diff --git a/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst b/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst index ec6c0fb477026bc66abe8fdfc7460f57191a5b31..ebe711bc93e6b5658d59e8a7b291ca392b0d9b8b 100644 --- a/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst +++ b/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst @@ -1,4 +1,5 @@ orig_name to_annotate gsize nb_conts L90 B2_A3_5.fasta-changeName.fna B2_A3_5.fasta-changeName.fna 120529 5 4 H299_H561.fasta-all.fna H299_H561.fasta-all.fna 13259 7 3 -A_H738.fasta-all.fna A_H738.fasta-all.fna 20031 5 1 +A_H738.fasta-all.fna A_H738.fasta-all.fna 20066 5 1 +complete_genome.fna complete_genome.fna 88 1 1 diff --git a/test/data/annotate/exp_files/exp_A_H738.fasta-all.fna_prokka-split3N.fna b/test/data/annotate/exp_files/exp_A_H738.fasta-all.fna_prokka-split3N.fna new file mode 100644 index 0000000000000000000000000000000000000000..f284e70de0bce8992f89f5d8611b735ef13b0680 --- /dev/null +++ b/test/data/annotate/exp_files/exp_A_H738.fasta-all.fna_prokka-split3N.fna @@ -0,0 +1,14 @@ +>1_H738_S10 L001_R1_001_(paired)_contig_1 +GAAATATAGGGGCAAATCCATTGTGTATTCCTGACGGCAAAAATAAGGAATATAAAGAAATGATTGCTTTGGTTTCTTACAACACATCATTCCCTTTTCATTTAATAAAGCGGCATGATACAAAGTGAACATGATTTCGATTTACATTGCCACCATACCGCTTCAGACAACCGGTACATTACTTTGTTATAAGACGTGATATATAATTCAAAACAACGTGGTTTTGATTATTCATATCTCATAATAAAAGTCGCGTCAGCATTTGCTTGCCCTGCTGATGCACTTGTACCGGTGCCTTTATAACGTGCAGAAAAATGAAGAACGTTGGTCCCGGGGATCAAGTTCTGGTTGGTTGAGAAGCTATTCCCATCAGGTTTGAGAATTGCGGATGTATTATCAAGTATTTCAATACCGACACCCGTTGCTGTTGTTGTATTGGTACTGGATGCAATGGCCAATAAATTATCATTGATTGCATCAGCCTGACCAGAAAATGCAACGGCAGCATTAGCGGCAACAACAGGATCGCAGTCGTTCAACTGAATGGTGAATGGAATTAATGCAGAGGTATTACCAACAGCATTGAAAATATCGGTACGATATTGACCGAGTGTGACAACCTGGTCTGCCGAGTCAGTATTCACTGAACAGGCAGCATTCACCAGTTCGCCTTCAAAGTGAATTGTACCGCCATCTACAACGGCAGCATAACTACCCGTAGCGGCGAATAGTGCGGCAGCCAGCGCAGACGAAATAAATCTTAATTTCATATATATTCCTTCAATCTCATTTATCGACTCCACATCCGTATATAACCGATTACTTTATTTAAGACACTGATAGTAGTAAATTCCTTTTTATCCTCTAAGAATGTCTTAATTGAAAATATGCACTCTATTCTAAAAAATAGAGAGCCCCGTTAGATGAATACTTCCGCGCAAAATATATTCAACACAAATATAGACCTGAAGCGGTAAATTACCAGGCTGAAAATTCTTTTTATATTGTCAGGTATTTCTTAAATTATCTTAATCCTTAGACAAGGAAATAAATCAGTTCCAGATTTACAACGCCATCATGGACGAAAAATGAAGCTTTCAGTCTCAGCGACGGTGCGCCTCACCTTCGCAAGAGGTCGCTTCACGCGATAAATCTGAAACGAAACCTGACAGCGCGCCCCGCTTCTGACAAAATAGGCGCATCCCCTTCGATCTACGTAACAGATGGAATCCTCTCTCTGATGGCAGCAAAGATTATTGACGGTAAAACGATTGCGCAGCAGGTGCGCTCTGAAGTTGCTCAAAAAGTTCAGGCGCGTATTGCAGCCGGACTGCGGGCACCAGGACTGGCCGTTGTGCTGGTGGGTAGTAACCCTGCATCGCAAATTTATGTCGCAAGCAAACGCAAGGCTTGTGAAGAAGTCGGGTTCGTCTCCCGCTCTTATGACCTCCCGGAAACCACCAGCGAAGCGGAGCTGCTGGAGCTTATCGATACGCTGAATGCCGACAACACCATCGATGGCATTCTGGTTCAACTGCCGTTACCGGCGGGTATTGATAACGTCAAAGTGCTGGAACGTATTCATCCGGACAAAGACGTGGACGGTTTCCATCCTTACAACGTCGGTCGTCTGTGCCAGCGCGCGCCGCGTCTGCGTCCCTGCACCCCGCGCGGTATCGTCACGCTGCTTGAGCGTTACAACATTGATACCTTCGGCCTCAACGCCGTGGTGATTGGCGCATCGAATATCGTTGGCCGCCCGATGAGCATGGAACTGCTGCTGGCAGGTTGCACCACTACAGTGACTCACCGCTTCACTAAAAATCTGCGTCATCACGTAGAAAATGCCGATCTATTGATCGTTGCCGTTGGCAAGCCAGGCTTTATTCCCGGTGACTGGATCAAAGAAGGCGCAATTGTGATTGATGTCGGCATCAACCGTCTGGAAAATGGCAAAGTTGTGGGCGACGTCGTGTTTGAAGACGCGGCTAAACGCGCCTCATACATTACGCCTGTTCCCGGCGGCGTTGGCCCGATGACGGTTGCCACGCTGATTGAAAACACGCTACAGGCGTGCGTTGAATATCATGATCCACAGGATGAGTAACATGGCGACATTTTCTTTAGGTAAACATCCGCACGTTGAGCTGTGCGACTTGCTGAAACTGGAAGGCTGGAGCGAAAGCGGCGCGCAGGCGAAAATCGCGATTGCCGAAGGCCAGGTGAAAGTCGACGGTGCGGTTGAAACGCGCAAACGCTGCAAAATCGTCGCCGGTCAGACAGTGAGTTTTGCAGGTCACAGCGTACAGGTTGTTGCCTGATCCCTTTCCCGGCCTGTATCAACAGGCCGGTTCTCTTTTCAGACTTTTGCCCTCTACGCCCCGTTCATCCATGCTGATAGCATCGACATTTTGCCGAAGCGACCATCATGCCAACCGTTATTACGCACGCCGCCGTTCCCCTATGCATTGGTTTAGGGTTGGGTTCGAAAGTCATCCCTCCGCGTCTGTTATTTGCCGGAATCATCCTGGCGATGCTGCCCGACGCCGACGTATTGTCGTTTAAATTTGGCGTTGCTTACGGCAATGTTTTTGGTCATCGCGGGTTTACCCATTCGCTGGTGTTTGCGTTTGTTGTCCCGCTGTTATGTGTGTTTATTGGACGCCGATGGTTCAGGGCTGGGCTGATTCGCTGCTGGCTGTTTTTAACCGTCTCGTTGCTATCGCACAGCTTGCTGGATTCGGTAACCACTGGCGGTAAAGGCGTTGGCTGGCTGTGGCCGTGGTCAGATGAACGCTTTTTCGCTCCCTGGCAGGTGATAAAAGTCGCGCCGTTTGCATTGTCTCGTTACACCACGCCGTACGGGCATCAGGTGATTATTTCTGAATTGATGTGGGTGTGGTTGCCGGGGATGCTACTGATGGGAATGTTGTGGTGGCGCAGACGATAACCGGATGCGAAAACTCGCATCCGGCAATAGCGCAATTACTTACGACGCCAGGTGGTCCCTTGCGGGCCATCTTCCAGCACGATCCCCATCTCGTTAAGACGATCACGCGCCGCATCCGCCGCCGCCCAGTCTTTCGCTTTACGGGCATCCAGACGCTGTTGAATTAACGCTTCAATCTCAGCCACTTCGCT +>2_H738_S10 L001_R1_001_(paired)_contig_1 +GTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGGTTCTTGCTCCAGCAGGCCCAATACAGCGGAAAGTTTACGCAGGTGAGATGCCATTGCATTCGCCGCTGCCATATCTTCTGCTTTCAGACGGTTTACTTCACGCGCCATATCAAACAGTACGGAATAGGCTTCCGGGGTGTTGAAATCGTCGTCCATCGCTTCAATAAAGCGCGCTTCAAACGCTTCGCCACCGGCAGGCGCAACGGTTTTATCTGTGCCGCGCAGCGCAGTGTAGAGACGCTCCAGCGCCGCACGCGCCTGCTTCAGGTTCTCTTCGCTGTAGTTCAACTGGCTGCGATAGTGGCCCGACATCAGGAAGTAACGCACGGTTTCCGCGTCGTAGTATTTCAGCACATCGCGCACGGTAAAGAAGTTACCCAGCGATTTGGACATCTTCTCGCGGTCAACCATCACCATCCCCGAGTGCATCCAGTAGTTCACATACTGACCATCATGGGCACAGGTGGACTGCGCGATTTCGTTTTCGTGGTGCGGGAACATCAGGTCTGAACCGCCGCCGTGGATATCAAAGTGGTTACCCAGCTGCTTGCAGTTCATTGCCGAACATTCAATGTGCCAGCCAGGACGACCCGCGCCCCACGGAGACGGCCAGCTCGGTTCGCCCTCTTTCGACATCTTCCACAGAACGAAGTCCATTGGGTTGCGTTTGTCGTCGACCACGTCAACGCGCGCGCCTGCCTGCAGCTGGTCGAGATCCTGACGCGACAGCACGCCATAAGTTGGATCGGTCGGGACGTCGAACATCACGTCGCCGTTGTCCGCCACATAAGCGTGACCTTTGGCGATCAGTTGTTCAGTGAGTTCAATAATTTCTGCGATATGGTGCGTCGCGCGCGGCTCCATATCCGGGCGCAGAATGTTCAAAGCATCAAAATCTTTGTGCATTTCGGCGATCATGCGATCCACCATCGCCACAAAGCTTTCGCCATTTTCATTGGCGCGTTTGATGATTTTGTCGTCGATATCGGTAATGTTGCGCACATACTTCAGTTTATAGCCGAGGAAACGCAGATAGCGCGCAACCACGTCAAAAGCAACAAAGGTACGCCCGTGACCGATATGACAGAGATCGTAAACGGTGATTCCACACACGTACATGCCGACTTCCCCGGCGTGAATAGGCTTAAATTCCTCTTTTTGGCGTGTCAGAGTATTGAAGATTTTTAGCATCGAAGATTCCGTTTAGACATGTGTGGGTAATTGAGTTGCGTATAATACCCATATTTCCCGCGCGAATCAGCATACATTGCGTGATGATCCGATCGTGCGGTTATGCTATAACACCACCCTATATATGACCCGAACTGGGTTGAAGCACCAATCAAACGGAACAGGATGCAAAAATGGTTACTTTCCACACCAATCACGGCGATATTGTCATCAAAACTTTTGACGATAAAGCACCTGAAACAGTTAAAAACTTCCTGGACTACTGCCGCGAAGGTTTTTACAACAACACCATTTTCCACCGTGTTATCAACGGCTTTATGATTCAGGGCGGCGGTTTTGAACCGGGCATGAAACAAAAAGCCACCAAAGAACCGATCAAAAACGAAGCCAACAACGGCCTGAAAAATACCCGTGGTACGCTGGCAATGGCACGTACTCAGGCTCCGCACTCTGCAACTGCACAGTTCTTCATCAACGTGGTTGATAACGACTTCCTGAACTTCTCTGGCGAAAGCCTGCAAGGTTGGGGCTACTGCGTGTTTGCTGAAGTGGTTGACGGCATGGACGTGGTAGACAAAATCAAAGGTGTTGCAACCGGTCGTAGCGGTATGCACCAGGACGTGCCAAAAGAAGACGTTATCATTGAAAGCGTGACCGTTAGCGAGTAATCGTGGCGACACTCTTTATTGCAGATCTTCATCTCTGCGTGGAAGAACCGGCGATCACCGCCGGTTTTCTGCGTTTTTTAGCGGGGGAAGCCCGCAAGGCCGACGCGCTGTATATTCTTGGCGATCTGTTTGAAGCATGGATTGGCGACGACGATCCCAACCCACTCCATCGCAAGATGGCGGCGGCGATCAAAGCGGTGTCCGATTCCGGCGTTCCCTGTTATTTCATTCATGGCAACCGTGATTTTCTGCTCGGCAAACGCTTTGCCCGTGAAAGTGGCATGACGTTATTGCCGGAAGAAAAGGTGCTCGAACTTTATGGTCGCCGGGTGTTGATTATGCATGGCGACACGCTGTGCACCGATGACGCGGGTTATCAGGCTTTTCGCGCCAAGGTCCACAAACCCTGGCTGCAGACGCTATTCCTCGCCCTGCCGTTGTTTGTGCGCAAACGCATTGCCGCGCGAATGCGCGCGAACAGCAAAGAAGCCAACAGCAGTAAATCGCTGGCGATCATGGACGTTAACCAAAACGCGGTGGTCAGTGCGATGGAAAAACATCAGGTGCAATGGCTGATCCACGGGCATACCCATCGCCCGGCGGTGCATGAACTTATCGCTAATCAGCAACCTGCTTTTCGCGTGGTACTGGGTGCCTGGCATACGGAAGGTTCAATGGTGAAAGTCACGGCGGATGACGTTGAGCTGATTCATTTTCCGTTTTAAAAAACCCGCAACTTTGCTGATTTCACAGCCACGCAACCGTTTTCCTTGCTCTCTTTCCGTGCTATTCTCTGTGCCCTCTAAAGCCGAGAGTTGTGCACCACAGGAGTTTTAAGACGCATGTCTTCCCGCAATAATCCGGCGCGTGTCGCCATCGTGATGGGGTCCAAAAGCGACTGGGCTACCATGCAGTTCGCCGCCGAAATCTTCGAAATCCTGAATGTCCCGCACCACGTTGAAGTGGTTTCTGCTCACCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAAGCGCCGAAGAGAACGGTTATCAGGTGATTATTGCGGGCGCAGGCGGCGCAGCGCATCTGCCAGGCATGATTGCCGCCAAAACGCTGGTGCCGGTGCTGGGCGTGCCAGTACAGAGCGCCGCACTGAGCGGTGTCGATAGCCTCTACTCCATCGTACAAATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATTGGTAAAGCTGGCGCGGCAAACGCGGCGTTACTGGCAGCACAAATTCTTGCGACTCATGATAAAGAACTGCACCAGCGTCTGAATGACTGGCGCAAAGCCCAGACCGACGAAGTGCTGGAAAACCCGGACCCGCGAGGTGCGGCATGAAACAGGTTTGCGTCCTCGGTAACGGGCAGTTAGGCCGTATGCTGCGTCAGGCAGGCGAACCGTTAGGCATTGCTGTCTGGCCAGTCGGGCTGGACGCTGAACCGGCGGCGGTGCCTTTTCAACAAAGCGTGATTACCGCTGAGATAGAACGCTGGCCGGAAACCGCATTAACCCGCGAGCTGGCGCGCCATCCGGCCTTTGTGAACCGCGATGTGTTCCCGATTATTGCTGACCGTCTGACTCAGAAGCAGCTTTTCGATAAGCTCCACCTGCCGACTGCACCGTGGCAGTTACTTGCCGAACGCAGCGAGTGGCCTGCGGTGTTTGATCGTTTAGGTGAGCTGGCGATTGTTAAGCGTCGCACTGGTGGTTATGACGGTCGCGGTCAATGGCGTTTACGCGCAAATGAAACCGAACAGTTACCGGCAGAGTGTTACGGCGAATGTATTGTCGAGCAGGGCATTAACTTCTCTGGTGAAGTGTCGCTGGTTGGCGCGCGCGGCTTTGATGGCAGCACCGTGTTTTATCCGCTGACGCATAACCTGCATCAGGACGGTATTTTGCGCACCAGCGTCGCTTTTCCGCAGGCCAACGCACAGCAGCAGGCGCAAGCCGAAGAGATGCTGTCGGCGATTATGCAGGAGCTGGGCTATGTGGGCGTGATGGCGATGGAGTGTTTTGTTACCCCGCAAGGTCTGTTGATCAACGAACTGGCACCGCGTGTGCATAACAGCGGTCACTGGACACAAAACGGTGCCAGCATCAGCCAGTTTGAGCTGCATCTGCGGGCGATTACCGATCTGCCGTTACCGCAACCAGTGGTGAATAATCCGTCGGTGATGATCAATCTGATTGGTAGCGATGTGAATTATGACTGGCTGAAACTGCCGCTGGTGCATCTGCACTGGTACGACAAAGAAGTCCGTCCGGGGCGTAAAGTGGGGCATCTGAATTTGACCGACAGCGACACATCGCGTCTGACTGCGACGCTGGAAGCCTTAATCC +>3_H738_S10 L001_R1_001_(paired)_contig_1 +CGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAGAGTAAGTTCGGTTAACTGGTGCTCTATTCTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACCGATCCGGTACCCATTGTAGGCCTGATAAGATGCGTCAAGCATCGCATCAGGCATTGTGCACCAATTGCCGGATGCGGCACCGGTTGTAGGCCTGATAAGACGCGTCAAGCGTCGCATCAGGCACAAATGTCTAATGCCTACGACTACAGCGAAATACAGGTCCCCGCTTCGCCCGCCAGCGTCTCTTCAATTCGCGATAACGCCCCAATCCACGCGGGTTTACCACGGCTTCTGACATAACCACTCACCGCCGTTACCTTCGGCCCCATCGAACCATCGGCTTTGGCAAATGGCGCTAACTCATCCGGTGTGGCATGGCGAATGGCACGTTGCTGCGGCGTTCCCCAGTTTTCATATACCGCATCAGCATCGGTGAGGATCACCAGTCCATCTGCATTAATCTGCTCGGCGAGCAACGCAGCGGCGAGATCTTTATCAATCACTGCTTCACTCCCTGCTCCGTCATCCGTCACAGGCACACCGCCGCCGCCACTGCAAATCACCACATGCCCCTCTTTTAGCAACAACTCGATGGCTTCGCTGTCGAGAATTTTACGCGGTTGCGGAGACGCCACCACCCGGCGCAAATATTTACCATCACGTTTCATCTGCCAGCCGTAAGCCGCTTCCAGTGCCTCTTGTTCTTCTGGCTGATAAACCGGACCAATAAATTTCTCTGGCTGCAAAAACGCCGGATCATCAGGCGAAACCTCAATGCGCGTCAGCACCGTCGTCACGGGCGGCATCTGCGGCTGTGCGCTCAAACTCTGCGCCAGCATATAGCCAATCATCCCCTGGCTTTCCGCAACCAGCACATCCAGCGGATACGGTTCTACCTCTTTCCACGCCAGATTCTGCAATGCCAGCAGCCCCACCTGCGGCCCGTTGCCGTGAACAATCGCCAACCGATAAGAACGGGCCAGGCGTGCCAGCGCGGGTACAGCACTGGCGATATTGCGATATTGATTTTCTGCCGTCAGCGCCTCACCGCGCTGGAGTAAGGCGTTGCCCCCAAGAGCCACAACCAGTGTTTTCATGGTTTTCCTTGTAATAATTGTTGGCCAAGCCAGAACCCCAGCAGCGTATCTGCCCCTGACGTATGCCCCAGCGCCAGCAGCGAATCAATCGCAACAGCGGTACGTTTCGGGCAACTCAGAGCATGAACAAAGTGCAGGAGTGGCGAGGCGAAATATCCTTGCGCGGCATAACGTAAATAACTGACGCTCACCGCTGTGGTAACGAGTTGCAGATTGTCGGAACAGGCAAAAAACGGACGACCGGAGCGCGCATCTAAAGCGCCATAATACCAGGCCGCCAGCAGCATTCCGCTCAGCGTGTCATCATGACTCGGCGTTAATCCGGGGCCTTTACCCAGCCAGTGCCGCCAGTCGGTCTTAACGCCATTGAGCGCGGCCTGAAAACAGTGACGAAACTGGCGTAACTCAGCAGGCAGCGGATCGCTTGCCGCCAACGCCAGTGGCCCGAAAAGCCCGGTTTCCTCCGCGCGTTGCATCCATGCAGCTGCAAGTGGTTGAGGATGCGCAGGCGGCGTAATACGCAGCAAACAATAACGCTGTGGCTGTTTAACCGTGAAACGCCCGAGGCGAATCCCTTGAGCCACAACCTGTGGTCGTTCATTGCCGCATAATCCACCGCATAACGCATCGAATTGCGCACGGCGAAGCACCCATCCTCCGGGGCCGAAACCACTACCCTGACGATGCAACGTTAACAGTTCGCCGCTTTCCGTCATCAGGTTAATCGCCCGCCGCCACACTCCCGCTAACCGCCAGGACTGGCGATAATTCGGTGCGCTACTACTGGCAAGCAGAGGATGGATGATCGTCATTGCGCGTTCCTCAACCAATACCCATGCTTTCAGCCAGTGCTTCCAGCGCCTGTTCAAAGCACGCCAGCGGTGCCCGCACGGTGCCTGCGCCAATCTGCCCGATCCCCGCCTCTTTATGGGCGATACCGGTATTGATGAGTGGCGTAATGCCGGTTTCTACCACGCGACGAATGTCCAGCCCCAGGCACGCGCCCTGAAAATCCCAGCTTGGGATCTGCAACTGCATATTGCGTTCAAGGTAAATTTCCGCCATCTCTTCAGATACCGCTCTTGCCGCTTCCATGCCACCCGCACCGACAAAGCGCGTTACGCCAGGCGCTGCGATCATTGCCGCACCTCCGATACCAAAGGTTTCGGTAATCGCGCTATCGCCCATATCCGGGTTCGCCTGCTCCTGCGAGAAGCCGGTGAAAAACAGACCTTGCGGAGTGTTTACAGGCGCAGTAAACCAGCGTTCGCCCAGCCCGCTTACCCGAATCCCGAACATATTGCCGTTGCGGGTCATTGCCGTGACGATGCTGCCTGCGCGGATCATCGCGCCAGCATCCATCGCCGCCTTGCAGTAAGCCATCGCGAGGTTGAGGAAGAACTGATCGGTCACGCTGAGGAAATCCATCACTTCGGCGATGTGCTGTTTATCATGATCGAGGCGAGCAATTTGTGGGGCCAGCGCACGCATTAACAGTGCAGAGGAAGCAATATTGCGTTGATGGAACTCATCGCCCATCGTAATGCCCTGCGCCATCATCGCCGTGAGATCGATACCGCGCTCCATGCGCCCCAGCGCCGCGCTTAATACTGGCATTAACACATCGCGCATCCAGCGATGGCGAGTCAGGACATCTTCGCCGTAAGCGCCAAAACGCATCACTTTGCCGATACCTTCGTTGAGGTTGCAGTACGCCCGGTTGCCGTCGGTCACGTTCTCAACCACCAGCATCGGCATACTGGCAGAAGTAATACCGCCCATTGGCCCGACGGCATTCACATGGTGACAAGGAATGAAGTTCACTTCCCCCTGCTCCAGTATTGCCAGCGCCTGCGCTTCATCTTTCGCCCAACCTTCGAACAGACATGCGCCCACGCACGCCCCTTTCATGGGTCCGGTCATCTCCTGCCAGCGCATTGGCGGCCCGGCGTGAAGCAGTGTTTTGCCCTCGTTTAGTTCGCTGATAAGTGAAGAAGCCGGTTGCACATCCAGCCAGTGTGGACGAGCGCGACGAATTTGTTCGATAACCGCAGCATTGGCTTGCGCCACTGATGTAAACATGGGAACCCCTTATTGCAAACGTTCTAATAAACGAGCCAGTTTTTTATTGCCACCGGCGACTGGCGACCATTGGTAATGCACAACCGGTTTGCTGGCGCTTTGTAGCTCCAGCGCAAAGCTGCGTAATCCGATGTTAATCACGGCGACGTTTTCCAGTAATGACGGTGTGTGTTGCTGTGCGGCAGGCGAGAGCGGATGAATTAACGCTGCCGCCAGCAAGGTGGCTTCCGGTAGCGAACTCACGACCGCAATCCCCGCATCTTCCAGCGTGGCGATTTGCTGCGAGCGGCATTGCGGGTCACGTTCAGTGCCTGTCACCGTGGCAATGGCATACAGTGGTTGATTATCTAAACGCGCGGCACAGGCTTTTTGCCAGGCGCTCACCAGCGAGGCGGCAGGATCGGCGGTCGCACCGAAGCCAATCACGACATCAAGCAGCAACACGCGCACTTGCGGTTTAGCGCCGAGATCGGCAATTAACTGGTTGCGTAAGGTTGGGTCGATCATCGGATGGGGACGCCCGACGGTGTAGAAATCATCGCCGAGGTCAATAATCTGGTGGCTATCGGCGTCCAGCATCATGCCATGTTGATGGGTATCGTCGGCTTCCACGCCAAGGTGTCCGGCAAGTAATCCCGCCGCTTCGGCAGCCAGCGTACCGCCGGTATACAAACCGCAAATAAATCCGCTGCTGACAGGCGCTATTGCGTTACGTCGCGCCGTGACGCGTGAAAGCAGGCAAGCCAGGCGTGCGGCCTCATCCAGCGAGGAGGCAAACCAGACATTCTCGTCGCGGGCCACCGCCGGGGTATAACCTAAAAACAGCGCCACCGTCGGTTTGCCGGTTGCTTTCATGGCATTAACAATTTTCAGACGCACAGCTTCGGCAGGTGGTTTTGAAACAAATGCCAGCACTTCGCTTTTCTCGTCTGCACTGAGCATTTCCAGCGCTGTTAGCGCACTGATGCCGCCCACTTCACGGCTGAGGTCGCGCCCGCCAAGGCCAATCGCGTGAGTAATTCCCTCCCCTGCCAGCGCAATCTGCGAACACAGCTCCTGAATCCCGGTACCGGAAGCGCCAATGACGCCAATATTGCCTTCCGGCATCACGTTAGCAAAAGCCAGCGGTGTGCCGGCAATCATCGACGTACCGCAGTCCGGCCCCATCACCAGCAAGCCTTTTTCCCGCGCGCGGGTTTTAAGTTGGATTTCATCTTCCAGCGTGACGTTATCGGAGAACATCATCACGTTGAGGTTGCGATCCAGCGCCTGGTTTGCCAGCTCCGCCGCATACTCGCCAGCCACTGAAATCAGCGCCAGATTGGCATCGGGTAATTTCTGACAGGCACTGTCCCAGCGACGCACCTGCATCAACGCCTGGCTGCTGCCTGACCCCTGCGCCAGTTGTTTTAGCGCCTCTTCAAGCTGCTGCATAATCGCCTGCGCGATCCCCGCATCCGCCGCTTCGCTACGAATTGCCACGCAAATATCGTTCGGCGTGGCGTTATTAAAATCGTCATGCCAGAAACCTGTGGTATCTAATAACGCTTTATTGGCGGGCGTACCCATCATTACGGAAACATCATCAACATTTTCTGATTCGCTGAGTTTTCGTGAAATAATCATTAAACTGACCGAATCCTGAAAACACCCTTTTTTAATAAAGGCGTGGATCATAACAACTCCTTAAAAATTGCACCCATGGCAATTGCACGAGCAGTGTTAATGTGGCGATTACGGTATCGATGACAACGAGTAAATAAGGTGATGAATATCACACAGGAATTATTAACAAAAGAATTCAAATAACCACCAGGCTATTACTCATTATTTTTTAATAAGCGTTGTTGTTTTAAAAATCAGGTTAAAAGTGAGCGGATTATCAAATAAATTCTAACTATATTTTTTTGCCTGTCTGGATCACATAATCCAGATATTTTCCCTGTATGTTAATTGCAGTCATGCTTCACACCGTCGTTAAAAAGGAAGACAGATGAAAATCAGTCGGGAAACACTCCACCAGCTAATTGAGAATAAACTCTGCCAGGCTGGGTTAAAACGTGAGCACGCTGCAACCGTGGCTGAAGTATTGGTTTACGCCGATGCCAGAGGGATCCACTCTCATGGCGCGGTGCGCGTGGAATACTACGCGGAACGCATTTCAAAAGGCGGCACCAACCGCGAACCGGAGTTTCGTCTTGAGGAAACCGGGCCGTGCTCGGCAATTTTACATGCCGACAATGCCGCCGGACAGGTCGCGGCGAAAATGGGTATGGAACATGCCATCAAAACCGCCCAGCAAAATGGCGTTGCGGTGGTCGGTATCAGCCGGATGGGTCACAGCGGCGCAATCTCTTATTTTGTGCAGCAGGCAGCCCGCGCCGGATTCATTGGCATTTCGATGTGCCAGTCCGATCCAATGGTGGTGCCGTTTGGCGGCGCGGAAATTTACTACGGTACTAACCCCCTGGCCTTTGCCGCGCCGGGAGAAGGCGACGAGATCCTTACCTTTGATATGGCGACTACCGTACAGGCATGGGGAAAAGTGCTCGACGCCCGCTCGCGTAATATGTCTATCCCGGATACCTGGGCGGTCGATAAAAACGGTGTACCAACAACCGATCCGTTCGCGGTACATGCTCTGCTCCCCGCCGCCGGGCCAAAAGGGTATGGCCTGATGATGATGATTGACGTCCTCTCAGGCGTCTTACTCGGCTTACCGTTCGGGCGACAGGTTAGTTCGATGTATGACGATTTACACGCAGGGCGTAATTTGGGGCAATTACATATAGTTATTAATCCGAACTTTTTCTCCTCCAGCGAATTATTCCGTCAACATCTTAGCCAGACCATGCGCGAATTAAATGCCATTACCCCCGCGCCCGGTTTTAATCAGGTTTATTATCCCGGACAGGATCAGGATATTAAACAACGCAAAGCCGCCGTCGAAGGCATCGAAATTGTTGATGATATTTACCAGTATTTAATTTCCGACGCGCTTTATAACACGTCATACGAAACGAAAAATCCCTTTGCGCAATAATTATTGAGACAGGACTTTCTTATGATTACACATTTCCGTCAAGCTATAGAAGAAACGCTGCCCTGGCTTTCCTCTTTTGGCGCTGACCCAGCGGGTGGGATGACCCGTTTACTTTATTCGCCGGAATGGCTGGAAACCCAGCAGCAATTTAAAAAAAGAATGGCAGCAAGCGGGCTGGAAACACGTTTCGATGAAGTGGGGAATTTATACGGTCGCCTGAATGGCACCGAATATCCACAGGAAGTGGTTCTGAGCGGTTCGCATATCGATACCGTGGTTAACGGCGGTAACCTTGACGGGCAATTCGGCGCGCTGGCGGCGTGGCTGGCAATTGACTGGCTGAAAACGCAATACGGCGCGCCGCTACGTACGGTCGAAGTGGTGGCGATGGCAGAAGAAGAAGGCAGCCGCTTCCCGTATGTCTTCTGGGGCAGTAAAAATATTTTTGGGCTGGCGAATCCTGACGACGTGCGGAATATCTGTGATGCCAAAGGAAATAGTTTTGTCGATGCGATGAAGGCTTGCGGATTTACTCTTCCGAACGCCCCACTAACTCCGCGTCAGGATATTAAAGCCTTTGTTGAACTGCATATTGAACAGGGCTGTGTGCTGGAAAGTAATGGGCAATCAATTGGCGTGGTGAATGCAATTGTCGGGCAGCGTCGTTATACGGTAACGCTGAACGGCGAATCAAACCATGCAGGCACCACGCCGATGGGTTATCGTCGTGATACAGTTTACGCTTTCAGTCGCATTTGCCATCAGTCGGTCGAAAAAGCGAAAAGGATGGGCGATCCGCTGGTTCTGACCTTTGGCAAAGTAGAGCCGCGCCCGAATACGGTAAATGTGGTGCCGGGTAAAACCACGTTCACCATTGATTGTCGTCATACCGACGCTGCCGTGCTGCGCGATTTCACCCAACAGTTAGAAAACGACATGCGGGCGATTTGCGATGAAATGGACATTGGTATTGATATCGATTTATGGATGGACGAAGAACCCGTGCCGATGAATAAGGAGCTGGTCGCCACCCTGACAGAATTGTGTGAAAGAGAAAAACTGAATTACCGGGTGATGCACAGTGGTGCCGGGCACGACGCGCAAATTTTCGCGCCTCGCGTACCAACCTGCATGATTTTTATCCCCAGCATCAACGGGATCAGCCATAACCCGGCGGAACGCACCAATATTACCGACCTTGCCGAAGGGGTCAAAACGTTGGCACTCATGCTTTATCAACTTGCCTGGCAGAAATAAGGAGTCATAAATGGGATATTTAAATAACGTCACCGGTTACCGCGAAGATTTACTGGCTAACCGTGCGATTGTTAAACACGGTAATTTCGCACTGTTAACCCCGGATGGTCTGGTAAAAAATATTATTCCGGGCTTTGAAAATTGTGACGCGACAATCCTCTCCACGCCAAAGCTGGGTGCCTCTTTTGTTGATTATCTGGTCACACTGCATCAAAACGGTGGCAACCAACAGGGCTTCGGTGGCGAAGGCATTGAAACGTTCCTGTATGTGATCTCTGGAAATATCACTGCCAAAGCCGAAGGCAAAACATTTGCCTTAAGCGAAGGTGGCTATCTTTATTGCCCGCCAGGCTCCTTAATGACGTTTGTTAACGCCCAGGCCGAAGACAGCCAAATCTTTTTATATAAGCGCCGCTATGTTCCGGTAGAAGGCTATGCACCGTGGCTGGTTTCTGGCAATGCCAGCGAACTGGAACGCATTCATTATGAAGGCATGGACGATGTTATTCTGCTGGATTTTCTGCCCAAAGAGTTAGGTTTTGATATGAACATGCATATCCTCTCTTTTGCACCAGGTGCCAGCCACGGTTATATCGAAACACACGTTCAGGAACACGGTGCCTATATTCTTTCCGGTCAGGGGGTTTATAACCTCGACAATAACTGGATCCCGGTGAAAAAAGGCGATTACATCTTTATGGGCGCTTATTCTTTACAGGCTGGTTATGGTGTAGGGCGTGGTGAAGCGTTCAGCTATATTTACTCGAAAGATTGTAACCGCGACGTAGAGATTTAAGTCATACCACTCGCCTGATTATTTTTAGCTATGTTGGATTTTGCCACGGTTTATACCGTGGCTTTTTTTGTAACATTGCCTGATGCGCTTCGCTTATCAGGCCTACATGATCTCTGCAATATATAGAATTTGCGCGATTTTCAGGAAGGATATGGTACTCATGCCGCATCCGGCATGAGTACTGCACTCTTATGCGATATAAATCGCATCCGCTTTAAAGGTAAGGGTTAGTTTTTAATTCCCTGACCTATTTTAATGGCGCAGGCAATATTTCGCGCGCTGTTGAAGAGATTGGTTTCACCGCTGGCGAGCACTTCGGCTAAAGGTGCCAGACGAGGCAAAATGCTGAATACCGCGTCAATGCCGTACTGGTGCACCACTTCCACGCCATCACCCAATACGCCAGCAATCCCAATCACCGGTACATTAAACTGCTTCGCCACCGACGCCACACCCAGCGGCGCTTTACCGCCTGCCGTTTGCGAGTCGATGCGCCCTTCCCCGGTAATCACCAGTGCTGCGCCCTGCACTGCCTGCGCAAGATTGACCGCATTCAACACAATTTCAATGCCCGGTTTAATATCCGCATTGAGAAATACCGCCGCCGCAATACCCATACCGCCCGCAGCGCCGCCGCCCGCCATCTGGCAGACATTAATTTCAGTTTGCTGTTGTAAAACACGGGCGTAATTTTGCAGCCCCTGTTCAAGTTCTTCGACCATCTCCGGCGTTGCCCCTTTTTGCGGGCCAAACACCGCCGCCGCGCCGCGTGCCCCTACCAGCGGGTTATCAACGTCACATGCTACTTCAATATGGCAATTCGCCAGACGCGGATCGCATTCATCCATCTCAATGCTTGCCACGCGCGCTAAATTACCACCGTTTGCCGCCAGCGCCTGACCGTCGGCATCAAGGAAACGCACACCGAGCGCCTGCGCCATGCCCATACCGCCGTCGACCGTCGCACTGCCGCCAATGCCGAGAATAATATGGCGAATGTCGTTATCCAGCGCATGACGAATTAACTCCCCCGTACCAAAACTGGAGGCCAGCAACGGATTACGCTTTTCAGGCGCGACCAGCATCAGGCCACTTGCTGCCGCCATCTCAATCACCGCCGTTTTCCCGTCGCCGGTAAGGCCATAAAAAGCATTCACTTTTTCGCCCATCGGCCCGCAGACTTCAAGCGTCACGATGTTGCCGCCCGTCGCGGCGACCATCGCATCCACCGTCCCTTCGCCGCCATCCGCTATCGGCAAACAGATATAGTTCGCATCGGGAAAGAGGGTCGAAAACCCGGCTTTAATTGCCTGACAACATTTTTCTGCACTTAAGCTCTCTTTAAAAGAGTCTGGCGCAATGACAATCTTCATTATCAATCCTTTTTCAACAAATTATTCGATGCGTTCCCACGGAATAAGGTTATCCATAAGAACAGCCAGTAAAATCCCGACCAATAAGCCGTTACTGAGCAGAGGACGAAGCGTTAATGGAAGGTCTTGCAGATACACAGGCGGTAATGCCATTAAAAATATGCCGACAAATAACGGCAATGCGAGTCGATAAATATTGCGAGCGGTAAACGTTATTTGCTGGCTAAACACCAGCGCGGAAAAGAGTAAAGGCAGATAAGAAACCAGCATGACCGCACTACTCACGGGTAAAGGGATACTGCAAAACAGTCGCGTGAGTGCAGGAACCAGCGCCACCAGCAGGCAAATAACGCTGCCATAAATAAACGAACGCCGCGTGTAATCGCCAGTCTGGGTTAATAAACCAATGGATGAAACAAACGGTGAAAATGGAATTACCGCCAGCGGTACGGTTATCAGCGTCATAAATCCGGTCGCCACAAAGCTACGACGATAACGCGTATTCCCTGCGCCCTGCTGCGGATAAAAAACATCCGTGCCCCGAATCGCACCGTAGGTATTGCTGATATTTACCAGACCTGTAATCACCGCCGTCAGAATAATTCCCGGCGACAAAGCACCGCCACTGCCGAGCGGGAACCACTGCCAGTGCAACTCACCGGAGAGCGAGTGCGAAGAAGGAAAGCAAAAGTACCACAACAACCAGCCGGTTATGGTGCCGACCAGCAGGCCATAACGGGCAAAACGTTGCGGCAGGAAGATAATCATCGCCAGTACCAGGCACATCACCGCCACCGAGAGCGCGAACGGCGGTAACTGAATTTTAAAATTCGGGTCGGCTATGCCAAACGGCAGCCCGAGCATACCTTTGAAAAAGATAGTGGTCAGCTGCGCGCCCAGCATCAACATAAACAAGACCATCACCGACGGCGTAAATAACCGTGCCAGGCGATGGCCTAATCCGCTAAAACCAATCAACATCGTCAGCACGCCGGAGAGTGCAATCCCCACTGCCAGGCTGGTGGCGATATCGTTGATCGGTGTCCCGCGCGATGCTTCACCAAGGGTGATAGTAAGGATGGTTCCCCACCACAGGCCACCTGGCCCTTCCATAATAGCGCGACGATGACCGCAAAACGCCTGAGCGAAGCAGGCCAGTGCGGTAGCAAGAAAAGCATATTGCGTGAGCGTAAGCAGGCTACTTTGCGGCAACTGAAAAGCAGAAAGTAGCGTAGGAGGAACCACAACCGTGTTGCAAAAAATAAAGAAAAACCACTGAAATCCTGATAACAGGCTTTCGCGGCTGACTGCAAAATTGAACATAAACACACCTTAACCGGAGAATGCCCGCCGCAAGGACGGGCATTGCAGGGGCCAGATTACTGCTGATGTTTAAGGATAAATTGACCTTTCGGCGCAACAGGGAAGCCCTGTTCAATGTCGTAAATCACATCACCACGTAAGATGGTTTTCGTGATACGCGCGCCAATGGTACGGCCAACATACGGGCTGACTTTGTGGCGATATTCCAGATCGTCATTGGTAAGAACATAGCTGCTATTCGGCTGAATGAAGACGAAGTCGGCATCTTTTCCTGGGGCGATACGGCCTTTTTGCTGCAGACCGAAAATATCTGCTGCGTTAGTCGCCATTAATTTGCCGAACATTGGCAGAGACATACCGCGTTTCTGTACCGCTTCATCGAACATCACGTCCATGCAGCTTTGCAGACCGGCGATACCGCCCCATGCTTTCATGATGTTACCGGCTTTCATTTCCGGCGGGCATGGAGAGTGGTCGGAAACCAGGCAGTCGATTTCACCGTTAAACAGTTTTTCCCACATGCCTTTCTGGTTTTCCAGATCGCGGATCGGCGGTGAACACTTCGCCAGAGTACCGATTTCTTCGAACTGATCGGTATCCAGTACAAAGTAATGCGGGCAGGATTCACAAGTAACGTCCTGACCTTCCTGACGTGCACGAGTCACTTCCTCAACACCTTCCGGGCTGCTGACGTGGCAAACGTGCAGACGGCAACCAGCAACTTTCGCCAGATACAGTACGCGGCGAATTGCTTCCACTTCGGTAAATACCGGACGCGAAGCCACATAGTCATGAGCGGTTACGCGACCTTCACGCTTCGCTTCTTCGCCCAGTTCGTCACAAATCAGCGCGTTTTCGCAGTGCACCAGCACCGGCTGACCCAGTTCGCCCAGCTTCTGCGCACCTTTGAAGAACTGCCAGTCGTTTACATCACGGAAGTCGTTGTCGATACCGCGATCGCCACAGGTCGCAACGAAGCATTTGAAGCCGACAACGCCCACTTCATCCAGCTCATGCAGACGGTCGATGTTGTAAGACACCAGGCCACCGAGTTGTGCCGCATCAATAGTCAGCTTGCCTTTAGCGGCATCGAACTTCAGTTCAATTGAAGCGCGGTCAACCGTTGCAGGCAGCTGGTTGAGCGGCATTTCGATCATGGTGGTGATACCACCTTTTGCCGCTGCGCGAGTACCGGTTTCATAACCTTCCCAGTGGCTACGACCCGGTTCAGAAATATGGGTGTGCGCATCAACCATGCCCGGCGAAACCACCAGACCAGACGCATCCATAACTTCTTTTGCATCGCCCAGATCCTGACCGATAGCAGCAATTTTTCCGCCTTTAACGGCGATATCTACAACGCGAGCTTCGTTTTCTAAAATAACGGTGCCGTTTTTAATGATTAAATCAAAAGACATAACAAACTCCTTGTAAAATACAGATTGGTTTTTAACTCAATGTTCAATATCGGGATTAATTAACCTATGGTTTTTTGCTCTCCTGTTTTTTCTGCTGTTGTACGTTTCTTTAATAAGGCGTAGGCCGCAAAGGCGACGATGACGC +>4_contig1 dgfdgd +ACGTTGCTGCGAATCGAGCTGTCTAGCGATCGAG +>5_contig2 +CGA +>6_contig3 +ATTCGGGCTTGA +>7_contig4 +AT diff --git a/test/data/annotate/exp_files/exp_complete_genome.fna_prokka-split3N.fna b/test/data/annotate/exp_files/exp_complete_genome.fna_prokka-split3N.fna new file mode 100644 index 0000000000000000000000000000000000000000..59df2730ff1596ed1c1fe1f3b4e332d9d85d0f67 --- /dev/null +++ b/test/data/annotate/exp_files/exp_complete_genome.fna_prokka-split3N.fna @@ -0,0 +1,2 @@ +>1_complete +CCGCTTAGGCTAGCGCCAGCTAGGAGCGCTCGAGAGACACAGCATTACNCCGATATTATAGAGGCCGCGCTTAGCACGCTAGGACGCG diff --git a/test/data/annotate/genomes/A_H738.fasta b/test/data/annotate/genomes/A_H738.fasta index 279640c2a0dce53162a643f852636f5fbd2779f7..d4e777a5beede0b80cbed518ace578d27777050e 100755 --- a/test/data/annotate/genomes/A_H738.fasta +++ b/test/data/annotate/genomes/A_H738.fasta @@ -51,7 +51,7 @@ TTCTGAATTGATGTGGGTGTGGTTGCCGGGGATGCTACTGATGGGAATGTTGTGGTGGCG CAGACGATAACCGGATGCGAAAACTCGCATCCGGCAATAGCGCAATTACTTACGACGCCA GGTGGTCCCTTGCGGGCCATCTTCCAGCACGATCCCCATCTCGTTAAGACGATCACGCGC CGCATCCGCCGCCGCCCAGTCTTTCGCTTTACGGGCATCCAGACGCTGTTGAATTAACGC -TTCAATCTCAGCCACTTCGCTGTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGG +TTCAATCTCAGCCACTTCGCTNNNNNNNNNGTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGG TTCTTGCTCCAGCAGGCCCAATACAGCGGAAAGTTTACGCAGGTGAGATGCCATTGCATT CGCCGCTGCCATATCTTCTGCTTTCAGACGGTTTACTTCACGCGCCATATCAAACAGTAC GGAATAGGCTTCCGGGGTGTTGAAATCGTCGTCCATCGCTTCAATAAAGCGCGCTTCAAA @@ -122,7 +122,7 @@ AACGGTGCCAGCATCAGCCAGTTTGAGCTGCATCTGCGGGCGATTACCGATCTGCCGTTA CCGCAACCAGTGGTGAATAATCCGTCGGTGATGATCAATCTGATTGGTAGCGATGTGAAT TATGACTGGCTGAAACTGCCGCTGGTGCATCTGCACTGGTACGACAAAGAAGTCCGTCCG GGGCGTAAAGTGGGGCATCTGAATTTGACCGACAGCGACACATCGCGTCTGACTGCGACG -CTGGAAGCCTTAATCCCGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAG +CTGGAAGCCTTAATCCNNNNNNNNNNNNNNNNNNNNNNNNNNCGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAG AGTAAGTTCGGTTAACTGGTGCTCTATTCTTGCCGGATGCGGCGTAAACGCCTTATCCGG CCTACCGATCCGGTACCCATTGTAGGCCTGATAAGATGCGTCAAGCATCGCATCAGGCAT TGTGCACCAATTGCCGGATGCGGCACCGGTTGTAGGCCTGATAAGACGCGTCAAGCGTCG diff --git a/test/data/annotate/genomes/complete_genome.fna b/test/data/annotate/genomes/complete_genome.fna new file mode 100644 index 0000000000000000000000000000000000000000..583e7b872877fbcb80e4a89ece5a0ce0371588ee --- /dev/null +++ b/test/data/annotate/genomes/complete_genome.fna @@ -0,0 +1,5 @@ +>complete +CCGCTTAGGCTAGCGCC +AGCTAGGAGCGCTCGAGAGACA +CAGCATTACNCCGATATTATAGAGGCCGCGCTTAGC +ACGCTAGGACGCG \ No newline at end of file diff --git a/test/data/annotate/test_files/list_genomes-func-test-default.txt b/test/data/annotate/test_files/list_genomes-func-test-default.txt index 0b6751d4ffbbbb196367df00254a07af68e0495e..ddd2dfb23d4a8ead62a49fb552101e7a03e377eb 100755 --- a/test/data/annotate/test_files/list_genomes-func-test-default.txt +++ b/test/data/annotate/test_files/list_genomes-func-test-default.txt @@ -1,3 +1,4 @@ B2_A3_5.fasta-changeName.fna::ESCO.1116 H299_H561.fasta genome6.fasta :: ESCO.1015 A_H738.fasta genome1.fasta toto.fst ::.1015 +complete_genome.fna \ No newline at end of file diff --git a/test/test_functional/test_annote.py b/test/test_functional/test_annote.py index c3cdfebfe420881bb474adc130496a9cf112640d..62d3053f6ff617d905a0a5807fe0c692f7f3165b 100755 --- a/test/test_functional/test_annote.py +++ b/test/test_functional/test_annote.py @@ -123,11 +123,11 @@ def test_main_given_tmp_verbose3(capsys): list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt") tmpdir = os.path.join(GENEPATH, "tmp_funcGivenTmp") name = "ESCO" - l90 = 1 + l90 = 10 date = "0417" verbose = 3 annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, l90, - cutn=0, tmp_dir=tmpdir, verbose=verbose) + cutn=3, tmp_dir=tmpdir, verbose=verbose) out, err = capsys.readouterr() # Check that warnings are written to stderr assert "WARNING" in err @@ -135,11 +135,22 @@ def test_main_given_tmp_verbose3(capsys): "concatenating ['A_H738.fasta', 'genome1.fasta', 'toto.fst']") in err # Check that tmp files exist in the right folder # -> 2 fna files created (concatenations) + # -> + 3 files created (split 5N) assert os.path.isfile(os.path.join(tmpdir, "A_H738.fasta-all.fna")) assert os.path.isfile(os.path.join(tmpdir, "H299_H561.fasta-all.fna")) + assert len(glob.glob(os.path.join(tmpdir, '*.fna'))) == 6 + assert len(glob.glob(os.path.join(tmpdir, '*split3N.fna'))) == 4 + # Check that split contigs were renamed with unique ID at the begining of the header + res_file = os.path.join(tmpdir, "A_H738.fasta-all.fna_prokka-split3N.fna") + exp_file = os.path.join(EXP_DIR, "exp_A_H738.fasta-all.fna_prokka-split3N.fna") + assert tutil.compare_order_content(exp_file, res_file) + # Check that even for complete genome, contig was renamed with ID + res_file = os.path.join(tmpdir, "complete_genome.fna_prokka-split3N.fna") + exp_file = os.path.join(EXP_DIR, "exp_complete_genome.fna_prokka-split3N.fna") + assert tutil.compare_order_content(exp_file, res_file) # Test that prokka folder is in the right directory # Only 1 genome annotated by prokka (the 2 others do not have appropriate L90/nbcont) - assert os.path.isdir(os.path.join(tmpdir, "A_H738.fasta-all.fna-prokkaRes")) + assert os.path.isdir(os.path.join(tmpdir, "A_H738.fasta-all.fna_prokka-split3N.fna-prokkaRes")) assert not os.path.isdir(os.path.join(tmpdir, "H299_H561.fasta-all.fna-prokkaRes")) @@ -150,7 +161,7 @@ def test_main_all_discard_nbcont(capsys): """ list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt") name = "ESCO" - nbcont = 1 + nbcont = 0 cutn = 0 date = "0417" annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, nbcont=nbcont, cutn=cutn) @@ -200,6 +211,7 @@ def test_main_existresdirforce(capsys): """ Test that, when the pipeline is run on an existing result directory, but force option is on, it removes the result folders and runs again. + Result folders contain expected files, the ones put before are removed """ list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt") # Create output directory with a prt file in Proteins folder @@ -209,28 +221,47 @@ def test_main_existresdirforce(capsys): assert os.path.isfile(os.path.join(protdir, "toto.prt")) name = "ESCO" date = "0417" - l90 = 1 + l90 = 5 + cutn = 3 annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, force=True, l90=l90, - prodigal_only=True) + prodigal_only=True, cutn = cutn, small=True) out, err = capsys.readouterr() + # Check that tmp files exist in the right folder + # -> 2 fna files created (concatenations) + # -> + 3 files created (split 5N) + assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "A_H738.fasta-all.fna")) + assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "H299_H561.fasta-all.fna")) + assert len(glob.glob(os.path.join(GENEPATH, "tmp_files", '*.fna'))) == 6 + assert len(glob.glob(os.path.join(GENEPATH, "tmp_files", '*split3N.fna'))) == 4 + # Check that split contigs were renamed with unique ID at the begining of the header + res_file = os.path.join(GENEPATH, "tmp_files", "A_H738.fasta-all.fna_prodigal-split3N.fna") + exp_file = os.path.join(EXP_DIR, "exp_A_H738.fasta-all.fna_prokka-split3N.fna") + assert tutil.compare_order_content(exp_file, res_file) + # Check that even for complete genome, contig was renamed with ID + res_file = os.path.join(GENEPATH, "tmp_files", "complete_genome.fna_prodigal-split3N.fna") + exp_file = os.path.join(EXP_DIR, "exp_complete_genome.fna_prokka-split3N.fna") + assert tutil.compare_order_content(exp_file, res_file) # Check that tmp files exist in the right folder (result/tmp_files) assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", - "B2_A3_5.fasta-changeName.fna_prodigal-split5N.fna")) + "B2_A3_5.fasta-changeName.fna_prodigal-split3N.fna")) assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", - "H299_H561.fasta-all.fna_prodigal-split5N.fna")) + "H299_H561.fasta-all.fna_prodigal-split3N.fna")) assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "H299_H561.fasta-all.fna")) assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", - "A_H738.fasta-all.fna_prodigal-split5N.fna")) + "A_H738.fasta-all.fna_prodigal-split3N.fna")) assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "A_H738.fasta-all.fna")) # Test all result folders are empty (in particular Proteins) as no genome is annotated assert os.path.isdir(protdir) - assert len(os.listdir(protdir)) == 1 + assert len(os.listdir(protdir)) == 4 assert not os.path.isfile(os.path.join(protdir, "toto.prt")) - assert os.path.isfile(os.path.join(protdir, "ESCO.1015.00001.prt")) + assert os.path.isfile(os.path.join(protdir, "ESCO.0417.00001.prt")) + assert os.path.isfile(os.path.join(protdir, "ESCO.1015.00002.prt")) + assert os.path.isfile(os.path.join(protdir, "ESCO.1015.00003.prt")) + assert os.path.isfile(os.path.join(protdir, "ESCO.1116.00004.prt")) def test_run_exist_resdir(caplog):