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Commit d27771e5 authored by Amandine PERRIN's avatar Amandine PERRIN
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fuctional tests for annotate: take into account new splitcontig header format

parent 2d5eaa31
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with 68 additions and 14 deletions
test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst
+ 2
− 1
View file @ d27771e5
orig_name to_annotate gsize nb_conts L90 orig_name to_annotate gsize nb_conts L90
B2_A3_5.fasta-changeName.fna B2_A3_5.fasta-changeName.fna 120529 5 4 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 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
test/data/annotate/exp_files/exp_A_H738.fasta-all.fna_prokka-split3N.fna 0 → 100644
+ 14
− 0
View file @ d27771e5
>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
test/data/annotate/exp_files/exp_complete_genome.fna_prokka-split3N.fna 0 → 100644
+ 2
− 0
View file @ d27771e5
>1_complete
CCGCTTAGGCTAGCGCCAGCTAGGAGCGCTCGAGAGACACAGCATTACNCCGATATTATAGAGGCCGCGCTTAGCACGCTAGGACGCG
test/data/annotate/genomes/A_H738.fasta
+ 2
− 2
View file @ d27771e5
...@@ -51,7 +51,7 @@ TTCTGAATTGATGTGGGTGTGGTTGCCGGGGATGCTACTGATGGGAATGTTGTGGTGGCG ...@@ -51,7 +51,7 @@ TTCTGAATTGATGTGGGTGTGGTTGCCGGGGATGCTACTGATGGGAATGTTGTGGTGGCG
CAGACGATAACCGGATGCGAAAACTCGCATCCGGCAATAGCGCAATTACTTACGACGCCA CAGACGATAACCGGATGCGAAAACTCGCATCCGGCAATAGCGCAATTACTTACGACGCCA
GGTGGTCCCTTGCGGGCCATCTTCCAGCACGATCCCCATCTCGTTAAGACGATCACGCGC GGTGGTCCCTTGCGGGCCATCTTCCAGCACGATCCCCATCTCGTTAAGACGATCACGCGC
CGCATCCGCCGCCGCCCAGTCTTTCGCTTTACGGGCATCCAGACGCTGTTGAATTAACGC CGCATCCGCCGCCGCCCAGTCTTTCGCTTTACGGGCATCCAGACGCTGTTGAATTAACGC
TTCAATCTCAGCCACTTCGCTGTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGG TTCAATCTCAGCCACTTCGCTNNNNNNNNNGTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGG
TTCTTGCTCCAGCAGGCCCAATACAGCGGAAAGTTTACGCAGGTGAGATGCCATTGCATT TTCTTGCTCCAGCAGGCCCAATACAGCGGAAAGTTTACGCAGGTGAGATGCCATTGCATT
CGCCGCTGCCATATCTTCTGCTTTCAGACGGTTTACTTCACGCGCCATATCAAACAGTAC CGCCGCTGCCATATCTTCTGCTTTCAGACGGTTTACTTCACGCGCCATATCAAACAGTAC
GGAATAGGCTTCCGGGGTGTTGAAATCGTCGTCCATCGCTTCAATAAAGCGCGCTTCAAA GGAATAGGCTTCCGGGGTGTTGAAATCGTCGTCCATCGCTTCAATAAAGCGCGCTTCAAA
...@@ -122,7 +122,7 @@ AACGGTGCCAGCATCAGCCAGTTTGAGCTGCATCTGCGGGCGATTACCGATCTGCCGTTA ...@@ -122,7 +122,7 @@ AACGGTGCCAGCATCAGCCAGTTTGAGCTGCATCTGCGGGCGATTACCGATCTGCCGTTA
CCGCAACCAGTGGTGAATAATCCGTCGGTGATGATCAATCTGATTGGTAGCGATGTGAAT CCGCAACCAGTGGTGAATAATCCGTCGGTGATGATCAATCTGATTGGTAGCGATGTGAAT
TATGACTGGCTGAAACTGCCGCTGGTGCATCTGCACTGGTACGACAAAGAAGTCCGTCCG TATGACTGGCTGAAACTGCCGCTGGTGCATCTGCACTGGTACGACAAAGAAGTCCGTCCG
GGGCGTAAAGTGGGGCATCTGAATTTGACCGACAGCGACACATCGCGTCTGACTGCGACG GGGCGTAAAGTGGGGCATCTGAATTTGACCGACAGCGACACATCGCGTCTGACTGCGACG
CTGGAAGCCTTAATCCCGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAG CTGGAAGCCTTAATCCNNNNNNNNNNNNNNNNNNNNNNNNNNCGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAG
AGTAAGTTCGGTTAACTGGTGCTCTATTCTTGCCGGATGCGGCGTAAACGCCTTATCCGG AGTAAGTTCGGTTAACTGGTGCTCTATTCTTGCCGGATGCGGCGTAAACGCCTTATCCGG
CCTACCGATCCGGTACCCATTGTAGGCCTGATAAGATGCGTCAAGCATCGCATCAGGCAT CCTACCGATCCGGTACCCATTGTAGGCCTGATAAGATGCGTCAAGCATCGCATCAGGCAT
TGTGCACCAATTGCCGGATGCGGCACCGGTTGTAGGCCTGATAAGACGCGTCAAGCGTCG TGTGCACCAATTGCCGGATGCGGCACCGGTTGTAGGCCTGATAAGACGCGTCAAGCGTCG
......
test/data/annotate/genomes/complete_genome.fna 0 → 100644
+ 5
− 0
View file @ d27771e5
>complete
CCGCTTAGGCTAGCGCC
AGCTAGGAGCGCTCGAGAGACA
CAGCATTACNCCGATATTATAGAGGCCGCGCTTAGC
ACGCTAGGACGCG
\ No newline at end of file
test/data/annotate/test_files/list_genomes-func-test-default.txt
+ 1
− 0
View file @ d27771e5
B2_A3_5.fasta-changeName.fna::ESCO.1116 B2_A3_5.fasta-changeName.fna::ESCO.1116
H299_H561.fasta genome6.fasta :: ESCO.1015 H299_H561.fasta genome6.fasta :: ESCO.1015
A_H738.fasta genome1.fasta toto.fst ::.1015 A_H738.fasta genome1.fasta toto.fst ::.1015
complete_genome.fna
\ No newline at end of file
test/test_functional/test_annote.py
+ 42
− 11
View file @ d27771e5
...@@ -123,11 +123,11 @@ def test_main_given_tmp_verbose3(capsys): ...@@ -123,11 +123,11 @@ def test_main_given_tmp_verbose3(capsys):
list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt") list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt")
tmpdir = os.path.join(GENEPATH, "tmp_funcGivenTmp") tmpdir = os.path.join(GENEPATH, "tmp_funcGivenTmp")
name = "ESCO" name = "ESCO"
l90 = 1 l90 = 10
date = "0417" date = "0417"
verbose = 3 verbose = 3
annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, l90, 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() out, err = capsys.readouterr()
# Check that warnings are written to stderr # Check that warnings are written to stderr
assert "WARNING" in err assert "WARNING" in err
...@@ -135,11 +135,22 @@ def test_main_given_tmp_verbose3(capsys): ...@@ -135,11 +135,22 @@ def test_main_given_tmp_verbose3(capsys):
"concatenating ['A_H738.fasta', 'genome1.fasta', 'toto.fst']") in err "concatenating ['A_H738.fasta', 'genome1.fasta', 'toto.fst']") in err
# Check that tmp files exist in the right folder # Check that tmp files exist in the right folder
# -> 2 fna files created (concatenations) # -> 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, "A_H738.fasta-all.fna"))
assert os.path.isfile(os.path.join(tmpdir, "H299_H561.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 # Test that prokka folder is in the right directory
# Only 1 genome annotated by prokka (the 2 others do not have appropriate L90/nbcont) # 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")) 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): ...@@ -150,7 +161,7 @@ def test_main_all_discard_nbcont(capsys):
""" """
list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt") list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt")
name = "ESCO" name = "ESCO"
nbcont = 1 nbcont = 0
cutn = 0 cutn = 0
date = "0417" date = "0417"
annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, nbcont=nbcont, cutn=cutn) annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, nbcont=nbcont, cutn=cutn)
...@@ -200,6 +211,7 @@ def test_main_existresdirforce(capsys): ...@@ -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, 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. 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") list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt")
# Create output directory with a prt file in Proteins folder # Create output directory with a prt file in Proteins folder
...@@ -209,28 +221,47 @@ def test_main_existresdirforce(capsys): ...@@ -209,28 +221,47 @@ def test_main_existresdirforce(capsys):
assert os.path.isfile(os.path.join(protdir, "toto.prt")) assert os.path.isfile(os.path.join(protdir, "toto.prt"))
name = "ESCO" name = "ESCO"
date = "0417" date = "0417"
l90 = 1 l90 = 5
cutn = 3
annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, force=True, l90=l90, 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() 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) # Check that tmp files exist in the right folder (result/tmp_files)
assert os.path.isfile(os.path.join(GENEPATH, "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", 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", assert os.path.isfile(os.path.join(GENEPATH, "tmp_files",
"H299_H561.fasta-all.fna")) "H299_H561.fasta-all.fna"))
assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", 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", assert os.path.isfile(os.path.join(GENEPATH, "tmp_files",
"A_H738.fasta-all.fna")) "A_H738.fasta-all.fna"))
# Test all result folders are empty (in particular Proteins) as no genome is annotated # Test all result folders are empty (in particular Proteins) as no genome is annotated
assert os.path.isdir(protdir) 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 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): def test_run_exist_resdir(caplog):
......
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