| Previous changeset 3:5c8ff92e38a9 (2017-06-14) Next changeset 5:24a7a95867b0 (2021-03-19) |
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Commit message:
"planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f" |
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modified:
sistr_cmd.xml test-data/alleles-output-13-1101.json test-data/alleles-output.json test-data/cgmlst-profiles-13-1101.csv test-data/cgmlst-profiles.csv test-data/novel-alleles-13-1101.fasta |
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added:
test-data/sistr-results-13-1101.tabular test-data/sistr-results.tabular |
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removed:
test-data/13-1101 Paratyphi_B.fasta test-data/sistr-results-13-1101.tab test-data/sistr-results.tab |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 sistr_cmd.xml --- a/sistr_cmd.xml Wed Jun 14 14:36:59 2017 -0400 +++ b/sistr_cmd.xml Thu Aug 06 11:48:49 2020 -0400 |
| [ |
| @@ -1,9 +1,12 @@ -<tool id="sistr_cmd" name="sistr_cmd" version="1.0.2"> +<tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@"> <description> - Salmonella In Silico Typing Resource commandline tool for serovar prediction + Salmonella In Silico Typing Resource commandline tool for serovar prediction </description> + <macros> + <token name="@VERSION@">1.1.1</token> + </macros> <requirements> - <requirement type="package" version="1.0.2">sistr_cmd</requirement> + <requirement type="package" version="@VERSION@">sistr_cmd</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -161,38 +164,42 @@ </outputs> <tests> <test> - <param name="input_fastas" value="AE014613-699860.fasta"/> + <param name="input_fastas" value="AE014613-699860.fasta" ftype="fasta"/> <param name="output_format" value="tab"/> <output name="cgmlst_profiles" value="cgmlst-profiles.csv" ftype="csv" - lines_diff="2"> - <assert_contents> - <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,"/> - </assert_contents> + compare="diff"> </output> - <output - name="output_prediction_tab" - value="sistr-results.tab" + <output name="output_prediction_tab" ftype="tabular" - lines_diff="2"> + value="sistr-results.tabular" + compare="sim_size"> <assert_contents> <has_text text="AE014613-699860" /> <has_text text="Typhi" /> <has_text text="enterica" /> - <has_text text="-:-:-" /> - <has_n_columns n="21" /> + <has_text_matching expression="FAIL\t-\t-:-:-\t-:-:-"/> + <has_text text="2014-LET-0419"/> + <has_n_columns n="22" /> </assert_contents> </output> <output name="alleles_output" value="alleles-output.json" ftype="json" - compare="sim_size"/> + compare="sim_size"> + <assert_contents> + <has_text text="NZ_AOXE01000059.1"/> + <has_text text="Salmonella enterica subsp. enterica serovar Typhi Ty2"/> + <has_text text="NZ_AOXE01000033.1"/> + <has_text text="NZ_AOXE01000052.1"/> + </assert_contents> + </output> </test> <test> - <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> + <param name="input_fastas" value="13-1101-Paratyphi_B.fasta" ftype="fasta"/> <param name="output_format" value="tab"/> <output name="novel_alleles" @@ -203,79 +210,32 @@ name="cgmlst_profiles" value="cgmlst-profiles-13-1101.csv" ftype="csv" - lines_diff="2"> + compare="diff"> </output> <output name="output_prediction_tab" - value="sistr-results-13-1101.tab" + value="sistr-results-13-1101.tabular" ftype="tabular" - lines_diff="2"> + compare="sim_size"> <assert_contents> - <has_text text="13-1101-Paratyphi_B" /> - <has_text text="Paratyphi B var. Java" /> - <has_text text="enterica" /> - <has_text text="1,4,[5],12" /> - <has_text text="PASS" /> - <has_n_columns n="21" /> + <has_text text="13-1101-Paratyphi_B"/> + <has_text text="Paratyphi B var. Java"/> + <has_text text="enterica"/> + <has_text text="1,4,[5],12"/> + <has_text text="PASS"/> + <has_n_columns n="22"/> </assert_contents> </output> <output name="alleles_output" value="alleles-output-13-1101.json" ftype="json" - compare="sim_size"/> - </test> - <test> - <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/> - <param name="output_format" value="tab"/> - <output - name="novel_alleles" - value="novel-alleles-13-1101.fasta" - ftype="fasta" - compare="sim_size"/> - <output - name="cgmlst_profiles" - value="cgmlst-profiles-13-1101.csv" - ftype="csv" - lines_diff="2"> - </output> - <output - name="output_prediction_tab" - value="sistr-results-13-1101.tab" - ftype="tabular" - lines_diff="2"> - <assert_contents> - <has_text text="13-1101 Paratyphi_B" /> - <has_text text="Paratyphi B var. Java" /> - <has_text text="enterica" /> - <has_text text="1,4,[5],12" /> - <has_text text="PASS" /> - <has_n_columns n="21" /> - </assert_contents> - </output> - <output - name="alleles_output" - value="alleles-output-13-1101.json" - ftype="json" - compare="sim_size"/> - </test> - <test> - <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> - <param name="output_format" value="json"/> - <param name="more_output" value="-MM"/> - <output - name="output_prediction_json" - value="sistr-results-13-1101.json" - ftype="json" compare="sim_size"> <assert_contents> - <has_text text="13-1101-Paratyphi_B" /> - <has_text text="Paratyphi B var. Java" /> - <has_text text="enterica" /> - <has_text text="1,4,[5],12" /> - <has_text text="PASS" /> + <has_text text="13-1101-Paratyphi_B"/> + <has_text text="NZ_AOXE01000059.1"/> </assert_contents> - </output> + </output> </test> </tests> <help> |
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| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/13-1101 Paratyphi_B.fasta --- a/test-data/13-1101 Paratyphi_B.fasta Wed Jun 14 14:36:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,126 +0,0 @@\n->10664704\n-CAATTCACGAATAACAGAGGTGATCTTTCTACCGAATTTAAAATAGAGCTCAATAGCACGAAGGCGCTCAGCTTTTGAATACATAAATTATCTCCTGAGAGTCCAGGAAATCGTCCGCACCCCCATTACCGTCTTATATCATTGGCGCTAACACCCGGGATAACGGAAGCCGCCTGCTGGGCTCATGCCCGCCGGAAGATCCACGATGTGCACGTCCGCACCCCGTCAGCTCTGACGGAAGAAGCCCTGAGGCAGATCGGTCAGTTGTACGCCATAGAGGCGAATATAAGGGGAATACCGGCGGAGCAGCGGCTTGCTGAACGTCAGCGAAAAACGAAACCGCTGCTGAAATCCCTGGAAAGCTGGTTGCGTGAAAAGATGAAGACCCTGTCGCGACACTCAGAGCTGGCGAAAGCGTTCGCGTACGCACTTAACCAGTGGCCGGCACTGACGTACTATGCGGACGATGGCTGGGCCGAAGCAGACAACAACAGTGCTGAAAATGCGCTGCGGACGGTCAGTCTGGGTCGTAAAAACTTCCTGTTCTTCGGCTCTGACCATGGTGGTGAGCGGGGAGCGCTGCTGTACAGCCTGATCGGGACGTGCAAACTGAACGGCGTGGGTCCAGAAAGCTACCTTCGCCATGTGCTTGGCGTCATAGCTGACTGGCCGGTCAACCGGGTCAGCGAACTGCTCCCCTGGCGCATAGCACTGCCAGCTGAATAACGCATCCCTGTCAATACGGCTCTCGCTGTACGCTTACGTTGAAGCAAGAAAGTAACATTAACTGGTGAGGCAACACGTTGGATAATATAAATGACGCCGGGTTATGCGAGTTTTCTTTCCTGTTGAATTTGAATCCGTGCATTTTTATTCAGTGCCTGAATAATACAGCTATAAAATCTGAAAAAAGTGAAAGTAATATGCCCGGGGCACTGGAAAAGCCGGTTACTCCCGGACATTAAGGCTCATAAATCAGTTAAGATCGTGAAGAATGCATATTAACGGCGCGTGGTGGTGGTTATTTTTGCCATCCTTTAAAAATAATTCTGTCCTGCTTTTCGATAACGACATGCTTCTCTATGCGAACATTTAAATACTGAGACGTGACCTGAAAACGACCTCTTGGTGCTTTAGATTGTGTGGATAACTGAGCGCCGGCATAGGCG\n->10664706\n-ACGATCAACAACCTGTTTGACTGCTTCAATTTTAAACTCTTCGGGATAACGTTTACCGCTCATGGGCACCTCTCTTTAAGTCATTTTAAATGACTCTGAGGTGTCTGTTAAACCCGTGGCGATTCAATCAGAGTAATTTAGTTCTATCGATATTTTTCGCACCACTGGTTCAGGATACAAAGGTGGCAATTGACGATGATCGCCGACCAGTAACACCCTGCGACCCGACTGAATTGCTATAGCCAATTCGCCAGGTGTCGCACGAGCAGCTTCGTCGACTATCACCCAATCATAGCGATTTTTTGCTACACCAAATTGTGAGCGTCCTAGACCCACACAAGTCCCACATACAAGTGATCGGGTCTTCGCAAGAAATTCTTCAAAGTTACCTCTCAGAGTGCCTAAGCGATCTACCCACTCTTGAGACATTGCAATTACTTGCTCCAGTCTAGACACTGCATCTAAAGAAGTTACACCAAACTGATTCATTGTCTCACGGCTTAATTGATTAATCACTTCCTCTGGAGTTCCCTCCCCCGCATAACCAAACTTTTCAGATGCAATTTTTTTAAATCGTTCAAGTCGCTGATTTATTCGAGCTATCAGAGGATTATTATTAGCTTCTGATATTTCATTTTTATTTAGTTTTGTGGTTAATCTTTCTATTTCACGATTCAAACGCTTAAGTTGATATTCAATATCGAACCATCTTTCTACAAATTTGTTAGGGAGACCTAAATTTCGGTTCATTGCTGAAATTCTAACTCGCATTTCTGAGCGGAATAAGTCTCGATAATTTTGCAAAATGGAAGATGAATGATATGGATGAAGTTTTTCTGAGACCATTCCTTCTGCACCGAACCTAACAACATCTAGGGGCAGATTGCTGTGCTGACAAAGTTCAATTACTTTTTCTGCAGCATTATTAACTGCTTCATGTGACTGGCTTGCAAGAAGTATACTTTGGGCTCCTTGTGAGAGAGCATAATGGATAAATGAAGCAATGAATGAAGTTTTACCAGTGCCTGGAGGGCCTTGCAAAAGACTCAATGGGCCGTATGACCAAAGTTTAGAAAAGGCATCTCGTTGCTGTCGATTGAGTGAAAAAGATAGCTCTCCATCTTTATCATATCGATTATAAGCATCAAGATCAGAATCATTTGGCTCTGGTTGTAGATATTGTGGATGAGGGCAAGTTAATGGTTCAAAGTAGTTGATTAATGAGGGGATAGCCGATTCAGCATTTAAAATACGTGTAACTGCATGACGCCTACGAATAAAAGATGATAGATCTTGTTGACTTCGTAATTTCAAAGTGTCGCCAATATTAGTCTGAATGCGAATCTTTGGATTTTCAAGTACGAGAGTAGATTGGGTAGTCTCTCTTATATCAACATTCCCTACACGAATCAGTTCACCGTTTATTTCTTGTAATGCCTCAACTTTTGCATCTGATTCATAGTCTAAAGACTCTCCCTCTTTTCTGTAAGGTATTCGCAATTTCTCATGACGCTTATCCATATCCCTGACAACTGATGAGGTGATTTCAATTTCAGGTAAGGAATCTTCTTCTGCATCTAAAATTGCACGCCAAAGTGATGCTGTATGTGGTCTTGTTTGAGAAACAGTTAAAGTTTCTGAGTTCTCAATTTCTTCCTCATCAGAAGAAAAATCGCCACCGAGAATTCTATTCTGAATTCTCGATATTGCAGAGATAACCTCAGGTATTTTTTTACATGTTCTAATAACTTGCTAGGGTCATCCGCGGATGAGGGTTCGAATAGTATATTAGCTTCGAGTTGTGTAATGGCTTGTGATGCCATTCGTACAAATAAGCTATGGGCTATATCTTTAGTTCGTAAAAATGCAAAATCTAATTGGGTCGCTTTAAGATAGATTTGTAACTGTTTACGTACTCCGGCAAAAGCTACGATAATATGAGGCTGCTGCTTTGGCGAACGGACTCGTTCTTCACTAATACTGATATGGTATACACCATTGTCATTTATTAATTTCTGGCTGGAGGTCAGTTGCCTCATTAATACTGACAACCTCACTCCCTCATTTATTTGTGGAGGGTTGATTAACATCTCTATTTCATCATTTATTCGGTCAAGAGAATAAATTTTAAAATCCCGCCCCATACAACTTCTGATCTCATTAAGTAAAGCTGATGGATCAATCCCTTCCCAGTTAACGTCGTGTTCTAAAATCTCATTACACACTTTGGCCACAGCGTAGCAATCACGTTCCTCCATAGGCAAAGATTCGTAATCTGTAGGTACATATGCAGGAGTGAATATTATATTCTCACCTGAACAAGGTATATCAAGTGCATCAATGAAGCGAACATCTCCCACTTCTATTAGAATATTGTTAGGGTGCAGATCCCCATGTTGTAATTGCATAGCATGTAAATGTAAGACTGCCCTAACTATTTTTTTGCATAGTAATATCAATTCACGACCAACATGACATGATTTGACAGCGTCATTTAGGAATTCCCCATTCAACCATTTTTGGACTAAATAGGTTCCTGCATCTGAAACACCAAAATCAATAACTTCAGCAAGAGAAGAACAGGGCTGGGATTTTATTAGGCGAGCTTTATCGAGAAAATTCTGAAGTTGTAAAGCCTCTTCCGGTCGCTTTATATCTGGTTTCCGCCCATACCATACTTTAACCGAAACACTCTCACCAGAAAAAGTCGATTTATATAAATGACTTATGCCCTGCTTTATATTTTCCTCAATAGGATAAATAACCATTGGAATCAACTCACTTCGA'..b'TTCAGCGCCCGTAGCAACTGACGACGGGTATCCATAGGTAACAATGCATTACTCATCGGCGCACCTCTAACTGGTTATTTATCACACAGCCAAAGTAACTATTTTAATGAGGCAACAGTGCGCGTTGGGTAACAAAAATGCTGAGTCAATTCGCCGGACTGAGTTATTGTCATCTCATAGAGGGCGGTATTGCAGGTTTACGCTCAAGCAGCAGCGCATTCTGACGCATGATGCGGTATACGCGTTTGGCATTGATAATGGCCATGTCGTCAGTTTCTGATTGTCTGCGCAGCAGTGCCCACACCCGACAATAACCATACCTTGGCAGCTCGCCGATAACGGTATGGATACGGTCCAGCGCTTCAGTATCATCAGGCTTGCGCTTGCGTCGACGATCCTGCCAGCTCTTCGACCGACGGGCCATGGCATGCAGTTGCACACGTGAGACCCGGAGGCAACGGCTGACAAGGCTTATTCACCATCCTCCGGCAACAAGGGCACGTGCGCTATCCACTTTTTTTGGCGACCATATTCAACAGCTTCTTTCAGCAGCTCGTTTTCCATAGTTTTCTTGCCCAGCAGGCGCTGCAGTTCTTTAATTTGCTTCATTGCCGATGCCAGTTCCGACGCGGGCACAACCTGTTCACCCGCGACTACGGCGGTAAGACTGCCTTCCTGATACTGCTTGCGCTACAGGAACAGCTGACTGGCGGCAACACCATGCTGCCGGGCGACCAGCGACACGGTCATACCGGGTTCAAAGCTCTGCTGAACAATGGCGATTTTTTCCTGAACACTGCACCGTCTGCGCTTCTCTGGACCTAAAACATCAATCATCCGGACTCCAACGACTAGTCTAAAAAATAGTATTAAGACTATCACTAACTTAAGTGATACCAACTGTCTGGAGATTCATGGGGCTAGTCTAGGAAGGATGAAGAATCTCCGGCTAACACGGGTTATACGGTATACAAATGCGAACAAGCAAACCGGTATCAAAACGCGCAGAGGTTTTGAGTGTTATGCTTCCCCCCAGCCGTTGAACACAGGTTTTTACAATCGATAACCCCAGCCCTGAACCCGGCAGTGAAGTTCCCGCTGTGCGATAAAATGCTCCGAAAACCTTTTCTCTTTCTGATTCTGAAATCCCGGGTCCACTGTCTTCGACCTCAATAACTAAAAAATCCCTTTCCCACCCTACTGACAAATCAATACGTCCCTGCGGAGGGGTAAACCGTACCGCGTTCTCCGTAACGTTTTTAATGGCGGTATAAAGGGCATTTTTGTCAGTAACAATAACCGTAAGGACTTCAGGTTCTGAGGACTGCAGAATACCAATGTCGATATCTTTTTCCGTCGCAAGAGGCAGGATTGTCTCAATTACGCTGCGAAACAGTGAAACAACATCAACGGAGTCGTGATGAGTTTTGTTCTCATTTTGTTGTTCCCGGGCCAGCGAAAGCAGTTGTTCAAGCAGTCTTTTTTCACGCGAGATGCCTGTCTGAAGGACCGCAAGCCGCTGACGAGCCTCCTCAGACATCTCTGACGCGGAAAGTCGTTCTGCCTGAAGCGAAAGTGCAGTTAAAGGCGTTCGTAATTCATGTGCCGCATCGGCTATAAAACGTTTTTGTGTCTGAATGACCGCATCAACTCTGCTCAGCAGATCGTTTATACTAACGATAAATGGTTGTATTTCATCGGGAATGTTTTTGTCTCTGACGGGTGTAAGGTCGTTGTCATGACGGGAGCAAACAGCGTCGGCCACACGTTGAAGCGGTATAAAGGCTTTTCTGACGACGAACCAGGCCACTAACATAAAAACCGGAAACAGAATGAGGAATGGGATCAGAGAACGCAAAGCGCTGCTAATTGCAATATCATCCCGGACATCGGATTGTTGTCCGACCACGACTTTTGCTTCGGGTGAATACTGGGTGATCAGTATACGGTAGCGTTTATTCCCGGACTCCACATCCTGGAATCCGTCGCTCACCGTTGAGGGTAATTCAAAATGCATCGTTGAGGCGTGTACATGAGCGGCATTATGCGGAAGATATTCAACCAAAATTTTATCCTCGTTATCCCCTTCCATGCTCCGGCCGATCTGTTGAGGAATACGCTCATTCCCTGACGAGTATTTCAGCACCAGGGTAATCTGTTTCAGCGTATTGTCCTGTAATTCATGGGATTCATCGAGCGCCAGAAAAAACGTGAGTGCAGCTGAAATCGTCCCGGTGAACAGAATGGCGATAAAAAGTGACAGCGAAAGCCGGTATTTAACTGATTTCATCATTTGTTTTTAGGGACCAGCCAGCCCACACCTCTCACGTTCCTGATTGCGTCTCGGCCAATTTTCTTTCTCAGTGAGTGGATTAAAAACTCTATCGCATTACTCTCCACCTCTTCACCCCAGCCATAGATACGATCTTCAAGGTCAGACCGGGATAAGATCCCCCCTGGTCTGATGAGAAGCGCCTCCAGCACTGCAAACTCACGGTTTGATAACAGAAAGGACAATCCGGAAGTGATGATCTGCACTTCATGGCTGTCAGGATCAAGTATCAGCTCGCCGTTGGTCAGCACCGGAGATTCGCTACCACTATTTCTGCGCAGAACAGCATGAATTCGAGCCACCAGTTCGCTCAAATCAAAGGGTTTAATAATATAATCATCGGCGCCGCCATTCAGTCCCCTGAGACGATCCTCCAGTGCATCACGTGCGGTCATTATCAGAACCGAAACCGTTGCGTTGTGTTTACGCATTCCGGCCATAACACTGAAGCCGTCCTTGCCTGGCAGACCAAGATCAAGCAGAACAAGATCATAATGTTGAGTACCAAAGGTTGAGAGGGCATCATTGCCATTTTTGACCCAGTCCACTGCAAATGAAGCTTCTCTCAGAGACTCCGCGACAATCTCACCAATCATGGCATCATCTTCAACGAGCAATATTCGCATTTAGGGGATCCCACACTAAAATTCGCCTCAACATCCGGCCGATAGCCTGAACCGGCAACGGTGATAAACCAGTACGTTTCGTTTATCCTGCCAGACAGTAGCCGATGAACCTTAACGTTTTATCTTATAAAAGCAGCAGGGTTGTAATTTTACAACCCTGCATATGGTTTACGGATTAATATGATCATGACCAATTGTAAATGGGGCTTCACAGCTGTGGTATGAAGGATTACAGTAGTTTTTATCCGCACCATTTTTTTTCGAAATCTTGTCCTTCCCGACAGTAAACGGGGCTTCACACTTATGCTGACCAGGGTTACAGTCAGCATTACCGGCATATGCTTCTGATGTCAGAACTGCCATTGTCAGCCCGGAGCAAAAGAGCATCATTGCTGCCGGCAATAATTTCTGTGTCTTTTTCATGTCAGTCACCTTATTTATACATATCGGCTTCGATGGTTTTATGGTCCTGATGGCCCTGTTCACCGATAATCACGTAATATTTACCGCCATGTTTTGCCACTGCATCTTTAAGATCCTGATTGTCCATTGTAAATCCATCCTGAGTTACGGCAATGTTTCCGATTTTATCAAGACCTGCAGCCCGGCTACGGGTAAGTTCCTGAGGGTGAATAGGTGACATGACAGAATTTGTCACGCTGGCATATACGCTGCCTGTTGCCGTAGCCATTAACAGTGCGGTTACAGCCATCAGTGTTGTACGTTTCATGATAAACCTCCTGCTGGGTGCTATTTATATTCAGGCTTTGTGGCCTGAAAGAAAAATTACAGGAGAAAACTTAGGGCATACTGAGCAACTCAATATTTTATGAAAAAATCGGGGGCGTACTACCGGTAATGATTGAAATCTGACGGTAGGGACATAACAGCAGATCTGTCAATACCTGCACAGCGATGAATCGCCACGGATAATCTAGACACTTCCGAGCCGTTGATAATACTGGTTTTCATATTCTGTCGGTGACATCTGATTGCTCGAACCATGCCGACGCTTACTGTTATAAAACATTTCGATGTAA\n' |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/alleles-output-13-1101.json --- a/test-data/alleles-output-13-1101.json Wed Jun 14 14:36:59 2017 -0400 +++ b/test-data/alleles-output-13-1101.json Thu Aug 06 11:48:49 2020 -0400 |
| b |
| b'@@ -1,1 +1,1 @@\n-{"13-1101-Paratyphi_B": {"NZ_AOXE01000059.1_60": {"name": 333445801, "seq": "ATGCCTTTTACACTTGGTCAACGCTGGATCAGCGATACAGAAAGCGAGCTGGGACTTGGAACCGTTGTTGCGATGGATGCGCGAACCGTCACCTTACTTTTCCCGTCCACGGGGGAAAACCGCCTGTATGCGCGCAGTGATTCTCCCGTGACCCGCGTCATGTTCAACCCTGGCGATACGATTACAAGCCATGAAGGCTGGCAGCTACATATCGATGAAGTAAAAGAAGAAAATGGCCTGCTTGTTTATGTCGGCACCCGCCTGGATACCGAAGAGACCAATGTGACGCTGCGCGAAGTTCTGCTCGACAGCAAGTTGGTTTTCAGTAAGCCCCAGGATCGTCTGTTCGCCGGTCAAATCGATCGAATGGATCGGTTCGCGCTGCGCTATCGCGCCCGTAAATTTCAGAGCGAGCAGTACCGGATGCCATACAGCGGCCTGCGCGGCCAGCGGACCAACCTGATCCCGCATCAGCTTAATATCGCTCATGATGTGGGTCGTCGCCACGCGCCGCGCGTACTGCTGGCGGATGAAGTGGGCTTAGGTAAAACCATTGAAGCCGGGATGATTCTGCATCAACAGTTATTATCCGGCGCGGCGGAACGCGTATTGATCATCGTGCCGGAAACCCTGCAACACCAGTGGCTGGTAGAAATGCTGCGCCGTTTCAACCTGCGCTTCGCGCTGTTCGATGACGAACGCTATACCGAAGCGCAGCACGACGCGTATAACCCGTTTGAAACCGAACAACTGGTGATCTGCTCGCTGGATTTCGCCCGCCGTAATAAGCAGCGTCTGGAACATTTGTGCGACGCCGAGTGGGATTTGCTGGTGGTCGACGAAGCGCATCATCTGGTGTGGAGTACCGATGCGCCGAGCCGTGAATATATGGCCATCGAACAGTTAGCTGAACGCGTACCGGGCGTGCTGCTGCTGACCGCCACGCCAGAACAGCTGGGGATGGAAAGCCATTTCGCCCGTCTGCGCCTGCTCGATCCGAACCGTTTCCACGATTTCGAACAGTTTGTCGAAGAACAGAAAAACTACCGTCCTGTCGCCGATGCGGTGGCCATGCTGCTGGCGGGCAATAAACTCAGCAACGACGAACTGAACAGGCTGGGCGATCTGATCGGCGAACAGGATATTGAACCGCTGTTGCAGGCCGCTAATAGCGATCGCGACGACGCGCAGGCCGCCCGTGATGAGCTGGTGTCGATGCTGATGGATCGCCACGGCACCAGCCGCGTTCTGTTCCGCAACACCCGTAACGGCGTCAAGGGGTTCCCGAAACGTGAACTGCATACGGTAAAACTGCCGCTGCCGACCCAGTATCAGACCGCCATTAAGGTCTCCGGCATTATGGGCGCGCGTAAAAGCGCGGAAGATCGCGCCCGCGATATGCTCTATCCGGAACAAATTTATCAGGAGTTCGAAGGCGATACCGGTACCTGGTGGAACTTCGACCCACGCGTTGAGTGGCTGATGGGCTATCTGACCAGCCATCGTTCGCAAAAAGTGCTGGTGATCTGCGCCAAAGCGACCACCGCGTTACAGCTGGAGCAGGTGCTGCGCGAACGCGAAGGCATCCGCGCCGCCGTGTTCCATGAGGGCATGTCTATTATCGAACGCGACCGCGCCGCCGCCTGGTTCGCCGAAGAAGATACCGGCGCGCAGGTGCTGTTATGTTCCGAAATCGGCTCCGAAGGACGTAACTTCCAGTTTGCCAGCAATCTGGTGATGTTCGACTTGCCGTTTAACCCGGATCTGCTGGAACAGCGTATTGGTCGTCTGGATCGCATCGGCCAGGCGCATGATATCCAGATCCACGTCCCGTACCTGGAAAAAACCGCCCAGTCGGTGCTGGTTCGCTGGTATCACGAAGGGCTGGACGCCTTTGAGCACACCTGTCCAACCGGCCGCGCGATTTATGATTCAGCCTACGCCAGTCTGATTAACTATCTGGCCGCGCCTGAAGAAACCGACGGGTTTGACGATCTGATCAAATCCTGCCGCGAGCAACATGAAGCGCTAAAAGCCCAGTTAGAACAGGGCCGCGACCGCCTGCTGGAGATCCACTCCAACGGTGGTGAAAAAGCCCAACAGCTTGCACAAAGCATTGAAGAACAGGACGACGACACCAACCTGATCGCGTTCGCCATGAACCTGTTCGATATCGTCGGCATTAACCAGGACGATCGCGGCGACAACCTGATCGTGCTGACGCCGTCCGACCACATGTTGGTGCCGGATTTCCCCGGCCTGCCGGAAGACGGCTGTACTATCACGTTTGAACGTGACGTAGCCCTGTCTCGCGAAGATGCGCAGTTTATTACCTGGGAACATCCGCTCATCCGTAACGGACTGGATCTGATCCTCTCCGGCGACACCGGCAGCAGCACCATTTCGCTGTTGAAAAATAAAGCGCTGCCCGTCGGCACGCTGCTGGTCGAACTGGTTTACGTCGTGGAAGCGCAGGCGCCGAAACAGCTACAACTGAACCGCTTCCTGCCGCCGACGCCGGTACGTATGCTGTTAGATAAAAACGGCAACAATCTGGCCGCCCAGGTCGAGTTTGAAACCTTCAACCGCCAGCTCAGCGCCGTGAATCGCCACACCGGTAGCAAACTGGTGAACGCCGTTCAACAGGACGTCCACGCCATTTTGCAACTGGGCGAGACGCAGATTGAAAAGTCCGCCAGAGCGCTGATTGATAACGCGCGCCGCGAGGCGGATGAAAAACTGTCCGGGGAACTGTCGCGTCTGGAAGCGCTGCGCGCCGTCAACCCGAACATTCGCGACGACGAACTTGCCGCTATCGACAGCAACCGTCAGCAGGTGCTGGAAAGCCTGAATCAGGCAGGCTGGCGTCTGGACGCGCTGCGTCTTATCGTCGTCACGCACCAATAA", "blast_result": {"qseqid": "NZ_AOXE01000059.1_60|2140847626", "stitle": 10664747, "pident": 99.897, "length": 2908, "mismatch": 2, "gapopen": 1, "qstart": 1, "qend": 2908, "sstart": 100409, "send": 103315, "evalue": 0.0, "bitscore": 5352.0, "qlen": 2908, "slen": 147648, "sseq": "ATGCCTTTTACACTTGGTCAACGCTGGATCAGCGATACAGAAAGCGAGCTGGGACTTGGAACCGTTGTTGCGATGGATGCGCGAACCGTCACCTTACTTTTCCCGTCCACGGGGGAAAACCGCCTGTATGCGCGCAGTGATTCTCCCGTGACCCGCGTCATGTTCAACCCTGGCGATACGATTACAAGCCATGAAGGCTGGCAGCTACATATCGATGAAGTAAAAGAAGAAAATGGCCTGCTTGTTTATGTCGGCACCCGCCTGGATACCGAAGAGACCAATGTGACGCTGCGCGAAGTTCTGCTCGACAGCAAGTTGGTTTTCAGTAAGCCCCAGGATCGTCTGTTCGCCGGTCAAATCGATCGAATGGATCGGTTCGCGCTGCGCTATCGCGCCCGTAAATTTCAGAGCGAGCAGTACCGGATGCCATACAGCGGCCTGCGCGGCCAGCGGACCAACCTGATCCCGCATCAGCTTAATATCGCTCATGATGTGGGTCGTCGCCACGCGCCGCGCGTACTGCTGGCGGATGAAGTGGGCTTAGGTAAAACCATTGAAGCCGGGATGATTCTGCATCAACAGTTATTATCCGGCGCGGCGGAACGCGTATTGATCATCGTGCCGGAAACCCTGCAACACCAGTGGCTGGTAGAAATGCTGCGCCGTTTCAACCTGCGCTTCGCGCTGTTCGATGACGAACGCTATACCGAAGCGC'..b'GGCGCTTGAGCACGTTGAAGCGGGTAAAACCGGTCAAGAAGAAAGCTAA", "coverage": 1.0, "is_trunc": false, "marker": "NZ_AOXE01000077.1_33", "allele": 4213771231, "is_match": true, "allele_name": 4213771231, "is_perfect": true, "has_perfect_match": true, "start_idx": 37676.0, "end_idx": 37789.0, "needs_revcomp": false, "trunc": false, "is_extended": false, "sseq_msa_gaps": 0, "sseq_msa_p_gaps": 0.0, "too_many_gaps": false}}, "NC_011149.1_467": {"name": 161888011, "seq": "ATGAAAAGCAACAAAAGCGCTGAAGCACACGAATCGCTGTTGCAATTGTCGTTCACAGCCAGTAAATTCGACCGTTTTCGAGCACAGGCGCAGGCGGTCAAAGAGTAA", "blast_result": {"qseqid": "NC_011149.1_467|161888011", "stitle": 10664711, "pident": 100.0, "length": 108, "mismatch": 0, "gapopen": 0, "qstart": 1, "qend": 108, "sstart": 146017, "send": 145910, "evalue": 1.7799999999999997e-52, "bitscore": 200.0, "qlen": 108, "slen": 345713, "sseq": "ATGAAAAGCAACAAAAGCGCTGAAGCACACGAATCGCTGTTGCAATTGTCGTTCACAGCCAGTAAATTCGACCGTTTTCGAGCACAGGCGCAGGCGGTCAAAGAGTAA", "coverage": 1.0, "is_trunc": false, "marker": "NC_011149.1_467", "allele": 161888011, "is_match": true, "allele_name": 161888011, "is_perfect": true, "has_perfect_match": true, "start_idx": 145909.0, "end_idx": 146016.0, "needs_revcomp": true, "trunc": false, "is_extended": false, "sseq_msa_gaps": 0, "sseq_msa_p_gaps": 0.0, "too_many_gaps": false}}, "NZ_AOXE01000059.1_333": {"name": 629769704, "seq": "ATGGTTCAGTGTGTACGACATTCTGTCTTACCGCGTCTGAAAAAAGACGCAGGCCTGCCGTTTTTCTTTCCGTTGAAAACCAATACCAAGCCCCTCAATTGA", "blast_result": {"qseqid": "NZ_AOXE01000059.1_333|629769704", "stitle": 10664754, "pident": 100.0, "length": 102, "mismatch": 0, "gapopen": 0, "qstart": 1, "qend": 102, "sstart": 141784, "send": 141683, "evalue": 3.6e-49, "bitscore": 189.0, "qlen": 102, "slen": 171064, "sseq": "ATGGTTCAGTGTGTACGACATTCTGTCTTACCGCGTCTGAAAAAAGACGCAGGCCTGCCGTTTTTCTTTCCGTTGAAAACCAATACCAAGCCCCTCAATTGA", "coverage": 1.0, "is_trunc": false, "marker": "NZ_AOXE01000059.1_333", "allele": 629769704, "is_match": true, "allele_name": 629769704, "is_perfect": true, "has_perfect_match": true, "start_idx": 141682.0, "end_idx": 141783.0, "needs_revcomp": true, "trunc": false, "is_extended": false, "sseq_msa_gaps": 0, "sseq_msa_p_gaps": 0.0, "too_many_gaps": false}}, "NZ_AOXE01000041.1_85": {"name": 708436169, "seq": "ATGAACCCTTCCATGCTGAACGCGACCCTACTAACAACTGCGCCATCTCGCGCAGTGGTCGTCGTGCGTGTGGTGGTGGTCGTCGGCAATGCGCCGTAG", "blast_result": {"qseqid": "NZ_AOXE01000041.1_85|708436169", "stitle": 10664772, "pident": 100.0, "length": 99, "mismatch": 0, "gapopen": 0, "qstart": 1, "qend": 99, "sstart": 14705, "send": 14803, "evalue": 1.61e-47, "bitscore": 183.0, "qlen": 99, "slen": 68361, "sseq": "ATGAACCCTTCCATGCTGAACGCGACCCTACTAACAACTGCGCCATCTCGCGCAGTGGTCGTCGTGCGTGTGGTGGTGGTCGTCGGCAATGCGCCGTAG", "coverage": 1.0, "is_trunc": false, "marker": "NZ_AOXE01000041.1_85", "allele": 708436169, "is_match": true, "allele_name": 708436169, "is_perfect": true, "has_perfect_match": true, "start_idx": 14704.0, "end_idx": 14802.0, "needs_revcomp": false, "trunc": false, "is_extended": false, "sseq_msa_gaps": 0, "sseq_msa_p_gaps": 0.0, "too_many_gaps": false}}, "NZ_AOXE01000041.1_84": {"name": 551814723, "seq": "ATGAGCGTAGTGGATATCACCATTCTTATCCTGAAACTCATTGTTGCAGCACTGCAACTGCTTGATGCTGTTCTGAAATACCTTAAGTAA", "blast_result": {"qseqid": "NZ_AOXE01000041.1_84|551814723", "stitle": 10664772, "pident": 100.0, "length": 90, "mismatch": 0, "gapopen": 0, "qstart": 1, "qend": 90, "sstart": 14071, "send": 13982, "evalue": 1.44e-42, "bitscore": 167.0, "qlen": 90, "slen": 68361, "sseq": "ATGAGCGTAGTGGATATCACCATTCTTATCCTGAAACTCATTGTTGCAGCACTGCAACTGCTTGATGCTGTTCTGAAATACCTTAAGTAA", "coverage": 1.0, "is_trunc": false, "marker": "NZ_AOXE01000041.1_84", "allele": 551814723, "is_match": true, "allele_name": 551814723, "is_perfect": true, "has_perfect_match": true, "start_idx": 13981.0, "end_idx": 14070.0, "needs_revcomp": true, "trunc": false, "is_extended": false, "sseq_msa_gaps": 0, "sseq_msa_p_gaps": 0.0, "too_many_gaps": false}}}}\n\\ No newline at end of file\n' |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/alleles-output.json --- a/test-data/alleles-output.json Wed Jun 14 14:36:59 2017 -0400 +++ b/test-data/alleles-output.json Thu Aug 06 11:48:49 2020 -0400 |
| b |
| b'@@ -1,1 +1,1 @@\n-{"AE014613-699860": {"NZ_AOXE01000059.1_60": {"name": 712233770, "seq": "ATGCCTTTTACACTTGGTCAACGCTGGATCAGCGATACAGAAAGCGAGCTGGGACTTGGAACCGTTGTTGCGATGGATGCGCGAACCGTCACCTTACTTTTCCCGTCCACGGGGGAAAACCGCCTGTATGCGCGCAGTGATTCTCCCGTGACCCGCGTCATGTTCAACCCTGGCGATACGATTACAAGCCATGAAGGCTGGCAGCTACATATCGATGAAGTAAAAGAAGAAAATGGCCTGCTTGTTTATGTCGGCACCCGCCTGGATACCGAAGAAACCAATGTGACGTTGCGCGAAGTTCTGCTCGACAGCAAGTTGGTTTTCAGTAAGCCCCAGGATCGTCTGTTCGCCGGTCAAATCGATCGAATGGATCGGTTCGCGCTGCGCTATCGCGCCCGTAAATTTCAGAGCGAGCAGTACCGGATGCCATACAGCGGCCTGCGCGGTCAGCGGACCAACCTGATCCCGCATCAGCTTAATATCGCTCATGATGTGGGTCGTCGCCACGCGCCGCGCGTACTGCTGGCGGATGAAGTGGGCTTAGGTAAAACCATTGAAGCCGGGATGATTCTGCATCAACAGTTATTATCCGGCGCGGCGGAACGCGTATTGATCATCGTTCCGGAAACCCTGCAACACCAGTGGCTGGTAGAAATGCTGCGCCGTTTCAACCTGCGCTTCGCGCTGTTCGATGACGAACGCTATACCGAAGCGCAGCACGACGCGTATAACCCGTTTGAAACCGAACAACTGGTGATCTGCTCGCTGGATTTCGCCCGCCGCAATAAGCAGCGTCTGGAACATTTGTGCGACGCCGAGTGGGATTTGCTGGTGGTCGACGAAGCGCATCATCTGGTGTGGAGCACCGATGCGCCGAGCCGTGAATATATGGCCATCGAACAGTTAGCTGAACGCGTGCCGGGCGTGCTGCTGCTGACCGCCACGCCAGAACAGCTGGGGATGGAAAGCCATTTCGCCCGTCTGCGCCTGCTCGATCCGAACCGTTTCCACGATTTCGAACAGTTTGTCGAAGAACAGAAAAACTACCGCCCTGTCGCCGATGCGGTGGCCATGCTGCTGGCGGGCAATAAACTCAGCAACGACGAACTGAACAGACTGGGCGATCTGATCGGCGAACAGGATATTGAACCGCTGTTACAGGCCGCTAATAGCGATCGCGACGACGCGCAGGCCGCCCGTGATGAGCTGGTGTCGATGCTGATGGATCGCCACGGTACCAGCCGCGTTCTGTTCCGCAACACCCGTAACGGCGTCAAGGGGTTCCCGAAACGTGAACTGCATACGGTAAAACTGCCGCTGCCGACCCAGTATCAGACCGCCATTAAGGTCTCCGGCATTATGGGCGCGCGTAAAAGCGCGGAAGATCGCGCCCGCGATATGCTCTATCCGGAACAAATTTATCAGGAGTTCGAAGGCGATACCGGCACCTGGTGGAACTTCGACCCACGCGTTGAGTGGCTGATGGGCTATCTGACCAGCCATCGTTCGCAAAAAGTGCTGGTGATCTGCGCCAAGGCGACCACCGCGTTACAGCTGGAGCAGGTGCTGCGCGAACGCGAAGGCATCCGCGCCGCCGTGTTCCATGAGGGCATGTCGATTATCGAACGCGACCGCGCCGCCGCCTGGTTCGCCGAAGAAGATACCGGCGCGCAGGTGCTGTTATGTTCCGAAATCGGCTCCGAAGGACGTAACTTCCAGTTTGCCAGCAATCTGGTGATGTTCGACTTGCCGTTTAACCCGGATCTGCTGGAACAGCGTATTGGTCGTCTGGATCGTATCGGCCAGGCGCATGATATCCAGATCCACGTCCCGTACCTGGAAAAAACCGCCCAGTCGGTGCTGGTTCGCTGGTATCACGAAGGGCTGGACGCCTTTGAGCACACTTGCCCGACCGGTCGCGCGATTTATGATTCAGCCTACGCCAGTCTGATTAACTATCTGGCCGCGCCTGAAGAAACCGACGGGTTTGACGATCTGATCAAATCCTGCCGCGAACAACATGAAGCGCTAAAAGCCCAGTTAGAACAGGGCCGCGACCGCCTGCTGGAGATCAACTCCAACGGTGGTGAAAAAGCCCAACAGCTTGCACAAAGCATTGAAGAACAGGACGACGACACCAACCTGATCGCGTTCGCCATGAACCTGTTCGATATCGTCGGCATTAACCAGGATGATCGCGGCGACAACCTGATCGTGCTGACGCCGTCCGACCACATGTTGGTGCCGGATTTCCCCGGCCTGCCGGAAGACGGTTGTACTATCACGTTTGAACGTGACGTAGCCCTGTCTCGCGAAGATGCGCAGTTTATTACCTGGGAACATCCGCTCATCCGTAACGGACTGGATCTGATCCTCTCCGGCGATACCGGCAGCAGCACCATTTCGCTGTTGAAAAATAAAGCGCTGCCCGTCGGCACGCTGCTGGTCGAACTGGTTTACGTCGTGGAAGCGCAGGCGCCGAAACAGCTACAACTGAACCGCTTCCTGCCGCCGACGCCGGTACGTATGCTGTTAGATAAAAACGGCAACAATCTGGCCGCCCAGGTCGAGTTTGAAACCTTCAACCGCCAGCTCAGCGCCGTGAATCGCCACACCGGTAGCAAACTGGTGAACGCCGTTCAACAGGACGTCCACGCCATTTTGCAACTGGGCGAGACGCAGATTGAACAGTCCGCCAGAGCGCTGATTGATAACGCGCGCCGCGAGGCAGATGAAAAACTGTCCGGGGAACTGTCGCGTCTGGAAGCGCTGCGCGCCGTCAACCCGAACATCCGCGACGACGAACTTGCCGCTATCGACAGCAACCGTCAGCAGGTGCTGGAAAGCCTGAATCAGGCAGGCTGGCGTCTGGACGCGCTGCGTCTTATCGTCGTCACGCACCAATAA", "blast_result": {"qseqid": "NZ_AOXE01000059.1_60|1987381665", "stitle": "gi|29140506|gb|AE014613.1| Salmonella enterica subsp. enterica serovar Typhi Ty2, complete genome", "pident": 99.96600000000001, "length": 2908, "mismatch": 0, "gapopen": 1, "qstart": 1, "qend": 2908, "sstart": 112697, "send": 109791, "evalue": 0.0, "bitscore": 5363.0, "qlen": 2908, "slen": 699860, "sseq": "ATGCCTTTTACACTTGGTCAACGCTGGATCAGCGATACAGAAAGCGAGCTGGGACTTGGAACCGTTGTTGCGATGGATGCGCGAACCGTCACCTTACTTTTCCCGTCCACGGGGGAAAACCGCCTGTATGCGCGCAGTGATTCTCCCGTGACCCGCGTCATGTTCAACCCTGGCGATACGATTACAAGCCATGAAGGCTGGCAGCTACATATCGATGAAGTAAAAGAAGAAAATGGCCTGCTTGTTTATGTCGGCACCCGCCTGGATACCGAAGAAACCAATGTGACGTTGCGCGAAGTTCTGCTCGACAGCAAGTTGGTTTTCAGTAAGCCCCAGGATCGTCTGTTCGCCGGTCAAATCGATCGAATGGATCGGTTCGCGCTGCGCTATCGCGCCCGTAAATTTCAGAGCGAGCAGTACCGGATGCCATACAGCGGCCTGCGCGGTCAGCGGACCAACCTGATCCCGCATCAGCTTAATATCGCTCATGATGTGGGTCGTCGCCACGCGCCGCGCGTACTGCTGGCGGATGAAGTGGGCTTAGGTAAAACCATTGAAGCCGGGATGATTCTGCATCAACAGTT-ATTATCCGGCGCGGCGGAACGCGTATTGATCA'..b'"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_209": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_210": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_211": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_212": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_214": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_215": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_220": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_223": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_249": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_251": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_262": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_264": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_267": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_272": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_282": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_283": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_286": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_294": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_40": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_48": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_49": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_52": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_55": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_59": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_62": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_64": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_76": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_79": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_83": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_87": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_92": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000081.1_97": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_10": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_17": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_20": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_34": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_57": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_60": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_62": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_63": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXE01000085.1_65": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXI01000002.1_306": {"blast_result": null, "name": null, "seq": null}, "NZ_AOXI01000016.1_73": {"blast_result": null, "name": null, "seq": null}, "NZ_AOYO01000084.1_456": {"blast_result": null, "name": null, "seq": null}, "NZ_AOYX01000009.1_43": {"blast_result": null, "name": null, "seq": null}, "NZ_AOYX01000031.1_11": {"blast_result": null, "name": null, "seq": null}, "NZ_AOYX01000060.1_42": {"blast_result": null, "name": null, "seq": null}, "NZ_AOYX01000075.1_47": {"blast_result": null, "name": null, "seq": null}, "NZ_AOYX01000092.1_135": {"blast_result": null, "name": null, "seq": null}, "NZ_APAO01000014.1_55": {"blast_result": null, "name": null, "seq": null}, "NZ_AYDA01000043.1_275": {"blast_result": null, "name": null, "seq": null}, "NZ_CM001471.1_3941": {"blast_result": null, "name": null, "seq": null}}}\n\\ No newline at end of file\n' |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/cgmlst-profiles-13-1101.csv --- a/test-data/cgmlst-profiles-13-1101.csv Wed Jun 14 14:36:59 2017 -0400 +++ b/test-data/cgmlst-profiles-13-1101.csv Thu Aug 06 11:48:49 2020 -0400 |
| b |
| b'@@ -1,2 +1,2 @@\n 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73887664,2983916931,3219814449,4276130360,1745976133,2077249876,2077738650,1430683295,2795082944,2904170129,1830292553,3712766732,1149384633,246770399,374122876,282105442,3473113586,4252575321,299233641,2651864740,1436693988,2545200385,225275747,1320460320,2353669245,1780432149,1667064808,4127891750,2307413670,1994382719,1324934990,912019826,767517378,300758334,2732360708,1476689272,316910970,726132721,2404196596,628816999,715723428,439814616,3868995612,3923470646,922813689,596464946,2068726690,514528221,1235021963,1738069373,2194946451,1542872411,4178717449,2356733911,3699174113,2832724106,3646752757,2770658758,431631459,3155517162,3250676045,1781281347,747567264,550964520,528121872,308073351,1638651814,593462775,3179271034,399278785,498374695,1439849948,1080346469,2094006958,551814723,708436169,828533582,2587507857,260803180,3578386263,3641973773,3721979689,119594086,2079191084,1524097055,4237193625,2084418558,2598101487,2243362473,132779259,2539563995,3147004960,1005413801,398274060,683371912,2311744161,2098379863,830225365,4090514893,3192866010,489837497,2392764491,4177019046,616151434,195979449,2688075180,571430577,3183061957,2253874773,1342053785,162097627,1109320307,664703088,4249405940,4228448746,791036150,629769704,3428477437,1226961299,21264588,2569933901,355071861,4175098203,2467894309,3206518183,3822365505,2170727246,2979506855,3572598511,257452301,2336031118,1809767828,3438653864,3027329430,3523309637,2590187629,2536338461,2306804434,3643876638,2409457196,3781645063,333445801,2424781734,1291136085,1047370225,698589548,2519701742,3276128843,3548183620,4289919471,1965001593,1842785664,3995669301,2390483285,3371174263,1245009874,2919271763,1854288580,3832041954,2672990925,4227342379,3643634927,333081518,2139774773,121039594,4267848688,1426386553,93691856,2617592815,2061334442,484067521,338226340,595233173,1246387686,1236556171,3165457710,649192555,3831614515,2226007812,2615307626,1822361792,1251756376,2953514645,226121950,3523430840,799742746,4250299083,1635467073,563085019,4033110422,2734837303,1982008089,2061617626,2494351896,3172400135,309774068,2754698655,2253744431,2081649483,3386486144,4213771231,352954861,216514641,744347523,2758229229,1743327588,406171140,1043329926,294538384,2505247376,4189957668,2899049638,2078682862,4109265911,2639318025,4269576185,3445065778,1716630297,3912522894,10121991,3254127745,3047220128,4248599762,353328767,1019572313,3239852751,2459342739,1547676029,2844497268,2203341188,4282035484,3699551722,121975481,3289785650,1171029009,4054067887,2414391967,3344082709,3523966715,3187079670,1371090518,2289872656,4200440493,3463404426,822043034,637470977,1500184554,3978410193,3572777440,2763485497,2649675872,625657224,2641882719,1619775958,1484137762,1613239859,3150901989,1366744981,504704912,1143941611,2475598021,3887842238,1839157263,3017501787,2881079752,3306151290,3554479089,128939352,2472742281,491087478,601432611,1671956993,938581157,486088087,2151397774,2972709081,3276924,4149206546,4185944080\n' |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/cgmlst-profiles.csv --- a/test-data/cgmlst-profiles.csv Wed Jun 14 14:36:59 2017 -0400 +++ b/test-data/cgmlst-profiles.csv Thu Aug 06 11:48:49 2020 -0400 |
| b |
| b'@@ -1,2 +1,2 @@\n ,NC_003198.1_3005,NC_006905.1_2841,NC_011149.1_467,NC_017623.1_3300,NZ_ABFH02000002.1_1303,NZ_AOXE01000003.1_37,NZ_AOXE01000003.1_39,NZ_AOXE01000003.1_57,NZ_AOXE01000003.1_7,NZ_AOXE01000003.1_70,NZ_AOXE01000004.1_10,NZ_AOXE01000004.1_101,NZ_AOXE01000004.1_12,NZ_AOXE01000004.1_134,NZ_AOXE01000004.1_135,NZ_AOXE01000004.1_14,NZ_AOXE01000004.1_140,NZ_AOXE01000004.1_154,NZ_AOXE01000004.1_35,NZ_AOXE01000004.1_36,NZ_AOXE01000004.1_39,NZ_AOXE01000004.1_59,NZ_AOXE01000004.1_68,NZ_AOXE01000004.1_74,NZ_AOXE01000004.1_87,NZ_AOXE01000007.1_13,NZ_AOXE01000007.1_18,NZ_AOXE01000007.1_20,NZ_AOXE01000007.1_48,NZ_AOXE01000008.1_59,NZ_AOXE01000008.1_63,NZ_AOXE01000009.1_17,NZ_AOXE01000011.1_101,NZ_AOXE01000011.1_77,NZ_AOXE01000011.1_82,NZ_AOXE01000011.1_83,NZ_AOXE01000011.1_85,NZ_AOXE01000016.1_13,NZ_AOXE01000016.1_8,NZ_AOXE01000017.1_117,NZ_AOXE01000017.1_118,NZ_AOXE01000017.1_130,NZ_AOXE01000017.1_4,NZ_AOXE01000017.1_40,NZ_AOXE01000017.1_43,NZ_AOXE01000017.1_54,NZ_AOXE01000017.1_59,NZ_AOXE01000017.1_80,NZ_AOXE01000017.1_82,NZ_AOXE01000017.1_96,NZ_AOXE01000019.1_13,NZ_AOXE01000019.1_14,NZ_AOXE01000019.1_24,NZ_AOXE01000021.1_10,NZ_AOXE01000021.1_11,NZ_AOXE01000021.1_165,NZ_AOXE01000021.1_29,NZ_AOXE01000021.1_38,NZ_AOXE01000021.1_49,NZ_AOXE01000021.1_6,NZ_AOXE01000021.1_61,NZ_AOXE01000021.1_79,NZ_AOXE01000023.1_11,NZ_AOXE01000023.1_25,NZ_AOXE01000023.1_30,NZ_AOXE01000024.1_3,NZ_AOXE01000024.1_35,NZ_AOXE01000024.1_38,NZ_AOXE01000025.1_13,NZ_AOXE01000025.1_14,NZ_AOXE01000025.1_20,NZ_AOXE01000031.1_102,NZ_AOXE01000031.1_106,NZ_AOXE01000031.1_70,NZ_AOXE01000031.1_80,NZ_AOXE01000033.1_11,NZ_AOXE01000033.1_12,NZ_AOXE01000033.1_14,NZ_AOXE01000033.1_17,NZ_AOXE01000033.1_19,NZ_AOXE01000033.1_2,NZ_AOXE01000033.1_21,NZ_AOXE01000033.1_26,NZ_AOXE01000033.1_3,NZ_AOXE01000033.1_30,NZ_AOXE01000033.1_34,NZ_AOXE01000033.1_38,NZ_AOXE01000033.1_43,NZ_AOXE01000033.1_51,NZ_AOXE01000034.1_103,NZ_AOXE01000034.1_106,NZ_AOXE01000034.1_111,NZ_AOXE01000034.1_112,NZ_AOXE01000034.1_113,NZ_AOXE01000034.1_119,NZ_AOXE01000034.1_126,NZ_AOXE01000034.1_127,NZ_AOXE01000034.1_133,NZ_AOXE01000034.1_134,NZ_AOXE01000034.1_164,NZ_AOXE01000034.1_173,NZ_AOXE01000034.1_53,NZ_AOXE01000034.1_82,NZ_AOXE01000035.1_13,NZ_AOXE01000035.1_21,NZ_AOXE01000036.1_108,NZ_AOXE01000036.1_116,NZ_AOXE01000036.1_15,NZ_AOXE01000036.1_157,NZ_AOXE01000036.1_16,NZ_AOXE01000036.1_2,NZ_AOXE01000036.1_3,NZ_AOXE01000036.1_31,NZ_AOXE01000036.1_39,NZ_AOXE01000036.1_43,NZ_AOXE01000036.1_58,NZ_AOXE01000036.1_66,NZ_AOXE01000036.1_98,NZ_AOXE01000040.1_19,NZ_AOXE01000040.1_28,NZ_AOXE01000040.1_31,NZ_AOXE01000041.1_33,NZ_AOXE01000041.1_73,NZ_AOXE01000041.1_75,NZ_AOXE01000041.1_76,NZ_AOXE01000041.1_84,NZ_AOXE01000041.1_85,NZ_AOXE01000041.1_87,NZ_AOXE01000043.1_4,NZ_AOXE01000047.1_56,NZ_AOXE01000047.1_57,NZ_AOXE01000050.1_18,NZ_AOXE01000050.1_44,NZ_AOXE01000052.1_115,NZ_AOXE01000052.1_128,NZ_AOXE01000052.1_131,NZ_AOXE01000052.1_137,NZ_AOXE01000052.1_141,NZ_AOXE01000052.1_23,NZ_AOXE01000052.1_36,NZ_AOXE01000052.1_38,NZ_AOXE01000052.1_41,NZ_AOXE01000052.1_43,NZ_AOXE01000052.1_78,NZ_AOXE01000052.1_92,NZ_AOXE01000053.1_113,NZ_AOXE01000053.1_128,NZ_AOXE01000053.1_130,NZ_AOXE01000053.1_166,NZ_AOXE01000053.1_173,NZ_AOXE01000053.1_180,NZ_AOXE01000053.1_190,NZ_AOXE01000053.1_217,NZ_AOXE01000053.1_86,NZ_AOXE01000059.1_11,NZ_AOXE01000059.1_129,NZ_AOXE01000059.1_133,NZ_AOXE01000059.1_15,NZ_AOXE01000059.1_174,NZ_AOXE01000059.1_182,NZ_AOXE01000059.1_184,NZ_AOXE01000059.1_189,NZ_AOXE01000059.1_229,NZ_AOXE01000059.1_31,NZ_AOXE01000059.1_32,NZ_AOXE01000059.1_325,NZ_AOXE01000059.1_328,NZ_AOXE01000059.1_333,NZ_AOXE01000059.1_335,NZ_AOXE01000059.1_336,NZ_AOXE01000059.1_338,NZ_AOXE01000059.1_35,NZ_AOXE01000059.1_353,NZ_AOXE01000059.1_363,NZ_AOXE01000059.1_37,NZ_AOXE01000059.1_370,NZ_AOXE01000059.1_372,NZ_AOXE01000059.1_38,NZ_AOXE01000059.1_395,NZ_AOXE01000059.1_396,NZ_AOXE01000059.1_408,NZ_AOXE01000059.1_411,NZ_AOXE01000059.1_418,NZ_AOXE01000059.1_42,NZ_AOXE01000059.1_427,NZ_AOXE01000059.1_430,NZ_AOXE01000059.1_433,NZ_AOXE0100005'..b'000072.1_3,NZ_AOXE01000072.1_41,NZ_AOXE01000072.1_42,NZ_AOXE01000072.1_60,NZ_AOXE01000072.1_65,NZ_AOXE01000072.1_73,NZ_AOXE01000072.1_8,NZ_AOXE01000072.1_82,NZ_AOXE01000072.1_83,NZ_AOXE01000072.1_86,NZ_AOXE01000072.1_93,NZ_AOXE01000073.1_11,NZ_AOXE01000073.1_130,NZ_AOXE01000073.1_144,NZ_AOXE01000073.1_15,NZ_AOXE01000073.1_19,NZ_AOXE01000073.1_48,NZ_AOXE01000073.1_79,NZ_AOXE01000073.1_85,NZ_AOXE01000073.1_98,NZ_AOXE01000077.1_25,NZ_AOXE01000077.1_28,NZ_AOXE01000077.1_29,NZ_AOXE01000077.1_33,NZ_AOXE01000077.1_35,NZ_AOXE01000079.1_15,NZ_AOXE01000079.1_4,NZ_AOXE01000080.1_12,NZ_AOXE01000080.1_13,NZ_AOXE01000080.1_20,NZ_AOXE01000081.1_103,NZ_AOXE01000081.1_105,NZ_AOXE01000081.1_124,NZ_AOXE01000081.1_136,NZ_AOXE01000081.1_179,NZ_AOXE01000081.1_186,NZ_AOXE01000081.1_190,NZ_AOXE01000081.1_193,NZ_AOXE01000081.1_195,NZ_AOXE01000081.1_200,NZ_AOXE01000081.1_201,NZ_AOXE01000081.1_209,NZ_AOXE01000081.1_210,NZ_AOXE01000081.1_211,NZ_AOXE01000081.1_212,NZ_AOXE01000081.1_214,NZ_AOXE01000081.1_215,NZ_AOXE01000081.1_220,NZ_AOXE01000081.1_223,NZ_AOXE01000081.1_249,NZ_AOXE01000081.1_251,NZ_AOXE01000081.1_262,NZ_AOXE01000081.1_264,NZ_AOXE01000081.1_267,NZ_AOXE01000081.1_272,NZ_AOXE01000081.1_282,NZ_AOXE01000081.1_283,NZ_AOXE01000081.1_286,NZ_AOXE01000081.1_294,NZ_AOXE01000081.1_40,NZ_AOXE01000081.1_48,NZ_AOXE01000081.1_49,NZ_AOXE01000081.1_52,NZ_AOXE01000081.1_55,NZ_AOXE01000081.1_59,NZ_AOXE01000081.1_62,NZ_AOXE01000081.1_64,NZ_AOXE01000081.1_76,NZ_AOXE01000081.1_79,NZ_AOXE01000081.1_83,NZ_AOXE01000081.1_87,NZ_AOXE01000081.1_92,NZ_AOXE01000081.1_97,NZ_AOXE01000083.1_45,NZ_AOXE01000083.1_47,NZ_AOXE01000083.1_53,NZ_AOXE01000083.1_74,NZ_AOXE01000083.1_86,NZ_AOXE01000085.1_10,NZ_AOXE01000085.1_17,NZ_AOXE01000085.1_20,NZ_AOXE01000085.1_34,NZ_AOXE01000085.1_57,NZ_AOXE01000085.1_58,NZ_AOXE01000085.1_60,NZ_AOXE01000085.1_62,NZ_AOXE01000085.1_63,NZ_AOXE01000085.1_65,NZ_AOXI01000002.1_306,NZ_AOXI01000005.1_72,NZ_AOXI01000016.1_73,NZ_AOYI01000008.1_9,NZ_AOYL01000006.1_89,NZ_AOYO01000084.1_456,NZ_AOYX01000009.1_43,NZ_AOYX01000031.1_11,NZ_AOYX01000060.1_42,NZ_AOYX01000075.1_47,NZ_AOYX01000092.1_135,NZ_APAO01000014.1_55,NZ_AYDA01000043.1_275,NZ_CM001471.1_3941\n-AE014613-699860,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,\n+AE014613-699860,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1562195475,926214622,2197498164,398274060,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,2516828756,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,\n' |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/novel-alleles-13-1101.fasta --- a/test-data/novel-alleles-13-1101.fasta Wed Jun 14 14:36:59 2017 -0400 +++ b/test-data/novel-alleles-13-1101.fasta Thu Aug 06 11:48:49 2020 -0400 |
| b |
| b'@@ -16,10 +16,10 @@\n ATGAGCCAGCAAGTCATTATTTTTGATACGACCTTACGCGACGGCGAACAAGCGTTACAGGCCAGCCTGAGCGCGAAAGAGAAGCTGCAGATTGCCCTGGCCCTTGAGCGCATGGGTGTTGATGTCATGGAAGTAGGCTTCCCGGTCTCTTCTCCGGGTGATTTTGAATCCGTCCAAACCATCGCCCGCACCATTAAAAACAGCCGCGTTTGCGCCCTGGCGCGTTGTGTAGAAAAAGACATCGACGTCGCGGCACAGGCGCTGAAGGTCGCCGACGCGTTTCGCATCCATACTTTTATCGCCACCTCGCCAATGCACATCGCCACCAAGCTGCGCAGCACGCTGGATGAGGTCATCGAACGCGCGGTATACATGGTTAAGCGGGCGCGTAATTACACTGATGACGTGGAGTTCTCCTGCGAAGATGCTGGCCGGACGCCTGTTGACGATCTGGCGCGCGTGGTGGAAGCCGCTATAAACGCCGGCGCGAGAACCATTAATATTCCCGATACCGTGGGCTATACCATGCCGTTTGAGTTCGCGGGAATCATTTCCGGCCTGTATGAACGCGTCCCCAATATCGACAAAGCCATCATCTCCGTTCATACCCACGACGATTTAGGGATAGCCGTAGGCAACTCGCTGGCGGCAGTACATGCGGGCGCGCGTCAGGTTGAAGGCGCGATGAACGGTATCGGAGAACGTGCCGGTAACTGCGCGCTGGAAGAAGTAATCATGGCGATTAAAGTGCGCAAAGACATCATGAACGTACACACCAATATCAATCACCACGAAATCTGGCGCACCAGCCAGACCGTCAGCCAGATCTGTAACATGCCGATCCCGGCCAACAAAGCAATTGTCGGCAGCGGCGCTTTCGCCCACTCTTCCGGCATCCACCAGGATGGCGTCCTCAAGAACCGCGAAAACTACGAAATCATGACGCCTGAGTCCATCGGTCTGAACCAGATACAGCTGAACCTGACCTCCCGCTCTGGCCGTGCCGCCGTGAAACATCGCATGGAAGAGATGGGTTACAAGGACACAGACTACAACATGGACCACCTGTACGACGCGTTCCTGAAGCTGGCGGACAAAAAAGGCCAGGTGTTCGACTATGACCTGGAAGCGCTGGCATTTATTAATAAACAGCAAGAAGAACCAGAGCATTTCCGCCTGGATTACTTCAGCGTGCAGTCCGGCTCCAGCGATATCGCCACTGCTTCCGTGAAGCTGGCCTGTGGTGAAGAGATCAAGGCCGAGGCGGCGAACGGCAACGGCCCGGTCGACGCCATCTATCAGGCGATTAACCGCATCACTGGCTACGACGTTGAGTTGGTTAAATACGACCTGAACGCCAAAGGCCAGGGCAAAGACGCGCTGGGTCAGGTCGATATCGTCGTGAACCATCATGGTCGCCGCTTCCACGGCGTCGGGCTGGCGACGGATATCGTCGAATCCTCCGCCAAAGCGATGGTGCACGTACTGAACAATATCTGGCGCGCCGCCGAAGTTGAAAAAGAATTGCAACGCAAAGCTCAAAATAAAGAGAACAACAAGGAAACCGTGTAA\n >NZ_AOXE01000085.1_34|504704912\n ATGTCTGAACAAAACGCACAGGGCGCTGACGAGGTAGTCGATCTTAACAATGAAATGAAGGCACGTCGCGAGAAGCTGGCTGCACTGCGTGAGCAGGGTATCCCGTTCCCGAACGATTTCCGTCGTGACCGTACCTCAGACCAACTGCACGCAGAGTTTGACGCGAAAGAAGCTGAAGAACTGGAAGCGCTGAATATTGAAGTGTCCGTCGCGGGCCGTATGATGACTCGCCGTATTATGGGTAAAGCCTCTTTTGTTACCCTGCAAGACGTAGGCGGCCGCATTCAGCTGTATGTGGCGCGCGATGATCTGCCGGAAGGCGTTTACAACGAGCAGTTCAAGAAGTGGGATCTTGGCGATATCCTCGGCGCGAAAGGTAAGCTGTTCAAAACCAAAACCGGCGAGCTGTCTATCCACTGCACCGAACTGCGCCTGCTGACGAAAGCGCTGCGTCCGTTGCCGGATAAATTCCACGGCCTGCAGGACCAGGAAGCGCGCTATCGCCAGCGTTATCTGGATCTCATCTCTAACGATGAATCCCGTAACACCTTCAAAACCCGTTCGAAGATCCTGGCCGGTATTCGCCAGTTTATGGTTGCTCGCGGCTTTATGGAAGTCGAAACGCCGATGATGCAGGTGATCCCAGGCGGCGCGTCTGCCCGTCCGTTTATCACCCATCACAACGCGCTGGATCTGGACATGTACCTGCGTATCGCGCCGGAACTGTACCTCAAGCGTCTGGTGGTTGGCGGCTTCGAACGCGTATTCGAAATTAACCGTAACTTCCGTAACGAAGGCATCTCCGTGCGCCATAATCCTGAGTTCACCATGATGGAACTCTATATGGCGTATGCGGACTACAAAGACCTGATCGAGCTGACGGAGTCTCTGTTCCGTACGCTGGCGCAGGATGTTCTGGGCACCACCCAGGTTCCGTACGGTGATGAAGTGTTTGACTTCGGTAAGCCGTTCGAAAAACTGACCATGCGTGAAGCGATCAAGAAATATCGTCCGGAAACGGATATGGCTGATCTGGACAACTTCGACTCCGCGAAGGCGATTGCTGAAAGCATCGGCATTCACGTCGAGAAGAGCTGGGGTCTGGGCCGTATCGTCACCGAGATCTTTGACGAAGTCGCTGAAGCGCATCTGATTCAGCCGACCTTCATCACCGAATATCCGGCTGAAGTGTCTCCGCTGGCGCGTCGTAATGATGTGAACCCGGAAATCACTGACCGCTTCGAGTTCTTTATCGGCGGTCGTGAAATCGGCAATGGCTTTAGCGAGTTGAACGATGCGGAAGACCAGGCGCAGCGTTTCCTGGATCAGGTTAATGCAAAAGCGGCGGGCGACGACGAAGCCATGTTCTACGACGAAGACTACGTGACGGCGCTGGAACACGGTTTACCGCCGACAGCGGGTCTGGGAATTGGTATCGACCGTATGGTGATGCTGTTTACTAACAGCCACACGATCCGCGACGTTATTCTGTTCCCGGCGATGCGTCCGGTGAAATAA\n+>NZ_AOXE01000059.1_32|4249405940\n+GTGGCAGATCGTAATTTGCGCGACCTTCTTGCTCCGTGGGTGGCTGGACTACCCGCGCGAGAACTGCGAGAGATGACGCTCGACAGCCGTGTGGCTGCGGCGGGCGATCTCTTTGTGGCAGTGGTGGGTCATCAGGCGGACGGGCGTCGATATATCCCGCAGGCGATAGCGCAAGGCGTAGCTGCCATTATTGCAGAGGCGAAAGACGAGGCGAGCGACGGTGAGATTCGCGAAATGCACGGCGTACCGGTCGTCTATCTCAGCCAGCTCAATGAGCGTTTATCTGCGCTGGCGGGCCGCTTTTACCATGAGCCATCTGAAAACATGCGTCTGGTGGCGGTGACCGGGACCAATGGCAAGACCACCACCACCCAACTACTGGCGCAGTGGAGCCAGTTGCTCGGCGAAACCAGCGCAGTGATGGGGACGGTAGGTAACGGACTGTTGGGTAAAGTGATCCCGACGGAGAACACAACCGGTTCCGCTGTGGATGTTCAGCATGTGCTGGCCAGCCTGGTTGCGCAGGGCGCGACCTTCGGCGCGATGGAAGTCTCTTCTCACGGCCTGGTGCAGCATCGCGTGGCGGCGCTGAAATTTGCCGCCTCCGTGTTTACTAATTTGAGCCGCGACCATCTCGACTATCATGGCGATATGGCGCATTACGAGGCGGCAAAATGGATGCTTTATTCCACCCACCATCACGGTCAGGCAATCGTCAACGCCGATGATGAAGTTGGACGCCGCTGGCTGGCGTCGCTACCCGATGCGGTCGCGGTATCAATGGAAGGGCATATCAACCCTAACTGTCACGGTCGTT'..b'GGTCAGGGAAAAGGCAGCTTATGCTGCCGCGAACTTACTGGTGAGCGATTATGTCAATGAATGA\n+>NZ_AOXE01000052.1_38|132779259\n+ATGGACTGGCTGGCAAAATATTGGTGGATTCTGGTATTGGTGTTTCTGGTAGGCGTACTGCTGAATGTGATCAAAGATCTCAAACGCATCGACCATAAGAAATTCCTTGCCAATAAACCTGAGCTGCCCCCGCATCGCGATTTTAACGATAAGTGGGACGATGAAGACGGCTGGCCGAAGAAAGATCAGCCGAAAAAGTAA\n >NZ_AOXE01000004.1_12|2932852483\n ATGGCAATCCGTAAACGTTTTATTGCAGGCGCGAAATGTCCGGCCTGTCAGGCGCAGGATACAATGGCGATGTGGCGTGAAAATAATGTCGATATTGTTGAATGCGTTAAGTGCGGGCATCAAATGCGGGAAGCGGATAAAGACGTCCGCGAGCATGTTCGCAAAGAAGAGCAAGTGATCGGGATTTTTCATCCGGACTAG\n->NZ_AOXE01000052.1_38|132779259\n-ATGGACTGGCTGGCAAAATATTGGTGGATTCTGGTATTGGTGTTTCTGGTAGGCGTACTGCTGAATGTGATCAAAGATCTCAAACGCATCGACCATAAGAAATTCCTTGCCAATAAACCTGAGCTGCCCCCGCATCGCGATTTTAACGATAAGTGGGACGATGAAGACGGCTGGCCGAAGAAAGATCAGCCGAAAAAGTAA\n->NZ_AOXE01000059.1_15|571430577\n-ATGTCTGACGTGACCGTCGTAAACTGTCCGACCTGCGGTAAACCGGTCGTCTGGGGGGAAATTAGCCCCTTCCGCCCATTTTGTTCTAAACGCTGTCAGTTAATTGATTTGGGCGAATGGGCCGCCGAAGAGAAACGAATCGCCAGCAGCGGCGACCAGTCTGATAGCGACGACTGGAGTGAAGAGCGCTAA\n >NZ_AOXE01000034.1_82|1542872411\n ATGCCAACCAGACCACCTTATCCGCGGGAAGCTTATATCGTCACCATTGAAAAAGGCACGCCGGGCCAGACGGTGACGTGGTATCAGCTACGGGCTGACCATCCGAAACCTGATTCGCTCATCAGCGAGCATCCGACCGCAGAAGAAGCGATGGATGCGAAAAAACGTTACGAAGATCCGGATAAATCATAG\n >NZ_AOXE01000008.1_63|1303226364\n ATGAAAATGAGTATTGCCATGCTGTCAGCGCTTGCGTCATTTATCGTGGTGGGGTGCACGCCACGTATTGAAGTCGCCGCGCCGGAACAGCCGATTACCATCAACATGAATGTAAAGATCGAGCATGAAATACATATCAAAGTCGATAAAGACGTTGAAGAACTCCTGAAATCACGCAGCGATCTATTCTGA\n >NZ_AOXE01000053.1_128|2311744161\n ATGTCTACTGATTTGGACCCAACCCAACTGGCGATTGAATTTTTACGCCGTGATAAAACCGAACTTTCTCCCGCGCAGTATTTGAAGCGTTTAAAACAGCTGGAGTTAGAGTTTGCCGATCTCCTCACCCTCTCTGCAACCGAACTGAAAGAAGAGATCTATTTCGCCTGGCGGTTGGGCGTGCATTAA\n+>NZ_AOXE01000059.1_15|571430577\n+ATGTCTGACGTGACCGTCGTAAACTGTCCGACCTGCGGTAAACCGGTCGTCTGGGGGGAAATTAGCCCCTTCCGCCCATTTTGTTCTAAACGCTGTCAGTTAATTGATTTGGGCGAATGGGCCGCCGAAGAGAAACGAATCGCCAGCAGCGGCGACCAGTCTGATAGCGACGACTGGAGTGAAGAGCGCTAA\n >NZ_AOXE01000072.1_104|1236556171\n ATGCTGATTCTGACTCGTCGAGTTGGTGAGACCCTCATGATTGGCGATGAGGTCACCGTGACAGTTTTAGGGGTGAAGGGCAACCAGGTGCGTATTGGCGTGAACGCCCCGAAAGAAGTTTCTGTCCATCGTGAAGAGATCTACCAGCGTATCCAGGCTGAAAAATCCCAGCAGTCCAGTTACTAA\n >NZ_AOXE01000036.1_16|431631459\n@@ -632,16 +632,16 @@\n ATGGCTAAAGGTATTCGTGAGAAAATCAAGCTGGTTTCTTCTGCTGGTACTGGTCACTTCTATACCACTACGAAGAACAAACGTACTAAACCGGAAAAACTGGAACTGAAAAAATTCGATCCAGTTGTCCGTCAGCACGTGATCTACAAAGAAGCGAAAATCAAATAA\n >NZ_AOXE01000064.1_26|3371174263\n ATGGGTTTCTGGAGAATTGTATTTACGATTATTTTGCCTCCGCTCGGCGTACTTTTAGGAAAAGGGTTCGGTTGGGCATTTATCCTTAATATCCTGCTGACATTACTCGGATATATTCCGGGGCTTATCCACGCATTTTGGGTTCAGATGCGTCATTAA\n->NZ_AOXE01000059.1_435|2536338461\n-ATGGTTAAAAAGACAATTGCAGCGATCTTTTCTGTTTTGGTACTTTCCACTGTATTAACTGCTTGTAATACCACGCGCGGCGTGGGCGAGGACATCTCGGACGGTGGTAGTGCGATCTCTGGCGCTGCAACCAGAGCTCAGCAGTAA\n >NZ_APAO01000014.1_55|3276924\n ATGTTATCCACAGAAAGTTGGGATAACTGTGTAAAACCACCACTACTGTTTCCATTTACAGCCTTGACGTGCGACGAAAATCGAAAATTCAGACAAATAGTGCGTAAGTTATTGGCACAATCTGTGGATAAAACCGACGCTGGTTGA\n+>NZ_AOXE01000059.1_435|2536338461\n+ATGGTTAAAAAGACAATTGCAGCGATCTTTTCTGTTTTGGTACTTTCCACTGTATTAACTGCTTGTAATACCACGCGCGGCGTGGGCGAGGACATCTCGGACGGTGGTAGTGCGATCTCTGGCGCTGCAACCAGAGCTCAGCAGTAA\n >NZ_AOXE01000036.1_31|1781281347\n GTGAAAAAATTTCGATGGGTCGTTCTCGGCATCGTGGTGGTAGTATGCCTGTTGCTGTGGGCGCAGGTGTTTAATATCATGTGCGATCAGGATGTACAATTTTTCAGCGGTATTTGCGCCATCAATAAATTTATTCCCTGGTAA\n+>NZ_AOYX01000060.1_42|486088087\n+ATGCGTAAGCGCAAAGAAAAAGCAGTAAAGGTGCGGCAGTATGTAAATAGTAATGAGAACGACTATCAATTCGACGTTGTTTTGATATTATTATGCTCAGATTTTGTGATTTGCGTCCTGGAGATACAGAGTGGGTAA\n >NZ_AOXE01000036.1_3|3250676045\n ATGTCTGAACGTCCTGATTTAGTCGATCCATTACCAGAGGATGAGCCGCTTCCTGGTGAAAATATTCCGGATACGCCAGAGGGAGACGATCCTCTCGACCCGGATACCCAGAATGAGGTTGAAGATCCTCGTAGATAG\n->NZ_AOYX01000060.1_42|486088087\n-ATGCGTAAGCGCAAAGAAAAAGCAGTAAAGGTGCGGCAGTATGTAAATAGTAATGAGAACGACTATCAATTCGACGTTGTTTTGATATTATTATGCTCAGATTTTGTGATTTGCGTCCTGGAGATACAGAGTGGGTAA\n >NZ_AOXE01000035.1_13|4178717449\n ATGCCTTCTGAAAACCAGGAACCGCGCCGCGACCCTGAGCTCAAACGTAAAGCATGGCTGGCGGTTTTTGTGGGTTCTGCGTTGTTCTGGGTAGTGGTAGCGCTTGTTATCTGGCATTGGTGGGGCTAA\n >NZ_AOXE01000073.1_79|3172400135\n' |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/sistr-results-13-1101.tab --- a/test-data/sistr-results-13-1101.tab Wed Jun 14 14:36:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,2 +0,0 @@ -cgmlst_ST cgmlst_distance cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar mash_subspecies o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst -1567171959 0.00303030303030305 SAL_HA5013AA 329 enterica /mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/13-1101-Paratyphi_B.fasta 13-1101-Paratyphi_B b 1,2 0.00178577 72308 929 Paratyphi B var. Java enterica 1,4,[5],12 PASS B Paratyphi B var. Java Paratyphi B|Paratyphi B var. Java Paratyphi B var. Java |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/sistr-results-13-1101.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sistr-results-13-1101.tabular Thu Aug 06 11:48:49 2020 -0400 |
| [ |
| @@ -0,0 +1,2 @@ +cgmlst_ST cgmlst_distance cgmlst_found_loci cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar mash_subspecies o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst +3782467861 0.045454545454545414 330 SRR2174054 315 enterica /galaxy/database/files/000/dataset_700.dat 13-1101-Paratyphi_B b 1,2 0.00178577 72308 929 Paratyphi B var. Java enterica 1,4,[5],12 INFO: Number of cgMLST330 loci found (n=330) PASS B Paratyphi B var. Java Paratyphi B|Paratyphi B var. Java|Limete Paratyphi B var. Java |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/sistr-results.tab --- a/test-data/sistr-results.tab Wed Jun 14 14:36:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -cgmlst_ST cgmlst_distance cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar mash_subspecies o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst - 0.8272727272727273 SAL_BA6036AA 57 enterica /mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/AE014613-699860.fasta AE014613-699860 - - 0.0637124 60369 151 Typhi - FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0 FAIL - -:-:- -:-:- Typhi |
| b |
| diff -r 5c8ff92e38a9 -r 17fcac7ddf54 test-data/sistr-results.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sistr-results.tabular Thu Aug 06 11:48:49 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +cgmlst_ST cgmlst_distance cgmlst_found_loci cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar mash_subspecies o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst + 0.8272727272727273 58 2014-LET-0419 57 enterica /galaxy/database/files/000/dataset_695.dat AE014613-699860 - - 1.0 0 - FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | INFO: Number of cgMLST330 loci found (n=58) | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0 FAIL - -:-:- -:-:- Typhi |