| Previous changeset 2:13632190a0ff (2017-04-20) Next changeset 4:17fcac7ddf54 (2020-08-06) |
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Commit message:
Update to 1.0.2 |
|
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 test-data/sistr-results-13-1101.tab test-data/sistr-results.tab |
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added:
test-data/sistr-results-13-1101.json |
| b |
| diff -r 13632190a0ff -r 5c8ff92e38a9 sistr_cmd.xml --- a/sistr_cmd.xml Thu Apr 20 14:33:38 2017 -0400 +++ b/sistr_cmd.xml Wed Jun 14 14:36:59 2017 -0400 |
| [ |
| @@ -1,9 +1,9 @@ -<tool id="sistr_cmd" name="sistr_cmd" version="0.3.6"> +<tool id="sistr_cmd" name="sistr_cmd" version="1.0.2"> <description> Salmonella In Silico Typing Resource commandline tool for serovar prediction </description> <requirements> - <requirement type="package" version="0.3.6">sistr_cmd</requirement> + <requirement type="package" version="1.0.2">sistr_cmd</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -25,8 +25,7 @@ --threads "\${GALAXY_SLOTS:-1}" -T "\${TMPDIR:-/tmp}" $keep_tmp - $full_output - $report_blast_results + $more_output $verbosity ]]></command> <inputs> @@ -86,21 +85,19 @@ label="Basic QC of results" /> <param - name="report_blast_results" - type="boolean" - checked="false" - truevalue="--report-blast-results" - falsevalue="" - label="Report all blastn results from antigen search" - /> - <param - name="full_output" - type="boolean" - checked="false" - truevalue="--full-output" - falsevalue="" - label="Report detailed results" - /> + name="more_output" + type="select" + label="Results verbosity"> + <option value="" selected="true"> + Basic results only + </option> + <option value="-M"> + Report top antigen BLAST results + </option> + <option value="-MM" > + Report all antigen BLAST results + </option> + </param> <param name="keep_tmp" type="boolean" @@ -167,17 +164,12 @@ <param name="input_fastas" value="AE014613-699860.fasta"/> <param name="output_format" value="tab"/> <output - name="novel_alleles" - value="novel-alleles.fasta" - ftype="fasta" - compare="sim_size"/> - <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,,,,,,,,,,1123870984,278162969,490843778,3950769715,,,,,,4203409135,3569491948,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,2019769394,1109678443,,,,,,,,,"/> + <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> </output> <output @@ -267,6 +259,24 @@ 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" /> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[ @@ -274,8 +284,7 @@ Usage:: usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT] - [-o OUTPUT_PREDICTION] [--full-output] - [--report-blast-results] [-p CGMLST_PROFILES] + [-o OUTPUT_PREDICTION] [-M] [-p CGMLST_PROFILES] [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K] [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS] [-v] [-V] @@ -305,9 +314,8 @@ Output format (json, csv, pickle) -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION SISTR serovar prediction output path - --full-output Produce full detailed output - --report-blast-results - Report blastn results for each antigen gene + -M, --more-results Output more detailed results (-M) and all antigen + search blastn results (-MM) -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES Output CSV file destination for cgMLST allelic profiles |
| b |
| diff -r 13632190a0ff -r 5c8ff92e38a9 test-data/alleles-output-13-1101.json --- a/test-data/alleles-output-13-1101.json Thu Apr 20 14:33:38 2017 -0400 +++ b/test-data/alleles-output-13-1101.json Wed Jun 14 14:36:59 2017 -0400 |
| b |
| b'@@ -1,1 +1,1 @@\n-{"13-1101-Paratyphi_B.fasta": {"NZ_AOXE01000034.1_82": {"blast_result": {"is_perfect": true, "slen": 345713, "pident": 100.0, "marker": "NZ_AOXE01000034.1_82", "qseqid": "NZ_AOXE01000034.1_82|1542872411", "qstart": 1, "is_trunc": false, "sseq_msa_gaps": 0, "sseq": "ATGCCAACCAGACCACCTTATCCGCGGGAAGCTTATATCGTCACCATTGAAAAAGGCACGCCGGGCCAGACGGTGACGTGGTATCAGCTACGGGCTGACCATCCGAAACCTGATTCGCTCATCAGCGAGCATCCGACCGCAGAAGAAGCGATGGATGCGAAAAAACGTTACGAAGATCCGGATAAATCATAG", "bitscore": 355.0, "sseq_msa_p_gaps": 0.0, "evalue": 6.989999999999998e-99, "gapopen": 0, "send": 244465, "has_perfect_match": true, "allele": 1542872411, "sstart": 244656, "allele_name": 1542872411, "start_idx": 244464.0, "qend": 192, "needs_revcomp": true, "is_extended": false, "mismatch": 0, "coverage": 1.0, "too_many_gaps": false, "end_idx": 244655.0, "trunc": false, "stitle": 10664711, "qlen": 192, "is_match": true, "length": 192}, "name": 1542872411, "seq": "ATGCCAACCAGACCACCTTATCCGCGGGAAGCTTATATCGTCACCATTGAAAAAGGCACGCCGGGCCAGACGGTGACGTGGTATCAGCTACGGGCTGACCATCCGAAACCTGATTCGCTCATCAGCGAGCATCCGACCGCAGAAGAAGCGATGGATGCGAAAAAACGTTACGAAGATCCGGATAAATCATAG"}, "NZ_AOXE01000016.1_8": {"blast_result": {"is_perfect": false, "slen": 277029, "pident": 99.344, "marker": "NZ_AOXE01000016.1_8", "qseqid": "NZ_AOXE01000016.1_8|2903172827", "qstart": 1, "is_trunc": false, "sseq_msa_gaps": 0, "sseq": "GTGGAAAAATATCTGCGTAGCGGTACCATGTTTGTGGTACTGGCATTTATATTATGGGGGTTAACACCTTTATATTATCAATATTTATCAGGGGGAAATCTCGCACAAATATTGATATACCGGGTGTTCTGGTCAATTCCATTATTACTGGCAGTAAGATTGTTATTTCGGCAGCGAACGCGATTTCATGATGCCTGGAAAGATAAAAAATCTTTTTTCTTCTGCATGATCGCCGGACTTTTGATGATTGTCTCATGGTCATCTTTTATTTATGCGCTAACCCATCATCTGGTACTTGATGCCAGCCTCGGCTATTTTATCAACCCGCTATTTGTTATTGCGCTGGGATGCATTTTTCTTAAAGAAAAACTGTCGTTGTTTCAGGCCATCGCCGTTTTTTCCGGTGTCTGCGGCCTGACTTTTCAAATTATCATGCTACGGCATTTCCCGGCGCTGGCGCTAACCATGGGATTATCATTTGCGCTATATGGCCTGGCGCGAAAGTTTATACATTATGATGTGATGACATCGATAACGATTGAAACATTATGGGCATTGCCTGTCTCACTATTAATTTTTCTCTTTAGCGATAGCGGACCAATTATATCCGCTAATACTCCTTTCTTTTTGTATGTCATGACGGCGCCAGTGACGATCATTCCACTGGTATTATTTGCCATCGCGTTAAATCACACCTCGTTGATTGTCACCGGACTGGCGCAATATATAGAGCCGTCGTTACAGTTCTTACTTGCCATTATGATATTTGGCGAACACATTAATTACGCAGAACTGCTCTGCTTTTGTGCGGTATGGTTCGGGTTGTTTCTATGCATATCTGAAAATTTATATTCCCATTATCTCCGCGCCCGTCTGAAACCGGTGTTCGGCAGGGTACAGCGCTTCTTTCGCTAA", "bitscore": 1657.0, "sseq_msa_p_gaps": 0.0, "evalue": 0.0, "gapopen": 0, "send": 53329, "has_perfect_match": false, "allele": 2903172827, "sstart": 54243, "allele_name": 717530117, "start_idx": 53328.0, "qend": 915, "needs_revcomp": true, "is_extended": false, "mismatch": 6, "coverage": 1.0, "too_many_gaps": false, "end_idx": 54242.0, "trunc": false, "stitle": 10664749, "qlen": 915, "is_match": true, "length": 915}, "name": 717530117, "seq": "GTGGAAAAATATCTGCGTAGCGGTACCATGTTTGTGGTACTGGCATTTATATTATGGGGGTTAACACCTTTATATTATCAATATTTATCAGGGGGAAATCTCGCACAAATATTGATATACCGGGTGTTCTGGTCAATTCCATTATTACTGGCAGTAAGATTGTTATTTCGGCAGCGAACGCGATTTCATGATGCCTGGAAAGATAAAAAATCTTTTTTCTTCTGCATGATCGCCGGACTTTTGATGATTGTCTCATGGTCATCTTTTATTTATGCGCTAACCCATCATCTGGTACTTGATGCCAGCCTCGGCTATTTTATCAACCCGCTATTTGTTATTGCGCTGGGATGCATTTTTCTTAAAGAAAAACTGTCGTTGTTTCAGGCCATCGCCGTTTTTTCCGGTGTCTGCGGCCTGACTTTTCAAATTATCATGCTACGGCATTTCCCGGCGCTGGCGCTAACCATGGGATTATCATTTGCGCTATATGGCCTGGCGCGAAAGTTTATACATTATGATGTGATGACATCGATAACGATTGAAACATTATGGGCATTGCCTGTCTCACTATTAATTTTTCTCTTTAGCGATAGCGGACCAATTATATCCGCTAATACTCCTTTCTTTTTGTATGTCATGACGGCGCCAGTGACGATCATTCCACTGGTATTATTTGCCATCGCGTTAAATCACACCTCGTTGATTGTCACCGGACTGGCGCAATATATAGAGCCGTCGTTACAGTTCTTACTTGCCATTATGATATTTGGCGAACACATTAATTACGCAGAACTGCTCTGCTTTTGTGCGGTATGGTTCGGGTTGTTTCTATGCATATCTGAAAATTTATATTCCCATTATCTCCGCGCCCGTCTGAAACCGGTGTTCGGCAGGGTACAGCGCTTCTTTCGCTAA"}, "NZ_AOXE01000061.1_3": {"blast_result": {"is_perfect": false, "slen": 146239, "pident": 99.14200000000001, "marker": "NZ_AOXE01000061.1_3", "qseqid": "NZ_AOXE01000061.1_3|1371632201", "qstart": 1, "is_trunc": false, "sseq_msa_gaps": 0, "sseq": "ATGAATAAAATCCTGTTAGTTGATGATGACCGAGAGCTGACTTCCCTGTTAAAAGAGCTCCTCGAAATGGAAGGTTTTAATGTCCTGGTGGCC'..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 13632190a0ff -r 5c8ff92e38a9 test-data/alleles-output.json --- a/test-data/alleles-output.json Thu Apr 20 14:33:38 2017 -0400 +++ b/test-data/alleles-output.json Wed Jun 14 14:36:59 2017 -0400 |
| b |
| b'@@ -1,1 +1,1 @@\n-{"AE014613-699860.fasta": {"NZ_AOXE01000059.1_338": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000017.1_96": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000059.1_370": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000021.1_61": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000034.1_164": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000016.1_8": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000011.1_85": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000036.1_31": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000036.1_39": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000011.1_83": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000031.1_80": {"blast_result": {"is_perfect": true, "slen": 699860, "pident": 100.0, "marker": "NZ_AOXE01000031.1_80", "qseqid": "NZ_AOXE01000031.1_80|2955003506", "qstart": 1, "is_trunc": false, "sseq_msa_gaps": 0, "sseq": "ATGAGTAAATGCAGTGCTGATGAAACCCCGGTTTGCTGCTGTATGGACGTTGGAACCATCATGGACAACTCCGATTGCACCGCGTCATACAGCCGCGTATTCGCTACCCGCGCAGAGGCTGAAGAGACGCTGGCGGCGTTAACCGAAAAAGCGCGTAGCGTGGAGTCTGAACCTTGCCAAATTACGCCAACCTTTACCGAGGAATCCGAAGGCGTTCGTCTGGATATTGATTTTGTTTTCGCCTGCGAAGCAGAAACGCTGATCTTCCAGCTCGGCCTGCGTTAA", "bitscore": 527, "sseq_msa_p_gaps": 0.0, "evalue": 3.18e-151, "gapopen": 0, "send": 548003, "has_perfect_match": true, "allele": 2955003506, "sstart": 547719, "allele_name": 2955003506, "start_idx": 547718.0, "qend": 285, "needs_revcomp": false, "is_extended": false, "mismatch": 0, "coverage": 1.0, "too_many_gaps": false, "end_idx": 548002.0, "trunc": false, "stitle": "gi|29140506|gb|AE014613.1| Salmonella enterica subsp. enterica serovar Typhi Ty2, complete genome", "qlen": 285, "is_match": true, "length": 285}, "name": 2955003506, "seq": "ATGAGTAAATGCAGTGCTGATGAAACCCCGGTTTGCTGCTGTATGGACGTTGGAACCATCATGGACAACTCCGATTGCACCGCGTCATACAGCCGCGTATTCGCTACCCGCGCAGAGGCTGAAGAGACGCTGGCGGCGTTAACCGAAAAAGCGCGTAGCGTGGAGTCTGAACCTTGCCAAATTACGCCAACCTTTACCGAGGAATCCGAAGGCGTTCGTCTGGATATTGATTTTGTTTTCGCCTGCGAAGCAGAAACGCTGATCTTCCAGCTCGGCCTGCGTTAA"}, "NZ_AOXE01000064.1_27": {"seq": null, "name": null, "blast_result": null}, "NZ_AOYX01000075.1_47": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000064.1_26": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000073.1_48": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000064.1_36": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000059.1_395": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000081.1_272": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000081.1_124": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000068.1_45": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000081.1_105": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000085.1_60": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000053.1_173": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000004.1_154": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000081.1_103": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000021.1_165": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000034.1_134": {"seq": null, "name": null, "blast_result": null}, "NZ_AOXE01000083.1_53": {"blast_result": {"is_perfect": false, "slen": 699860, "pident": 99.56700000000001, "marker": "NZ_AOXE01000083.1_53", "qseqid": "NZ_AOXE01000083.1_53|1998597791", "qstart": 1, "is_trunc": false, "sseq_msa_gaps": 0, "sseq": "ATGATTGACTGGCAGGATCTCCACCATAGCGAACTTACTGTTCCTCAACTTTACGCGTTACTCAAATTGCGCTGCGCGGTCTTTGTGGTAGAACAGCGCTGTCCTTACCTGGATGTGGATGGCGATGATTTAGTCGGCGACAATCGGCATATTCTGGGCTGGCATCAGGATGAGCTGGTGGCGTATGCGAGGATTCTGAAAAGTGATAACGAATCAGACCCGGTTGTCATTGGCCGGGTGATCGTCAGCGATGCCTGGCGAGGGGCGAAACTGGGCCAGCAATTAATGGCGAAAACGCTGGAATCTTGTGGGCGGCACTGGCCGGATAAGCCGCTATATCTGGGGGCGCAGGCGCATCTGCAACCTTTTTATGCGCGGTTTGGTTTT'..b'{"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": 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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_58": {"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 13632190a0ff -r 5c8ff92e38a9 test-data/cgmlst-profiles-13-1101.csv --- a/test-data/cgmlst-profiles-13-1101.csv Thu Apr 20 14:33:38 2017 -0400 +++ b/test-data/cgmlst-profiles-13-1101.csv Wed Jun 14 14:36:59 2017 -0400 |
| b |
| b'@@ -1,2 +1,2 @@\n 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3887664,2983916931,3219814449,4276130360,3574020847,2077249876,2077738650,1430683295,2795082944,2904170129,1830292553,3712766732,1898052981,246770399,2246059591,282105442,3473113586,4252575321,299233641,2651864740,1436693988,2545200385,225275747,1320460320,2353669245,1780432149,1667064808,4127891750,2307413670,1994382719,1324934990,912019826,767517378,300758334,2732360708,1476689272,316910970,726132721,2404196596,628816999,715723428,439814616,3868995612,3923470646,922813689,596464946,2068726690,514528221,1235021963,1738069373,2194946451,1542872411,4178717449,2356733911,3699174113,2832724106,3646752757,2770658758,431631459,3155517162,3250676045,1781281347,747567264,550964520,528121872,308073351,1638651814,593462775,3179271034,399278785,498374695,1439849948,1080346469,2094006958,551814723,708436169,828533582,2587507857,260803180,3578386263,3641973773,3721979689,119594086,2079191084,1524097055,4237193625,2084418558,2598101487,2243362473,132779259,2539563995,3147004960,1005413801,398274060,683371912,2311744161,2098379863,830225365,4090514893,3192866010,489837497,2392764491,4177019046,616151434,195979449,2688075180,571430577,3183061957,2253874773,1342053785,162097627,1109320307,664703088,4249405940,4228448746,791036150,629769704,3428477437,1226961299,21264588,2569933901,4239412284,4175098203,2467894309,3206518183,3822365505,2170727246,2979506855,3572598511,257452301,2336031118,986292687,3438653864,3027329430,4212855923,2590187629,2536338461,2306804434,3643876638,2409457196,3781645063,333445801,2424781734,1291136085,1047370225,698589548,2519701742,3276128843,3548183620,4289919471,1965001593,1842785664,3995669301,2390483285,3371174263,1245009874,2919271763,1854288580,3832041954,2672990925,4227342379,3643634927,333081518,2139774773,121039594,4267848688,1426386553,93691856,2617592815,2061334442,484067521,338226340,595233173,1246387686,1236556171,3165457710,649192555,3831614515,2226007812,2615307626,1822361792,1251756376,2953514645,226121950,3523430840,799742746,4250299083,1635467073,563085019,4033110422,2734837303,1982008089,2061617626,2494351896,3172400135,309774068,2754698655,2253744431,2081649483,3386486144,4213771231,352954861,216514641,744347523,2758229229,1743327588,406171140,1043329926,294538384,2505247376,4189957668,2899049638,2078682862,4109265911,2639318025,4269576185,3445065778,1716630297,3912522894,10121991,3254127745,3047220128,4248599762,353328767,1019572313,3239852751,2459342739,1547676029,2844497268,2203341188,4282035484,3699551722,121975481,3289785650,1171029009,4054067887,2414391967,3344082709,3523966715,3187079670,1371090518,2289872656,4200440493,3463404426,822043034,637470977,1500184554,3978410193,3572777440,2763485497,2649675872,625657224,2641882719,1619775958,1484137762,1613239859,3150901989,1366744981,504704912,1143941611,2475598021,3887842238,1839157263,3017501787,2881079752,3306151290,3554479089,128939352,2472742281,491087478,601432611,1671956993,938581157,486088087,2151397774,2972709081,3276924,4149206546,4185944080\n' |
| b |
| diff -r 13632190a0ff -r 5c8ff92e38a9 test-data/cgmlst-profiles.csv --- a/test-data/cgmlst-profiles.csv Thu Apr 20 14:33:38 2017 -0400 +++ b/test-data/cgmlst-profiles.csv Wed Jun 14 14:36:59 2017 -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'2.1_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.fasta,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,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,,,,,,,,,,1123870984,278162969,490843778,3950769715,,,,,,4203409135,3569491948,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,2019769394,1109678443,,,,,,,,,\n+AE014613-699860,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,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' |
| b |
| diff -r 13632190a0ff -r 5c8ff92e38a9 test-data/novel-alleles-13-1101.fasta --- a/test-data/novel-alleles-13-1101.fasta Thu Apr 20 14:33:38 2017 -0400 +++ b/test-data/novel-alleles-13-1101.fasta Wed Jun 14 14:36:59 2017 -0400 |
| b |
| b'@@ -1,660 +1,660 @@\n->NZ_AOXE01000034.1_82|1542872411\n-ATGCCAACCAGACCACCTTATCCGCGGGAAGCTTATATCGTCACCATTGAAAAAGGCACGCCGGGCCAGACGGTGACGTGGTATCAGCTACGGGCTGACCATCCGAAACCTGATTCGCTCATCAGCGAGCATCCGACCGCAGAAGAAGCGATGGATGCGAAAAAACGTTACGAAGATCCGGATAAATCATAG\n->NZ_AOXE01000016.1_8|717530117\n-GTGGAAAAATATCTGCGTAGCGGTACCATGTTTGTGGTACTGGCATTTATATTATGGGGGTTAACACCTTTATATTATCAATATTTATCAGGGGGAAATCTCGCACAAATATTGATATACCGGGTGTTCTGGTCAATTCCATTATTACTGGCAGTAAGATTGTTATTTCGGCAGCGAACGCGATTTCATGATGCCTGGAAAGATAAAAAATCTTTTTTCTTCTGCATGATCGCCGGACTTTTGATGATTGTCTCATGGTCATCTTTTATTTATGCGCTAACCCATCATCTGGTACTTGATGCCAGCCTCGGCTATTTTATCAACCCGCTATTTGTTATTGCGCTGGGATGCATTTTTCTTAAAGAAAAACTGTCGTTGTTTCAGGCCATCGCCGTTTTTTCCGGTGTCTGCGGCCTGACTTTTCAAATTATCATGCTACGGCATTTCCCGGCGCTGGCGCTAACCATGGGATTATCATTTGCGCTATATGGCCTGGCGCGAAAGTTTATACATTATGATGTGATGACATCGATAACGATTGAAACATTATGGGCATTGCCTGTCTCACTATTAATTTTTCTCTTTAGCGATAGCGGACCAATTATATCCGCTAATACTCCTTTCTTTTTGTATGTCATGACGGCGCCAGTGACGATCATTCCACTGGTATTATTTGCCATCGCGTTAAATCACACCTCGTTGATTGTCACCGGACTGGCGCAATATATAGAGCCGTCGTTACAGTTCTTACTTGCCATTATGATATTTGGCGAACACATTAATTACGCAGAACTGCTCTGCTTTTGTGCGGTATGGTTCGGGTTGTTTCTATGCATATCTGAAAATTTATATTCCCATTATCTCCGCGCCCGTCTGAAACCGGTGTTCGGCAGGGTACAGCGCTTCTTTCGCTAA\n->NZ_AOXE01000061.1_3|2390483285\n-ATGAATAAAATCCTGTTAGTTGATGATGACCGAGAGCTGACTTCCCTGTTAAAAGAGCTCCTCGAAATGGAAGGTTTTAATGTCCTGGTGGCCCACGACGGCGAGCAGGCGCTTGAGCTTTTGGATGACAGCATCGATTTACTTTTGCTTGACGTCATGATGCCGAAGAAAAACGGTATCGATACGTTGAAAGCGCTTCGCCAGACACACCAGACGCCTGTCATTATGCTGACCGCGCGCGGCAGCGAGCTGGATCGCGTTCTCGGCCTTGAGCTGGGCGCGGACGACTATTTACCCAAACCATTTAACGACCGCGAGCTGGTAGCGCGCATCAGGGCTATTTTGCGCCGTTCCCACTGGAGCGAACAGCAGCAGAGCAGCGACAACGGCTCGCCGACGCTGGAAGTCGATGCGCTAAGCCTTAATCCGGGTCGCCAGGAAGCCAGTTTCGATGGCCAAACGCTGGAGCTGACCGGTACGGAATTCACCCTGCTCTATTTGCTGGCCCAGCACCTCGGCCAGGTGGTTTCCCGTGAACATTTAAGTCAGGAAGTGCTGGGCAAGCGCCTGACGCCGTTCGATCGCGCCATTGATATGCATATTTCTAACCTGCGCCGCAAACTGCCGGAACGCAAAGACGGTCACCCGTGGTTTAAAACATTGCGTGGTCGCGGCTATCTGATGGTTTCCGCTTCATGA\n->NZ_AOXE01000036.1_39|747567264\n-TTGAGCAAGAACGCATTTAATGCTTATTTTAATAGCCTGTGTTTAGGAGTAAGACCACGAAGTGATTATATAATGAGCAAAACAGAACTATACGCGGCGTTAAACCGCGATTTTCAGTCGTTAATGGCAGGTGAAACCAGCTTTCTGGCCACGCTGGCGAATACCAGCGCGCTACTGTTCGAACGCCTTACCGAGGTGAACTGGGCGGGATTTTATCTCCTCGAAGGCGATACGCTGGTGTTGGGGCCGTTTCAGGGGCGAATCGCCTGTGTGCGGATTCCGGTTGGTCGCGGCGTGTGTGGCGCAGCGGTAGCGCAGAATAAGGTTCAACGTATTGATGATGTTCATGCGTTTGACGGCCATATTGCCTGTGATGCCGCCAGCAACGCCGAAATTGTGCTGCCTGTCACGGTTGGCGAACGGATTATCGGCGTGCTGGATATAGATAGCACGGCGTTTGGCCGTTTTACCGAAGAAGATGAACACGGCCTGCGTACGCTGGTCGCACAGCTTGAAACCGTGCTTGCAACGACGGATTACAAAAAATTCTTTGCGAGCGTTGCAGGATAA\n->NZ_AOXE01000031.1_80|1320460320\n-ATGAGTAAATGCAGTGCTGATGAAACCCCGGTTTGCTGCTGTATGGATGTTGGAACCATCATGGACAACTCCGATTGCACCGCGTCATACAGCCGCGTATTCGCTACCCGCGCAGAGGCTGAAGGGACGCTGGCGGCGTTAACCGAAAAAGCGCGTAGCGTGGAGTCTGAGCCTTGCCAAATTACGCCAACCTTTACCGAGGAATCCGAAGGCGTTCGTCTGGATATTGATTTTGTTTTCGCCTGCGAAGCAGAAACGCTGATCTTCCAGCTCGGCCTGCGTTAA\n->NZ_AOXE01000059.1_395|2979506855\n-ATGATAGCGATTGAAACACGGCAATTAGCCGGAGGCGTCGTACTACATGCCTTCCCGGAAGGGAAACGCGCCGTGCCGCTTCCCTGTGTGGTGTTCTATCATGGCTTCACCTCCTCCAGCCTGGTTTATAGTTATTTTGCCGTTGCCCTGGCACAGGCAGGATTCCGGGTAGTCATGCCGGATGCGCCGGAGCATGGCGCTCGCTTCGGCGGCGACTCACAGGGACGGATACACCGATTCTGGCAGATTCTGCACCAAAACATGCAGGAATTTACGACGTTACGTGCGGCGATTCAGGAGGAAAACTGGCTACTTGACGGGCGGTTGGCGGTGGGCGGCGCATCCATGGGCGGTATGACGGCGCTGGGCATTATGACGCGTCACCGTGAGGTAAAATGCGGGGCCAGTTTAATGGGGTCGGGCTATTTTACCGGGCTTGCCCGGACGCTTTTCCCGCCGTTATCCCCGCAGAACCCGGCGCAGCAGGCGGAATTCGACAATATCATCGCGCCGCTACGTGAATGGGAAGTCACACACCAGTTGGAGCGACTGGCCGACAGGCCGCTTCTGTTGTGGCATGGTCAGGAGGATGACGTGGTGCCTGCTATCGAAACCTTCCGGCTCCAGCAGGCACTCGCCGGGGCGAAGCTGGATAAGCATGTGACCTGTTTATGGGCCGCAGGCGTGCGGCATCGCATTACGCCAGAAGCGTTGTCGGCGACGGTAGCGTTTTTCCGACAGCATCTTTAA\n->NZ_AOXE01000081.1_105|294538384\n-ATGAGCGATATGCACTCGCTGCTGATAGCGGCAATTTTGGGTGTGGTCGAAGGATTGACGGAGTTTTTGCCGGTATCCAGCACGGGCCATATGATTATTGTGGGTCATCTGCTGGGGTTTGAAGGCGATACGGCCAAGACATTCGAAGTGGTGATTCAACTTGGATCTATTCTGGCGGTCGTGGTGATGTTCTGGCGGCGGTTGTTTGGTCTCATCGGTATTCACTTTGGCCGCCCGCTACAGCGTGAAGGTGAAAGTAAAGGTCGATTAACGTTGATTCACATCCTGCTGGGCATGATTCCGGCGGTGGTGCTGGGGTT'..b'CGGATAAATCATAG\n+>NZ_AOXE01000008.1_63|1303226364\n+ATGAAAATGAGTATTGCCATGCTGTCAGCGCTTGCGTCATTTATCGTGGTGGGGTGCACGCCACGTATTGAAGTCGCCGCGCCGGAACAGCCGATTACCATCAACATGAATGTAAAGATCGAGCATGAAATACATATCAAAGTCGATAAAGACGTTGAAGAACTCCTGAAATCACGCAGCGATCTATTCTGA\n+>NZ_AOXE01000053.1_128|2311744161\n+ATGTCTACTGATTTGGACCCAACCCAACTGGCGATTGAATTTTTACGCCGTGATAAAACCGAACTTTCTCCCGCGCAGTATTTGAAGCGTTTAAAACAGCTGGAGTTAGAGTTTGCCGATCTCCTCACCCTCTCTGCAACCGAACTGAAAGAAGAGATCTATTTCGCCTGGCGGTTGGGCGTGCATTAA\n+>NZ_AOXE01000072.1_104|1236556171\n+ATGCTGATTCTGACTCGTCGAGTTGGTGAGACCCTCATGATTGGCGATGAGGTCACCGTGACAGTTTTAGGGGTGAAGGGCAACCAGGTGCGTATTGGCGTGAACGCCCCGAAAGAAGTTTCTGTCCATCGTGAAGAGATCTACCAGCGTATCCAGGCTGAAAAATCCCAGCAGTCCAGTTACTAA\n+>NZ_AOXE01000036.1_16|431631459\n+ATGTTTGCAGGTTTACCTTCACTCAGTCATGAACAACAGCAAAAAGCCGTAGAACGTATCCAGGAATTGATGTCGCAAGGTATGAGCAGCGGAGAAGCGATTGCCCAGGTGGCGGGCGAACTTCGCGCCAACCATACCGGCGAACGGATAGTGGCGCGTTTTGAGGATGAAGACGAATAA\n+>NZ_AOXE01000007.1_13|2980577262\n+ATGGATCATCGTCTGCTTGAAATCATCGCCTGCCCGGTATGTAACGGCAAACTCTGGTATAACCAGGAACAGCAAGAATTAATTTGCAAACTGGACAATCTCGCTTTCCCGTTACGCGACGGCATTCCTGTATTGCTGGAAAATGAAGCTCGCGCCCTGACATCTGATGAGAGTAAATCATGA\n+>NZ_AOXE01000003.1_57|1721939526\n+ATGGCCGTACAACAGAATAAACCAACCCGTTCCAAACGTGGCATGCGTCGTTCCCATGACGCTCTGACCGCAGTCACCAGCCTGTCTGTAGACAAAACTTCTGGTGAAAAACACCTGCGTCACCACATCACTGCCGACGGTTACTACCGCGGCCGTAAGGTCATCGCTAAGTAA\n+>NZ_AOXE01000036.1_2|3155517162\n+ATGAACAGCGAAGAGTTGACACATAAAGCAGAAGAGGAAATCGCGGCACTCATTAGCAAAAAGGTCGCCGAACTACGGAAGAAAACCGGGCAAGAGGTTTCCGAAATAGAGTTCGCGCCGCGAGAAACGATGAAAGGGCTTGAGGGATACCACGTTAAAATTAAACTACTCTAG\n+>NZ_AOXE01000017.1_54|3756506314\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_AOXE01000036.1_31|1781281347\n+GTGAAAAAATTTCGATGGGTCGTTCTCGGCATCGTGGTGGTAGTATGCCTGTTGCTGTGGGCGCAGGTGTTTAATATCATGTGCGATCAGGATGTACAATTTTTCAGCGGTATTTGCGCCATCAATAAATTTATTCCCTGGTAA\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+ATGAACGAATTTAAGAGGTGTATACGCGTGTTCACTCACTCTCCCTTTAAAGTCCGGTTAATGCTGCTCTCTATGTTGTGCGATATGATCAACGGCAAACCGGAACAGGATAACCCTTCCACGAAATAA\n+>NZ_AOYX01000009.1_43|1671956993\n+ATGACACATGCAGACTGGCTGATTCTTGGGTATACAACTGTTATTATTATTTTTGGTATTGTATGTTATATCGGATTGCTTAAATTGATAACGAAAGGCAAGCATGAAAAATAA\n+>NZ_AOXE01000077.1_33|4213771231\n+ATGTGGTATTTCGCATGGATTCTGGGAACGCTTCTTGCCTGTGCATTCGGGATCATTACCGCCCTGGCGCTTGAGCACGTTGAAGCGGGTAAAACCGGTCAAGAAGAAAGCTAA\n+>NC_011149.1_467|161888011\n+ATGAAAAGCAACAAAAGCGCTGAAGCACACGAATCGCTGTTGCAATTGTCGTTCACAGCCAGTAAATTCGACCGTTTTCGAGCACAGGCGCAGGCGGTCAAAGAGTAA\n+>NZ_AOXE01000059.1_333|629769704\n+ATGGTTCAGTGTGTACGACATTCTGTCTTACCGCGTCTGAAAAAAGACGCAGGCCTGCCGTTTTTCTTTCCGTTGAAAACCAATACCAAGCCCCTCAATTGA\n+>NZ_AOXE01000041.1_85|708436169\n+ATGAACCCTTCCATGCTGAACGCGACCCTACTAACAACTGCGCCATCTCGCGCAGTGGTCGTCGTGCGTGTGGTGGTGGTCGTCGGCAATGCGCCGTAG\n+>NZ_AOXE01000041.1_84|551814723\n+ATGAGCGTAGTGGATATCACCATTCTTATCCTGAAACTCATTGTTGCAGCACTGCAACTGCTTGATGCTGTTCTGAAATACCTTAAGTAA\n' |
| b |
| diff -r 13632190a0ff -r 5c8ff92e38a9 test-data/sistr-results-13-1101.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sistr-results-13-1101.json Wed Jun 14 14:36:59 2017 -0400 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"cgmlst_ST": 1567171959, "cgmlst_distance": 0.00303030303030305, "cgmlst_genome_match": "SAL_HA5013AA", "cgmlst_matching_alleles": 329, "cgmlst_subspecies": "enterica", "fasta_filepath": "/mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/13-1101-Paratyphi_B.fasta", "genome": "13-1101-Paratyphi_B", "h1": "b", "h1_flic_prediction": {"blast_results": {"qseqid": {"976": "2|b", "973": "1|b", "1497": "183|b", "1378": "136|b", "1488": "180|b", "1500": "184|b", "430": "111-16-1-184|b", "28": "584-11-1-1-180|b", "534": "145-1-2-183|b", "253": "54-1-2-183|b", "601": "166-3-5-183|b", "630": "175-1-7-183|b", "233": "48-1-8-184|b", "61": "584-23-2-4-166-3-5-183|b", "619": "172-1-8-60|b", "756": "214-4-8-60|b", "1506": "186|b", "1109": "60|b", "1503": "185|b", "604": "167-1-18-184|b", "279": "61-1-18-180|b", "34": "584-13-1-17-167-1-18-184|b", "910": "266-5-22-60|b", "470": "125-1-20-185|b", "799": "228-1-31-184|b", "814": "233-1-29-76|b", "679": "190-3-32-183|b", "110": "7-1-33-184|b", "959": "281-1-34-180|b", "732": "207-3-34-183|b", "633": "176-14-28-60|b", "2044": "HM142048.1|Salmonella_bongori_strain_CDC_2405_flagellin_fliC_gene|b", "1509": "187|b", "345": "82-2-29-76|b", "1146": "76|b", "172": "27-2-9-35|b", "1045": "35|b", "1042": "34|b", "467": "124-1-72-354|z39", "1512": "188|b", "1048": "36|b", "1944": "354|z39", "1941": "353|e,n,x,z15", "1022": "HM142003|II_40:-:1,5,(7)|-", "1932": "350|e,n,x,z15", "1019": "27|e,n,x", "1025": "29|e,n,x", "1016": "26|e,n,x", "1935": "351|e,n,x", "1920": "346|e,n,x", "1917": "345|e,n,x", "1926": "348|-", "1938": "352|z6", "1923": "347|z6", "1088": "52|z", "1929": "349|z", "2033": "11-2580|c", "1990": "373|c", "1999": "376|g,z51", "2004": "380|g,m,s,t", "2008": "382|g,m,s,t", "282": "63-14-1-248|i", "139": "17-1-1-171|i", "202": "39-7-1-0|i", "1994": "374|f,g,t", "1607": "247|i", "1338": "125|i", "1318": "120|i", "286": "64-4-9-294|z10", "1322": "121|i", "1226": "97|i", "1330": "123|i", "99": "4-1-1-0|i", "1222": "96|i", "1310": "118|i", "1246": "102|i", "1334": "124|i", "1595": "244|i", "1250": "103|i", "1342": "126|i", "1346": "127|i", "1358": "130|i", "969": "AY649720|Typhimurium|i", "1362": "131|i", "580": "159-1-14-137|c", "1611": "248|i", "1238": "100|i", "1234": "99|i", "936": "274-1-1-248|i", "1366": "132|i", "1354": "129|i", "1350": "128|i", "1242": "101|i", "1230": "98|i", "190": "35-2-2-157|i", "1314": "119|i", "132": "15-2-1-0|i", "1326": "122|i", "1463": "171|i", "68": "584-26-1-1-156|i", "1413": "158|i", "1298": "115|i", "1274": "109|i", "302": "68-3-1-159|i", "1417": "159|i", "1405": "156|i", "1278": "110|i", "1282": "111|i", "1258": "105|i", "1270": "108|i", "1306": "117|i", "1294": "114|i", "1266": "107|i", "1302": "116|i", "1409": "157|i", "1262": "106|i", "1286": "112|i", "1290": "113|i", "889": "258-1-2-0|i", "718": "203-1-1-281|r", "1254": "104|i", "95": "3-2-7-142|e,h", "777": "220-4-4-288|y", "1701": "273|l,z13", "763": "216-47-8-172|z10", "759": "215-3-1-248|i", "742": "210-1-2-290|z", "1432": "163|l,z13", "1729": "281|r", "221": "45-1-9-172|z10", "47": "584-19-1-2-35-2-2-157|i", "1697": "272|l,z13", "290": "65-3-5-288|y", "366": "89-1-1-0|i", "194": "36-3-1-248|i", "374": "91-1-1-281|r", "294": "66-1-6-294|z10", "929": "272-2-10-202|e,h", "198": "38-5-5-288|y", "54": "584-21-1-0-220-4-4-288|y", "833": "240-6-7-281|r", "1906": "Abaetetuba|SRR1212374|k", "229": "47-2-1-203|e,h", "506": "135-1-1-168|r", "699": "197-38-11-202|e,h", "79": "584-32-1-1-47-2-1-203|e,h", "358": "86-1-6-202|e,h", "703": "199-1-1-290|z", "695": "196-1-1-202|e,h", "217": "44-16-1-141|e,h", "691": "195-18-9-288|y", "3": "584-2-1-4-294|z10", "637": "178-1-7-276|l,z13,z28", "13": "584-7-1-1-57-1-9-203|e,h", "983": "5|a", "788": "224-4-55-203|e,h", "810": "232-1-8-289|y", "784": "222-23-1-278|l,z28", "1565": "203|e,h", "1381": "137|c", "547": "149-2-1-203|e,h", "661": "184-1-1-141|e,h", "1753": "287|r,[i]", "568": "156-4-1-202|e,h", "264": "57-1-9-203|e,h", "121": "12-1-1-203'..b'0000000002e-21}, "bitscore": {"3": 1862, "1": 106, "4": 106, "5": 106, "0": 100, "2": 100}, "qlen": {"3": 1224, "1": 1176, "4": 1176, "5": 1176, "0": 1176, "2": 1176}, "slen": {"3": 418912, "1": 284629, "4": 284629, "5": 284629, "0": 284629, "2": 284629}, "sseq": {"3": "TTATTTATTGTTTCTTAGTAAAACGAATCTTATATGCTCTGAAAAAACAAAGGAAGATGCAATGTATACCATAAAAGCAATCATCAAATGCTCAGGGAACAACCATCCCATGCTAACAGGAATCACACTTATTCCAATGCAAAATAGGAACATTATGAAATAATGCGCTGACTTTGTTTCCTGAGTTTTATTGGAGAAATACTTAGCTAGGACGCCTTTAAATACTCCAGATATAACTAACCAAACTGGTGTAAAAAGCCCGAAATCTGCGTATAGTTCACCATACCCGAAAGCAGGAGCGCCCTGATTTCTGTAGAATGCATCAGGGAAAAATACTTTTGCCAGATACAATGCGCCAAAATCTTCAGGCTTATCAGGCCAAATAGCCCTCGGAATCCTCGAGTAAACCTCGCTCTCCATTAGTAATTTTCCGTACATAAAGTCAAAGTTTGAGGAAGCAACAAGAACAGCATTACGGGTATAATCCGAGTAATTCGCCATATTTTCTATCGGATTCCCATCAGTAAACGTATATGCAAAGAATGCCGTTACAATGACTGCTATAACAGCAAACGATTTTACCAGGAACATAAATTTAATTTTTTTATTTTCAATATATGAAAGGTAAAGGATGAATGCTATAAATATACTAAATATTGGTCCTTTGTTACCATGCAAGAAAATAAGTATACAGTTAAATAAAACTATGGAAATACAAAATAACTTTGATTTTTTGTATGTAAAGAACGCGCAAATAGAAGCGACAAGAGAAAACATTAATGAAGGATAGAAGTATATACCATACCCTGTTCTGGTTAATTCGTATATTCTTCTTGGGCTAAGTATATACTCTCTGAACTCCATCAACACTGGAAGGTAAATGATAAAAGCAAGGAAGGTGAATAACAATGAAGTAAACACATACCTTGGTTTATTTTTCGTGTTTGATTTGTTGTATATGGGTTTTCTTTGTGTGTAAAGATAAGAAATAACAAATGATGCTATGTATGTTATATAGCAAGTATAGAAAAACAAATATTCCACTGTATAATTCTGCACCTCTGAGAGGTATACAAATATACCTTCAAACACGTACAGTGTAGGGACTGTTATTATCAGGTATGGGACCATTACATTTATTATTTTTCCCTCAATTCTTACGGAAAGAGTATAGAGATAAACTATAAATAATAAGCATAATGCAATGTATGAAATTATAAGCAT", "1": "ATATTATTTATCCTTATGATTATTGCTTTAAAGATGCGTATGGAAAAACGGAGAGCTATTCAATGA", "4": "ATATTATTTATCCTTATGATTATTGCTTTAAAGATGCGTATGGAAAAACGGAGAGCTATTCAATGA", "5": "TCATTGAATAGCTCTCCGTTTTTCCATACGCATCTTTAAAGCAATAATCATAAGGATAAATAATAT", "0": "ATATTATTTATCCTTATGATTATTGCTTTAAAGATGCGTATGGAAAAACGGAGAGCTATTCAATGA", "2": "ATATTATTTATCCTTATGATTATTGCTTTAAAGATGCGTATGGAAAAACGGAGAGCTATTCAATGA"}, "coverage": {"3": 1.0, "1": 0.05612244897959184, "4": 0.05612244897959184, "5": 0.05612244897959184, "0": 0.05612244897959184, "2": 0.05612244897959184}, "is_trunc": {"3": false, "1": false, "4": false, "5": false, "0": false, "2": false}}, "is_missing": false, "is_perfect_match": false, "is_trunc": false, "serogroup": "B", "top_result": {"qseqid": "gb|AY064418.1|514_1737|Salmonella_enterica_subsp._salamae_serovar_4_12_z_1_7_O_antigen_polymerase_Wzy_wzy_gene_complete_cds|B", "stitle": 10664758, "pident": 94.118, "length": 1224, "mismatch": 72, "gapopen": 0, "qstart": 1, "qend": 1224, "sstart": 84515, "send": 85738, "evalue": 0.0, "bitscore": 1862, "qlen": 1224, "slen": 418912, "sseq": "TTATTTATTGTTTCTTAGTAAAACGAATCTTATATGCTCTGAAAAAACAAAGGAAGATGCAATGTATACCATAAAAGCAATCATCAAATGCTCAGGGAACAACCATCCCATGCTAACAGGAATCACACTTATTCCAATGCAAAATAGGAACATTATGAAATAATGCGCTGACTTTGTTTCCTGAGTTTTATTGGAGAAATACTTAGCTAGGACGCCTTTAAATACTCCAGATATAACTAACCAAACTGGTGTAAAAAGCCCGAAATCTGCGTATAGTTCACCATACCCGAAAGCAGGAGCGCCCTGATTTCTGTAGAATGCATCAGGGAAAAATACTTTTGCCAGATACAATGCGCCAAAATCTTCAGGCTTATCAGGCCAAATAGCCCTCGGAATCCTCGAGTAAACCTCGCTCTCCATTAGTAATTTTCCGTACATAAAGTCAAAGTTTGAGGAAGCAACAAGAACAGCATTACGGGTATAATCCGAGTAATTCGCCATATTTTCTATCGGATTCCCATCAGTAAACGTATATGCAAAGAATGCCGTTACAATGACTGCTATAACAGCAAACGATTTTACCAGGAACATAAATTTAATTTTTTTATTTTCAATATATGAAAGGTAAAGGATGAATGCTATAAATATACTAAATATTGGTCCTTTGTTACCATGCAAGAAAATAAGTATACAGTTAAATAAAACTATGGAAATACAAAATAACTTTGATTTTTTGTATGTAAAGAACGCGCAAATAGAAGCGACAAGAGAAAACATTAATGAAGGATAGAAGTATATACCATACCCTGTTCTGGTTAATTCGTATATTCTTCTTGGGCTAAGTATATACTCTCTGAACTCCATCAACACTGGAAGGTAAATGATAAAAGCAAGGAAGGTGAATAACAATGAAGTAAACACATACCTTGGTTTATTTTTCGTGTTTGATTTGTTGTATATGGGTTTTCTTTGTGTGTAAAGATAAGAAATAACAAATGATGCTATGTATGTTATATAGCAAGTATAGAAAAACAAATATTCCACTGTATAATTCTGCACCTCTGAGAGGTATACAAATATACCTTCAAACACGTACAGTGTAGGGACTGTTATTATCAGGTATGGGACCATTACATTTATTATTTTTCCCTCAATTCTTACGGAAAGAGTATAGAGATAAACTATAAATAATAAGCATAATGCAATGTATGAAATTATAAGCAT", "coverage": 1.0, "is_trunc": false}}}, "serovar": "Paratyphi B var. Java", "serovar_antigen": "Paratyphi B|Paratyphi B var. Java", "serovar_cgmlst": "Paratyphi B var. Java"}]\n\\ No newline at end of file\n' |
| b |
| diff -r 13632190a0ff -r 5c8ff92e38a9 test-data/sistr-results-13-1101.tab --- a/test-data/sistr-results-13-1101.tab Thu Apr 20 14:33:38 2017 -0400 +++ b/test-data/sistr-results-13-1101.tab Wed Jun 14 14:36:59 2017 -0400 |
| [ |
| @@ -1,2 +1,2 @@ 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 -2375035975 0.069696969697 SRR1097806 307 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 +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 13632190a0ff -r 5c8ff92e38a9 test-data/sistr-results.tab --- a/test-data/sistr-results.tab Thu Apr 20 14:33:38 2017 -0400 +++ b/test-data/sistr-results.tab Wed Jun 14 14:36:59 2017 -0400 |
| b |
| @@ -1,2 +1,2 @@ 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 73530 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 + 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 |