAATTGTGTACGTCCCAATAATGAATGGCGATAAATTTGTCGGTTCTATCGTGCTGAATTCACCCATTAGCGGTAC
+GGAGCAAGTAATTGGCACGATTAACCGCTATATGTTCTACACTATTTTACTTTCTATAACGGTAGCACTTATTCTTAGCG
+CAATCTTGTCCAAACTACAAGTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGGCAATTACAAC
+GCTCGCTTGAAGGAAAATAATTTTGATGAAATTGGTGCACTCGCCATTGATTTCAATAAAATGACACAAACCCTTGAAAC
+ATCTCAAGAAGAAATTGAACGACAAGAGAAACGGAGACGCCAGTTTATTGCTGATGTTTCTCATGAAATGCGTACCCCGC
+TCACAACGATTAGTGGCCTCACGGAAGGTTTAGTAAATGATATTATCCCAAAAAGTGAAACCGATCGTTGCATAGCACTC
+ATTGATACAGAAGCTAGACGTTTAACGAAACTAGTCAATGAAAATTTAGATTATGAAAAAATACGCAGTAACAAAATCAA

modules/trueCoverage_rematch/streptococcus_dysgalactiae.config

@@ -0,0 +1,20 @@
+#reference_file (fasta file full path)
+/home/mpmachado/INNUca/modules/trueCoverage_rematch/streptococcus_dysgalactiae.fasta
+#length_extra_seq (int)
+200
+#maximum_number_absent_genes (int)
+0
+#maximum_number_genes_multiple_alleles (int)
+1
+#minimum_read_coverage (x, int)
+25
+#minimum_depth_presence (x, int)
+5
+#minimum_depth_call (x, int)
+10
+#minimum_depth_frequency_dominant_allele (0-1, double)
+0.60
+#minimum_gene_coverage (0-100, int)
+80
+#minimum_gene_identity (0-100, int)
+70