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README.rst kaptive.xml test-data/Klebsiella_k_locus_primary_reference_db.gbk test-data/input.fasta test-data/result.json test-data/result_input.fasta test-data/result_table.txt |
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| diff -r 000000000000 -r bda1fd5c651d README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Apr 10 14:47:17 2017 -0400 |
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| @@ -0,0 +1,27 @@ +Kaptive wrapper for Galaxy +============================== + +Galaxy wrapper for +`Kaptive <https://github.com/katholt/Kaptive>`_ + +Installation +------------ + +Installation directly from the `Galaxy Toolshed <http://toolshed.g2.bx.psu.edu/view/nml/kaptive>`_ is +recommended. + + + + +Citation +------------ + +If you use Kaptive in your research, please cite this paper: Wyres, K. et al. Identification of Klebsiella capsule synthesis loci from whole genome data. bioRxiv (2016). + +License +------------ + +GNU General Public License, version 3 + +http://dx.doi.org/10.5281/zenodo.55773 + |
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| diff -r 000000000000 -r bda1fd5c651d kaptive.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kaptive.xml Mon Apr 10 14:47:17 2017 -0400 |
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| @@ -0,0 +1,96 @@ +<tool id="kaptive" name="Kaptive" version="0.3.0"> + <description>reports information about capsular (K) loci found in genome assemblies.</description> + <requirements> + <requirement type="package" version="0.3">kaptive</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> + </stdio> + <command><![CDATA[ + + ln -s "$assembly" "$assembly.name" && + + kaptive.py --assembly "$assembly.name" + + + --k_refs "$references" + -o 'result' + + -t "\${GALAXY_SLOTS:-4}" + + #if $allelic_typing: + --allelic_typing "$allelic_typing" + #end if + + + #if $start_end_margin: + --start_end_margin "$start_end_margin" + #end if + + #if $min_gene_cov: + --min_gene_cov "$min_gene_cov" + #end if + + #if $min_gene_id: + --min_gene_id "$min_gene_id" + #end if + + #if $low_gene_id: + --low_gene_id "$low_gene_id" + #end if + + #if $gap_fill_size: + --gap_fill_size "$gap_fill_size" + #end if + + ]]></command> + <inputs> + + <param name="assembly" type="data" format="fasta" label="Assembly fasta file"/> + + <param name="references" type="data" format="genbank" label="Genbank referece K loci"/> + + <param name="allelic_typing" type="data" format="fasta" label="Allelic Typing genes" help="SRST2-formatted file of allelic typing genes to include in results" optional="True"/> + + <param name="start_end_margin" type="integer" label="Start end margin" help="Missing bases at the ends of K locus allowed in a perfect match. (default: 10)" value="10"/> + + <param name="min_gene_cov" type="float" label="Minimum % coverage for genes" help="minimum required % coverage for genes (default: 90.0)" value="90.0"/> + + <param name="min_gene_id" type="float" label="Minimum % identity for genes" help="minimum required % identity for genes (default: 80.0)" value="80.0"/> + + <param name="low_gene_id" type="float" label="Flag gene with % identity below" help="genes with a % identity below this value will be flagged as low identity (default: 95.0) " value="95.0"/> + + <param name="gap_fill_size" type="integer" label="Distance to merge assemblies" help="when separate parts of the assembly are found within this distance, they will be merged (default: 100) " value="100"/> + + + + </inputs> + + <outputs> + <data format="tabular" name="results" label="Report Results" from_work_dir="result_table.txt"/> + <data format="txt" name="json" label="JSON Results" from_work_dir="result.json"/> + <data format="fasta" name="fasta" label="Fasta Hit Results" from_work_dir="result_*.fasta" /> + </outputs> + <tests> + <test> + <param name="assembly" value="input.fasta" /> + <param name="references" value="Klebsiella_k_locus_primary_reference_db.gbk" /> + <output name="results" file="result_table.txt" /> + <output name="json" file="result.json" /> + <output name="fasta" file="result_input.fasta" /> + </test> + </tests> + <help> + <![CDATA[ + +Documentation available @ https://github.com/katholt/Kaptive/blob/master/README.md + + +**Acknowledgments** + Tool Wrapper Author: Philip Mabon +]]> + </help> + <citations> + <citation type="doi">10.5281/zenodo.55773</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r bda1fd5c651d test-data/Klebsiella_k_locus_primary_reference_db.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Klebsiella_k_locus_primary_reference_db.gbk Mon Apr 10 14:47:17 2017 -0400 |
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| b'@@ -0,0 +1,101640 @@\n+LOCUS AB924547 24985 bp DNA linear BCT 13-MAY-2015\n+DEFINITION Klebsiella pneumoniae DNA, capsular polysaccharide synthesis gene\n+ cluster, serotype: K1.\n+ACCESSION AB924547\n+VERSION AB924547.[1]\n+KEYWORDS .\n+SOURCE Klebsiella pneumoniae\n+ ORGANISM Klebsiella pneumoniae\n+ Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;\n+ Enterobacteriaceae; Klebsiella.\n+REFERENCE 1 (bases 1 to 28658)\n+ AUTHORS Pan,Y.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (15-APR-2014) to the DDBJ/EMBL/GenBank databases.\n+ Contact:Yi-Jiun Pan\n+ National Taiwan University College of Medicine, Department of\n+ Microbiology; 1, Sec 1, Jen-Ai Rd., Taipei 100, Taiwan\n+REFERENCE 2 \n+ AUTHORS Pan,Y.\n+ TITLE Genetic analysis of capsular polysaccharide synthesis gene\n+ clusters in 79 capsular types of Klebsiella\n+ JOURNAL Unpublished (2014)\n+FEATURES Location/Qualifiers \n+ source <1..>24985\n+ /db_xref="taxon:573"\n+ /mol_type="genomic DNA"\n+ /organism="Klebsiella pneumoniae"\n+ /serotype="K1"\n+ /note="K locus: KL1"\n+ /strain="NTUH-K2044"\n+ CDS 1..897\n+ /codon_start=1\n+ /gene="galF"\n+ /product="UDP-glucose pyrophosphorylase"\n+ /protein_id="########.[1]"\n+ /transl_table=11\n+ /translation="MANLKAVIPVAGLGMHMLPATKAIPKEMLPIVDKPMIQYIVDEI\n+ VAAGIKEIVLVTHSSKNAVENHFDTSYELEALLEQRVKRQLLAEVQAICPPGVTIMNV\n+ RQAQPLGLGHSILCARPVVGDNPFVVVLPDIILDGGTADPLRYNLAAMIARFNETGRS\n+ QVLAKRMPGDLSEYSVIQTKEPMVAEGQVARIVEFIEKPDEPQTLDSDLMAVGRYVLS\n+ ADIWAELERTEPGAWGRIQLTDAIAELAKKQSVDAMLMTGESYDCGKKMGYMQAFVTY\n+ GMRNLKEGAKFRESIKKLLA"\n+ CDS 1290..1919\n+ /codon_start=1\n+ /gene="cpsACP"\n+ /note="orf2"\n+ /product="acid phosphatase homologue"\n+ /protein_id="########.[1]"\n+ /transl_table=11\n+ /translation="MNWQLISFFGDSTVLLPSAAALFIVLMLRKTSRLLAWQWSLLFG\n+ ITGAIVCASKLAFMGWGLGIRELDYTGFSGHSALSAAFWPIFLWLLSARFSAGLQKAA\n+ VATGYILAAVVGYSRLVIHAHSVSEVIAGLLLGAAGSALFLVLQKRTSAPESVNISWG\n+ GVACLVMVPLILLHSGSKAPTQSLLGQIATAVGPLDKPFTRTDLHKQVW"\n+ CDS 2879..4312\n+ /codon_start=1\n+ /gene="wzi"\n+ /product="surface assembly of capsule"\n+ /protein_id="########.[1]"\n+ /transl_table=11\n+ /translation="MIKIARIAVTLGLLSSLGAQAYAAGLVVNDNDLRNDLAWLSDRG\n+ VIHLSLSTWPLSQEEIARALKKAKPSYSSEQVVLARINQRLSALKADFRVTGYTSTDQ\n+ PGTPQGFGQTQPADNSLGLAFNNSGEWWDVHLQGNVEGGERISNGSRFNANGAYGAVK\n+ FWNQWLSFGQVPQWWGPGYEGSLIRGDAMRPMTGFLMQRAEQAAPETWWLRWVGPWQY\n+ QISASQMNQYTAVPHTKIIGGRFTFTPFQSLELGASRIMQWGGEGRPESFSSFWDGLT\n+ GKDNTGTENEPGNQLAGFDFKFKLEPTLGWPVSFYGQMVGEDESGYLPSANMFLGGVE\n+ GHHGWGKDAVNWYIEAHDTRTNMNRTGYSYWHHIYTDGYYQQGYSLGDAMGGDGQLFA\n+ GKIEIITEDNQRWSTRLVYAKVNPENQLINKAFPQSDTLKGVQLGWSGDVYQSVRLNT\n+ SLWYTNANNSDSDDVGASAGIEIPFSL"\n+ CDS 4455..5588\n+ /codon_start=1\n+ /gene="wza"\n+ /product="putative capsule polysaccharide export protein"\n+ /protein_id="########.[1]"\n+ /transl_table=11\n+ /translation="MKKKIVKISALALVIGFLSGCTIIPGQGLNSLRKNVVELPDSDY\n+ DLDKLVNVYPMTP'..b'taacacag tttttttcgt taacaatttt taactatccg ttcaaaaagg gagtggtctt\n+ 18361 taaacttcat ttgaaaacta tcttttttag agttaaaggc taagtttttt ttgaaatatt\n+ 18421 taaaataaat aatatttaaa attagcttgt ctctaaaatg ttaaaaatta ttttgtagca\n+ 18481 ttttttgctt ttcttctagg ttcatgcata tctttgagct aatatattta atactttcta\n+ 18541 agctgcgaaa agtcgcagcg accacaccag acaggagtat gtaatgtcca agcaacagat\n+ 18601 cggggttgtc ggtatggcag tgatggggcg caacctcgcg ctcaacatcg aaagccgtgg\n+ 18661 ttataccgtc tctgttttca accgctcccg tgataagact gaggaagtga ttgccgagaa\n+ 18721 ccctggcaag aaactggtcc cacattatac cgtcaaagag tttgttgaat ccctcgaaac\n+ 18781 tccgcgccgt atcctgttaa tggtgaaagc aggtgctggt acggatagtg ctatcgactc\n+ 18841 cctcaagccg tatctggata aaggcgacat catcattgat ggtggtaaca ctttcttcca\n+ 18901 ggataccatc cgacgcaatc gtgaactgtc tgctgatggt tttaacttca tcggtaccgg\n+ 18961 tgtttctggt ggagaagagg gcgcacttaa gggcccatct attatgcctg gcggtcagaa\n+ 19021 agaggcctat gagctggtag cgccaatcct tgagcagatc gccgcccgtg cggaagacgg\n+ 19081 ggaaccttgt gttgcctata ttggtgctga tggtgctggc cactatgtga aaatggttca\n+ 19141 taacggcatt gaatacggtg acatgcagct cattgcagaa gcgtacgctt tgctgaaagg\n+ 19201 cggccttgca ctgtcaaatg aagaactggc tacgaccttc accgagtgga atcagggtga\n+ 19261 gttaagtagc tatctgatag atatcactaa agacatcttc actaaaaaag atgacgaagg\n+ 19321 taaatacttg gttgacgtga ttcttgatga agcggcgaac aaaggtaccg gtaaatggac\n+ 19381 tagccagagt tctctggatt tgggtgaacc tctgtccctt atcaccgagt ccgtattcgc\n+ 19441 tcgttacatc tcttctctca aagatcagcg tgttgccgct tctaaagtgt tgactggtcc\n+ 19501 tcaggcacaa ccggctagtg ataaaacaga atttatcgag aaagtgcgtc gtgctcttta\n+ 19561 tctgggtaaa attgtttcct atgcgcaggg cttctctcaa ctgcgtgctg catctaatga\n+ 19621 atacggctgg gatctgaact acggcgaaat tgccaaaata ttccgtgcgg gttgcattat\n+ 19681 tcgagcccaa ttcctgcaga aaattactga tgcttatgaa gagaatgcag ggattgctaa\n+ 19741 cctgttactg gcaccgtact tcaaacagat tgcggatgaa taccagcagg cactgcgtga\n+ 19801 tgtagttgct tatgctgtgc agaatggtat tccggtacca actttctctg ctgctatcgc\n+ 19861 atactacgac agctatcgtt ctgcagttct gccggctaac ctgattcagg ctcaacgtga\n+ 19921 ttatttcggt gcccatactt ataagcgtac tgataaagat ggagtattcc atactgagtg\n+ 19981 gatggaataa acatcaatcg ttaaagtaat taaatcccgg ttatttgaga gccgggtttt\n+ 20041 ttctatgaat atctttcaac ctaaaactat tgttacgatt attcatctcc tctttaaagc\n+ 20101 tttgctattt gctctcaccc tgaaatctat gaccttgaca tacaccaggt tgaagcataa\n+ 20161 aactgctaca agtattgatt acctgggtgg ccagctgcca ttatcccgtt aactgattaa\n+ 20221 agtgtgaacg aatgaaaatt actatttccg gtaccggtta tgttggttta tcgaacggca\n+ 20281 tccttattgc gcaaaaccat gaagtggtcg cgcttgatat cgttcagtcc aaagtagata\n+ 20341 tgcttaacca gaaaatttct ccgattgtcg acaaagagat ccaggaatat ctggctgaaa\n+ 20401 aaacgttgaa ttttcgtgcg acaactgaca agcaggacgc ttatcgtaat gcggactatg\n+ 20461 tcattatcgc taccccgact gactacgatc caaaaacgaa ctatttcaat acttctaccg\n+ 20521 ttgaagccgt cattcgtgat gtcgcagaaa ttaaccctgc tgcggtgatg attgttaaat\n+ 20581 caaccgttcc tgttggtttt atccgtgata ttaaagagcg tctaggaatt gataacgtta\n+ 20641 ttttctctcc agagttcctg cgcgaaggcc gtgcgttgta tgacaacctg cacccgtccc\n+ 20701 gtatcgttat tggtgagcgt tccgaacgtg ctgaacgatt tgccaatctt ctgaaagaag\n+ 20761 gggcgattaa acaggatatc ccaacgctgt ttactgattc gaccgaagcc gaagcgatta\n+ 20821 aattgtttgc taatacctat cttgcactgc gtgttgccta tttcaatgaa ctggacagct\n+ 20881 atgctgagag tcagggcctt aacactaaac agatcattga aggtgtgtgc ctggatccgc\n+ 20941 gcattgggaa tcactataac aatccgtcgt ttggctatgg tggctactgc ttaccaaaag\n+ 21001 ataccaagca actgctggca aactacgaat cggtaccgaa caacatcatc ggcgctattg\n+ 21061 ttgatgctaa ccgtactcgt aaagacttca tcgccgattc tatcctcgcc cgtaagccac\n+ 21121 aggtggttgg tatttatcgt ctgataatga agagtggttc tgataatttc cgtgcttcat\n+ 21181 cgatccaggg aataatgaaa cgcatcaaag ctaaagggat ttctgttatt atttatgagc\n+ 21241 cagccatgca ggaagatgag ttctttaatt cccgagtgat tagcgacttg aacgtgttta\n+ 21301 agcaggaagc ggatgttatt gtctctaatc gtatggctga agaactggct gacgtcaaag\n+ 21361 ataaggttta cactcgtgat ctgtttggta gcgactga\n+//\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r bda1fd5c651d test-data/input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Mon Apr 10 14:47:17 2017 -0400 |
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| b'@@ -0,0 +1,435 @@\n+>AB924555 Klebsiella pneumoniae DNA, capsular polysaccharide synthesis gene cluster, serotype: K13.\n+GTGAATATGAATATGGCGAATTTGAAAGCGGTTATTCCGGTCGCAGGACTAGGCATGCAT\n+ATGCTGCCGGCCACAAAGGCAATTCCAAAGGAGATGCTGCCGATCGTTGATAAGCCAATG\n+ATTCAGTACATCGTTGACGAAATCGTCGCCGCCGGGATCAAAGAGATTGTTCTGGTGACG\n+CACTCCTCGAAGAACGCGGTGGAAAACCACTTCGACACCTCCTACGAGCTGGAAGCCCTG\n+CTGGAACAGCGCGTGAAGCGCCAGCTGCTGGCGGAAGTGCAGGCCATTTGCCCGCCGGGC\n+GTGACCATCATGAACGTGCGTCAGGCGCAGCCGCTGGGTCTGGGCCACTCCATCCTCTGC\n+GCCCGCCCGGTAGTCGGCGACAACCCGTTTGTGGTGGTCCTGCCGGATATCATCCTTGAC\n+GGCGGCACCGCTGACCCGCTGCGCTATAACCTCGCCGCTATGATCGCCCGCTTTAACGAG\n+ACCGGCCGCAGCCAGGTGCTGGCGAAACGTATGCCGGGCGATCTCTCCGAATACTCCGTC\n+ATCCAGACCAAAGAGCCGATGGTGGCTGAAGGCCAGGTGGCGCGTATCGTTGAGTTTATT\n+GAAAAACCGGACGAACCGCAGACCCTGGACTCCGATCTGATGGCGGTGGGGCGCTACGTG\n+CTGTCGGCGGATATCTGGGCCGAACTGGAACGTACCGAGCCGGGCGCATGGGGCCGTATC\n+CAACTGACCGACGCCATTGCCGAACTGGCGAAGAAGCAGTCCGTCGACGCGATGCTGATG\n+ACCGGCGAAAGCTACGACTGCGGGAAGAAAATGGGCTACATGCAGGCCTTCGTCACCTAC\n+GGGATGCGTAACCTGAAAGAAGGCGCCAAATTCCGCGAAAGCATTAAAAAACTGCTGGCC\n+TGAGCGCCAGCCTGAAACCGAGCGGCAAGGCTGAAGCATTCGTCCTGCCGCTCATAACGT\n+TATGCAGAAATTATTCATAACGCGAATGTTATAACGATTGTAAAGAAACGTATGGCTTCG\n+GAGACTTCTGGTAGTTTGTCTCTGGCCTCTGTGGTGCAATGGTCGGAGTAGCGGCAATAA\n+TGCTTTATGAATAGTCACTTAGTGCGACAATTCCTAAAGCGCAGGGAAAGCGGTCAACGT\n+CAGCCAAAAATAAAACTTGACTGCGATCATGTTTACGCTTTAAACAACTCACTTGCATGC\n+ATAAAAATGTGAAATGAATTGGCATGCGAGCTGGTACAGACATTACGGATAATCCCTGAG\n+CACGGCAGTGGACATCATCGAAGGATCACAGGTATTTGAACTGGCAACTCATCTCATTTT\n+TTGGCGATAGCACCGTTTTGCTGCCCAGCGCAGCGGCGCTGTTTATTGTCCTGATGCTGC\n+GTAAAACGTCGCGGTTGCTGGCGTGGCAGTGGAGTTTGCTGTTCGGCATCACCGGCGCTA\n+TCGTCTGCGCCTCCAAACTGGCCTTTATGGGCTGGGGTCTGGGTATTCGCGAGCTGGATT\n+ACACCGGCTTCAGCGGCCACTCCGCGCTCTCCGCGGCCTTCTGGCCTATCTTCCTGTGGC\n+TGCTCAGCGCCCGTTTCTCCGTCGGTCTGCGTAAAGCGGCCGTTATTACCGGCTATGTTC\n+TGGCCGCCGTGGTGGGCTATTCGCGGCTGGTCATCCATGCGCATTCCGTCTCGGAAGTGA\n+TTGCCGGCCTGCTGCTGGGCGCTGCTGGCAGCGCTTTGTTCCTGCTGCTGCAAAAATGCA\n+CTTCTGACTGCGATTATAAGACAATACCCTGGGGTGGAATTGCATGCCTGGTAATGGTCC\n+CACTGATACTGTTGTATAGCGGCAGTAAAGCGCCGACACAGACCCTGCTGGGGCAAATCG\n+CCACCGCAATTGGGCCGCTGGATAAACCTTTTACCAGAGAGGACCTGCACAAGCAGGCCT\n+GGTAATCGCCGTTTGTTTTACAGGGGAAATTAAATTTTCGCCGGTTAATTAGACAAATAA\n+GAAAATAATCTACTATATACCCGGTAATTGATAATTCATATTTATGAAATAATGAAGTGC\n+TACTACATTGTTATTGCATATTTGCCTGGATATAGCCTTGATCAGACGTTTCTTAAATGC\n+GCTGAGACGTTACCTGATGGACATTCAATGAATATCCAGATTCAGGAAACTATTAGAAAT\n+TGTAGTTGACTACAACGCCATCATCTGATTTTTGCATGTTGATGAGCTATGGAAAAAGAC\n+GTTTTTTTACAGTCAGTTAGCTGCATATGTGATGTTGTAGCAGTACCGGGAAGATCTTTA\n+ACCCTGGAAGCCAGTGAATAATCTTAATTGGTGACCCGCTTATTTTTTGTCAGTAGAACG\n+ACAGGCGGCATTAATTGGCAGATATTCGGTAACAACACTCCCAATTGTGACCGAAATCCC\n+GTAAACTTAACGCCGCCAAAAATAATGGCCTGACCAATTATTCATCCACAGGTCGATAAA\n+AAAATTAAGCCGTTCAGGTAGTCAGTGCGCTGGTAGCTGTTAAGCCAGGGGCGGTAGCGT\n+CGCTGAAGCCGCTTGCTGCTGCACAGAGGTTCTCTTCGACGGCTGAAAAATCGTCCCGGT\n+CAGGATGATCGCCCTCAATCGATATCTATCAATTTTCTACGGATATCCTCAGAAGTTGGC\n+CAGGAACGGCTGCTGATATCGCCTGGAGATTAACTTTCCTGTCTCATCGATAGCCTGTAG\n+GGTAAAATTCGCCTACATTGTGAGCTGAGTGGATGTTATAAGGCTAACAAGCAGCTTAGG\n+GTAAATGTACTTGCCTCGCCGGTGTTGCACAGCGAAGTCAGCTGGTGCCGCGAGCGCTTT\n+CTATCTTGGTATTCCCCTCATTCTCATTGAGATACGACAGCGGGGCTGAAAATGGATCTT\n+GTACAATGATAAAAATTGCGCGCATTGCCGTGACGTTGGGTTTGCTTTCCTCACTGGGAG\n+CCCAGGCTTACGCGGCCGGGTTAGTGGTAAATGACAACGACTTGCGTAACGACCTGGCCT\n+GGCTTTCCGATCGCGGGGTCATCCATCTGAGCCTGTCGACGTGGCCGCTGAGCCAGGAAG\n+AGATCGCCCGGGCGCTGAAAAAGGCCAAACCTTCCTACTCTTCTGAGCAAGTTGTGCTGG\n+CGCGTATCAACCAGCGACTGTCTGCCTTAAAAGCGGATTTCCGGGTCACCGGCTACACTT\n+CAACCGATCAGCCGGGCACTCCGCAGGGGTTTGGTCAGACACAGCCGGCGGATAACTCGT\n+TAGGCCTGGCATTCAACAACAGCGGCGAGTGGTGGGATATCCATCTCCAGGGCAACGTTG\n+AAGGGGGAGAGCGGATTAGCAACGGATCGCGCTTCAACGCCAACGGCGCATACGGCGCGG\n+TGAAGTTCTGGAACCAGTGGCTCTCTTTTGGCCAGGTACCACAGTGGTGGGGGCCTGGCT\n+ATGAAGGTAGCCTGATTCGCGGGGATGCAATGCGACCGATGACCGGTTTCCTGATGCAGC\n+GAGCCGAGCAGGCGGCGCCAGAGACCTGGTGGCTGCGCTGGGTGGGGCCATGGCAGTATC\n+AAATCTCCGCAAGCCAGATGAATCAATATACCGCGGTACCTCATGCCAAAATTATCGGCG\n+GTCGTTTCACTTTCTCACCTTTCCAGTCACTGGAACTAGGCGCGTCGCGCATTATGCAGT\n+GGGGGGGGGAAGGGCGGCCGCAATCCTTTAGCAGCTTCTGGGATGGGTTTACTGGTCATG\n+ATAATACCGGGACTAATAATGAACCTGGTAACCAA'..b'CATCGCCCTGGCGGCCCTCCAGGCCACCCGCCACGGCGACGACC\n+CGCTGATGCTGGTCCTCGCCGCCGACCATATCATCAATAACCAGCCGGTCTTCCACGACG\n+CCATCCGCGTCGCCGAGCAGTATGCCGATGAAGGCCATCTGGTCACCTTCGGTATCGTGC\n+CGAACGCCCCGGAAACCGGCTACGGCTACATCCAGCGCGGCGTGGCCCTCACCGACAGCG\n+CCCATACTCCGTACCAGGTGGCCCGCTTCGTGGAGAAGCCGGACCGCGAGCGCGCCGAGG\n+CTTACCTCGCCTCCGGGGAGTACTACTGGAACAGCGGCATGTTTATGTTCCGCGCCAAAA\n+AATACCTTTCCGAGCTGGCCAAATTCCGCCCGGATATCCTCGAAGCCTGCCAGGCCGCGG\n+TCAATGCCGCCGATAACGGCAGCGACTTCATCAGTATCCCGCATGACATTTTCTGCGAGT\n+GTCCGGACGAGTCTGTGGACTACGCGGTGATGGAGAAAACCGCCGACGCGGTGGTGGTCG\n+GTCTCGATGCCGACTGGAGCGACGTCGGCTCCTGGTCCGCCCTGTGGGAGGTCAGCCCGA\n+AAGACGGGCAGGGTAACGTCCTCAGCGGCGACGCGTGGGTGCACAACAGCGAAAACTGCT\n+ACATCAACAGCGACGAGAAGCTGGTGGCGGCCATCGGCGTGGAGAATCTGGTGATTGTCA\n+GCACCAAGGACGCCGTGCTGGTGATGAACCGCGAGCGTTCCCAGGACGTGAAGAAGGCGG\n+TCGAGTTTCTCAAGCAGAACCAGCGCAGCGAGTACAAGCGCCACCGCGAGATTTACCGTC\n+CCTGGGGCCGCTGCGACGTGGTGGTCCAGACCCCGCGCTTCAACGTCAACCGCATTACGG\n+TGAAACCGGGCGGCGCCTTCTCGATGCAGATGCATCACCACCGCGCCGAGCACTGGGTCA\n+TTCTCGCCGGCACCGGCCAGGTGACCGTCAACGGCAAGCAGTTCCTGCTGACCGAGAACC\n+AGTCCACCTTTATTCCGATTGGCGCCGAGCACAGCCTGGAAAACCCGGGCCGCATTCCGC\n+TGGAAGTGCTGGAGATCCAGTCGGGGTCGTACCTCGGCGAGGACGACATTATTCGTATTA\n+AAGACCAGTATGGTCGTTGCTAATTTTTTCGGGACAAAACGCAGAATGACACAGTTAACA\n+TGCTTTAAGGCTTATGACATCCGTGGTGAACTGGGCGAGGAGCTGAACGAGGACATCGCC\n+TACCGTATCGGCCGCGCCTACGGCGAATTTCTGAAACCCGGGAAGATAGTGGTGGGGGGC\n+GATGTGCGCCTCACCAGCGAGTCGCTGAAGCTGGCGCTGGCCCGCGGGCTGATGGACGCC\n+GGCACCGACGTGCTGGATATCGGCCTGAGCGGCACGGAAGAGATTTACTTCGCCACTTTC\n+CACCTCGGGGTGGATGGCGGTATCGAGGTGACGGCCAGCCACAACCCGATGAACTACAAC\n+GGCATGAAGCTGGTGCGCGAGAACGCGAAGCCCATCAGCGGCGACACCGGCCTGCGGGAT\n+ATCCAGCGCCTGGCGGAGGAGAACCAGTTCCCGCCGGTGGACCCGGCGCGTCGCGGGACC\n+CTGCGCCAGATTTCGGTGCTGAAGGAGTACGTCGACCACCTGATGGGCTACGTGGACCTG\n+GCGAACTTCACCCGTCCGCTGAAGCTGGTGGTGAACTCCGGCAACGGGGCGGCGGGGCAC\n+GTAATTGATGAGGTGGAGAAACGCTTCGCGGCGGCCGGGGCGCCGGTGACCTTTATCAAG\n+GTGCATCACCAGCCGGACGGCCATTTCCCGAACGGTATCCCGAACCCGCTGCTGCCGGAG\n+TGCCGCCAGGACACCGCCTACGCGGTGCGTGCGCATCAGGCGGACATGGGGATCGCCTTT\n+GACGGCGACTTCGACCGCTGCTTCCTGTTCGATGACGAGGCGTCGTTTATCGAGGGGTAC\n+TACATTGTCGGCCTGCTGGCGGAAGCGTTCCTGCAGAAGCAGCCGGGGGCGAAAATCATT\n+CACGACCCGCGTCTGACATGGAACACGGTGGACATCGTGACCCGCAGCGGCGGCCAGCCG\n+GTGATGTCGAAGACCGGGCATGCGTTCATCAAGGAGCGGATGCGCCAGGAAGACGCCATC\n+TACGGCGGGGAGATGAGCGCGCACCATTACTTCCGCGACTTTGCCTACTGCGACAGCGGG\n+ATGATCCCGTGGCTGCTGGTGGCGGAGCTGCTGTGCCTGAAGAACAGCTCGCTGAAATCG\n+CTGGTGGCGGACCGCCAGGCGGCGTTCCCGGCGTCGGGGGAGATCAACCGCAAGCTGGGA\n+AATGCAGCGGAGGCGATAGCGCGCATCCGGGCGCAGTATGAGCCGGCGGCCGCACACATC\n+GACACAACGGACGGTATCAGTATTGAATACCCTGAGTGGCGCTTTAACCTGCGCACGTCC\n+AATACCGAGCCGGTGGTGCGTCTGAACGTTGAGTCCAGAGCGGATACTGCGTTAATGAAT\n+GCAAAAACCGAAGAGATTTTAGCTCTTCTCAAGTAATGCATTATCCATAATGGAAGCCAT\n+AGGGTCAGATTTTAATCGTATTTTTGACCTTATGGCTTATTCTTGACATCCCACTGGTCA\n+AAGCGTAAAACCGCCCACAGAATTATTTAATTTCGTGGCTATCCGCCATTATCCAGTTAA\n+CTGATTAAAGTGTAATCTCATGAAAATTACTATTTCCGGTACAGGTTATGTTGGTTTATC\n+GAACGGTGTCCTGATCGCGCAAAACCACGAAGTGGTGGCCCTGGATATCGTACAGGCCAA\n+AGTGGATATGCTTAACCAGAAGATCTCTCCGATTGTCGATAAAGAGATTCAGGAATATCT\n+GGCAGAAAAACCGTTAAATTTCCGTGCCACCACGGATAAGCACGACGCGTACCGCAATGC\n+CGACTACGTGATCATTGCCACGCCGACCGATTACGATCCCAAAACTAACTACTTTAACAC\n+CTCTACGGTGGAAGCGGTTATTCGCGATGTCACAGAGATCAACCCGAACGCGGTAATGAT\n+CATTAAATCGACCATCCCGGTGGGGTTCACCCGCGACATCAAAGAACGTTTAGGGATTGA\n+TAATGTTATTTTCTCTCCGGAGTTCCTGCGTGAAGGACGTGCGCTGTACGACAACCTACA\n+TCCGTCGCGTATTGTCATCGGTGAGCGCTCCGCGCGTGCCGAACGTTTCGCTGATCTGCT\n+GAAAGAAGGCGCGATCAAGCAGGATATCCCGACCCTGTTTACCGACTCTACCGAAGCGGA\n+AGCGATCAAACTGTTCGCTAACACCTATCTGGCGCTGCGCGTTGCCTATTTCAACGAGCT\n+CGACAGCTATGCTGAAAGCCAGGGGCTGAACAGCAAGCAGATTATCGAAGGGGTATGCCT\n+GGATCCGCGTATCGGCAACCACTATAACAACCCGTCCTTTGGCTACGGCGGCTACTGCCT\n+GCCAAAAGATACCAAGCAGCTGCTGGCGAACTACGAATCGGTCCCGAACAATATCATCGC\n+GGCTATCGTCGATGCCAACCGTACCCGTAAAGACTTTATCGCGGATTCTATTCTCGCTCG\n+TAAGCCGAAAGTAGTGGGTGTGTATCGCCTGATCATGAAGAGTGGTTCGGACAACTTCCG\n+TGCCTCTTCTATTCAGGGCATTATGAAGCGCATCAAGGCGAAAGGTATTCCGGTTATTAT\n+CTATGAACCGGTGATGCAGGAAGATGAGTTCTTCAACTCCCGCGTCGTGCGCGACCTGAA\n+TGCCTTCAAGCAAGAAGCTGATGTGATCATTTCTAACCGTATGGCGGAAGAGTTGGCGGA\n+TGTGGCGGACAAGGTCTACACCCGCGATCTGTTTGGTAACGATTAA\n' |
| b |
| diff -r 000000000000 -r bda1fd5c651d test-data/result.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.json Mon Apr 10 14:47:17 2017 -0400 |
| [ |
| b'@@ -0,0 +1,550 @@\n+[\n+ {\n+ "Assembly name": "input",\n+ "Best match": {\n+ "Locus name": "KL13",\n+ "Match confidence": "Perfect",\n+ "Reference": {\n+ "Length": 26026,\n+ "Sequence": "GTGAATATGAATATGGCGAATTTGAAAGCGGTTATTCCGGTCGCAGGACTAGGCATGCATATGCTGCCGGCCACAAAGGCAATTCCAAAGGAGATGCTGCCGATCGTTGATAAGCCAATGATTCAGTACATCGTTGACGAAATCGTCGCCGCCGGGATCAAAGAGATTGTTCTGGTGACGCACTCCTCGAAGAACGCGGTGGAAAACCACTTCGACACCTCCTACGAGCTGGAAGCCCTGCTGGAACAGCGCGTGAAGCGCCAGCTGCTGGCGGAAGTGCAGGCCATTTGCCCGCCGGGCGTGACCATCATGAACGTGCGTCAGGCGCAGCCGCTGGGTCTGGGCCACTCCATCCTCTGCGCCCGCCCGGTAGTCGGCGACAACCCGTTTGTGGTGGTCCTGCCGGATATCATCCTTGACGGCGGCACCGCTGACCCGCTGCGCTATAACCTCGCCGCTATGATCGCCCGCTTTAACGAGACCGGCCGCAGCCAGGTGCTGGCGAAACGTATGCCGGGCGATCTCTCCGAATACTCCGTCATCCAGACCAAAGAGCCGATGGTGGCTGAAGGCCAGGTGGCGCGTATCGTTGAGTTTATTGAAAAACCGGACGAACCGCAGACCCTGGACTCCGATCTGATGGCGGTGGGGCGCTACGTGCTGTCGGCGGATATCTGGGCCGAACTGGAACGTACCGAGCCGGGCGCATGGGGCCGTATCCAACTGACCGACGCCATTGCCGAACTGGCGAAGAAGCAGTCCGTCGACGCGATGCTGATGACCGGCGAAAGCTACGACTGCGGGAAGAAAATGGGCTACATGCAGGCCTTCGTCACCTACGGGATGCGTAACCTGAAAGAAGGCGCCAAATTCCGCGAAAGCATTAAAAAACTGCTGGCCTGAGCGCCAGCCTGAAACCGAGCGGCAAGGCTGAAGCATTCGTCCTGCCGCTCATAACGTTATGCAGAAATTATTCATAACGCGAATGTTATAACGATTGTAAAGAAACGTATGGCTTCGGAGACTTCTGGTAGTTTGTCTCTGGCCTCTGTGGTGCAATGGTCGGAGTAGCGGCAATAATGCTTTATGAATAGTCACTTAGTGCGACAATTCCTAAAGCGCAGGGAAAGCGGTCAACGTCAGCCAAAAATAAAACTTGACTGCGATCATGTTTACGCTTTAAACAACTCACTTGCATGCATAAAAATGTGAAATGAATTGGCATGCGAGCTGGTACAGACATTACGGATAATCCCTGAGCACGGCAGTGGACATCATCGAAGGATCACAGGTATTTGAACTGGCAACTCATCTCATTTTTTGGCGATAGCACCGTTTTGCTGCCCAGCGCAGCGGCGCTGTTTATTGTCCTGATGCTGCGTAAAACGTCGCGGTTGCTGGCGTGGCAGTGGAGTTTGCTGTTCGGCATCACCGGCGCTATCGTCTGCGCCTCCAAACTGGCCTTTATGGGCTGGGGTCTGGGTATTCGCGAGCTGGATTACACCGGCTTCAGCGGCCACTCCGCGCTCTCCGCGGCCTTCTGGCCTATCTTCCTGTGGCTGCTCAGCGCCCGTTTCTCCGTCGGTCTGCGTAAAGCGGCCGTTATTACCGGCTATGTTCTGGCCGCCGTGGTGGGCTATTCGCGGCTGGTCATCCATGCGCATTCCGTCTCGGAAGTGATTGCCGGCCTGCTGCTGGGCGCTGCTGGCAGCGCTTTGTTCCTGCTGCTGCAAAAATGCACTTCTGACTGCGATTATAAGACAATACCCTGGGGTGGAATTGCATGCCTGGTAATGGTCCCACTGATACTGTTGTATAGCGGCAGTAAAGCGCCGACACAGACCCTGCTGGGGCAAATCGCCACCGCAATTGGGCCGCTGGATAAACCTTTTACCAGAGAGGACCTGCACAAGCAGGCCTGGTAATCGCCGTTTGTTTTACAGGGGAAATTAAATTTTCGCCGGTTAATTAGACAAATAAGAAAATAATCTACTATATACCCGGTAATTGATAATTCATATTTATGAAATAATGAAGTGCTACTACATTGTTATTGCATATTTGCCTGGATATAGCCTTGATCAGACGTTTCTTAAATGCGCTGAGACGTTACCTGATGGACATTCAATGAATATCCAGATTCAGGAAACTATTAGAAATTGTAGTTGACTACAACGCCATCATCTGATTTTTGCATGTTGATGAGCTATGGAAAAAGACGTTTTTTTACAGTCAGTTAGCTGCATATGTGATGTTGTAGCAGTACCGGGAAGATCTTTAACCCTGGAAGCCAGTGAATAATCTTAATTGGTGACCCGCTTATTTTTTGTCAGTAGAACGACAGGCGGCATTAATTGGCAGATATTCGGTAACAACACTCCCAATTGTGACCGAAATCCCGTAAACTTAACGCCGCCAAAAATAATGGCCTGACCAATTATTCATCCACAGGTCGATAAAAAAATTAAGCCGTTCAGGTAGTCAGTGCGCTGGTAGCTGTTAAGCCAGGGGCGGTAGCGTCGCTGAAGCCGCTTGCTGCTGCACAGAGGTTCTCTTCGACGGCTGAAAAATCGTCCCGGTCAGGATGATCGCCCTCAATCGATATCTATCAATTTTCTACGGATATCCTCAGAAGTTGGCCAGGAACGGCTGCTGATATCGCCTGGAGATTAACTTTCCTGTCTCATCGATAGCCTGTAGGGTAAAATTCGCCTACATTGTGAGCTGAGTGGATGTTATAAGGCTAACAAGCAGCTTAGGGTAAATGTACTTGCCTCGCCGGTGTTGCACAGCGAAGTCAGCTGGTGCCGCGAGCGCTTTCTATCTTGGTATTCCCCTCATTCTCATTGAGATACGACAGCGGGGCTGAAAATGGATCTTGTACAATGATAAAAATTGCGCGCATTGCCGTGACGTTGGGTTTGCTTTCCTCACTGGGAGCCCAGGCTTACGCGGCCGGGTTAGTGGTAAATGACAACGACTTGCGTAACGACCTGGCCTGGCTTTCCGATCGCGGGGTCATCCATCTGAGCCTGTCGACGTGGCCGCTGAGCCAGGAAGAGATCGCCCGGGCGCTGAAAAAGGCCAAACCTTCCTACTCTTCTGAGCAAGTTGTGCTGGCGCGTATCAACCAGCGACTGTCTGCCTTAAAAGCGGATTTCCGGGTCACCGGCTACACTTCAACCGATCAGCCGGGCACTCCGCAGGGGTTTGGTCAGACACAGCCGGCGGATAACTCGTTAGGCCTGGCATTCAACAACAGCGGCGAGTGGTGGGATATCCATCTCCAGGGCAACGTTGAAGGGGGAGAGCGGATTAGCAACGGATCGCGCTTCAACGCCAACGGCGCATACGGCGCGGTGAAGTTCTGGAACCAGTGGCTCTCTTTTGGCCAGGTACCACAGTGGTGGGGGCCTGGCTATGAAGGTAGCCTGATTCGCGGGGATGCAATGCGACCGATGACCGGTTTCCTGATGCAGCGAGCCGAGCAGGCGGCGCCAGAGACCTGGTGGCTGCGCTGGGTGGGGCCATGGCAGTATCAAATCTCCGCAAGCCAGATGAATCAATATACCGCGGTACCTCATGCCAAAATTATCGGCGGTCGTTTCACTTTCTCACCTTTCCAGTCACTGGAACTAGGCGCGTCGCGCATTATGCAGTGGGGGGGGGAAGGGCGGCCGCAATCCTTTAGCAGCTTCTGGGATGGGTTTACTGGTCATGATAATACCGGGACTAATAAT'..b'h": 389,\n+ "Nucleotide sequence": "ATGAAAATTACTATTTCCGGTACAGGTTATGTTGGTTTATCGAACGGTGTCCTGATCGCGCAAAACCACGAAGTGGTGGCCCTGGATATCGTACAGGCCAAAGTGGATATGCTTAACCAGAAGATCTCTCCGATTGTCGATAAAGAGATTCAGGAATATCTGGCAGAAAAACCGTTAAATTTCCGTGCCACCACGGATAAGCACGACGCGTACCGCAATGCCGACTACGTGATCATTGCCACGCCGACCGATTACGATCCCAAAACTAACTACTTTAACACCTCTACGGTGGAAGCGGTTATTCGCGATGTCACAGAGATCAACCCGAACGCGGTAATGATCATTAAATCGACCATCCCGGTGGGGTTCACCCGCGACATCAAAGAACGTTTAGGGATTGATAATGTTATTTTCTCTCCGGAGTTCCTGCGTGAAGGACGTGCGCTGTACGACAACCTACATCCGTCGCGTATTGTCATCGGTGAGCGCTCCGCGCGTGCCGAACGTTTCGCTGATCTGCTGAAAGAAGGCGCGATCAAGCAGGATATCCCGACCCTGTTTACCGACTCTACCGAAGCGGAAGCGATCAAACTGTTCGCTAACACCTATCTGGCGCTGCGCGTTGCCTATTTCAACGAGCTCGACAGCTATGCTGAAAGCCAGGGGCTGAACAGCAAGCAGATTATCGAAGGGGTATGCCTGGATCCGCGTATCGGCAACCACTATAACAACCCGTCCTTTGGCTACGGCGGCTACTGCCTGCCAAAAGATACCAAGCAGCTGCTGGCGAACTACGAATCGGTCCCGAACAATATCATCGCGGCTATCGTCGATGCCAACCGTACCCGTAAAGACTTTATCGCGGATTCTATTCTCGCTCGTAAGCCGAAAGTAGTGGGTGTGTATCGCCTGATCATGAAGAGTGGTTCGGACAACTTCCGTGCCTCTTCTATTCAGGGCATTATGAAGCGCATCAAGGCGAAAGGTATTCCGGTTATTATCTATGAACCGGTGATGCAGGAAGATGAGTTCTTCAACTCCCGCGTCGTGCGCGACCTGAATGCCTTCAAGCAAGAAGCTGATGTGATCATTTCTAACCGTATGGCGGAAGAGTTGGCGGATGTGGCGGACAAGGTCTACACCCGCGATCTGTTTGGTAACGATTAA",\n+ "Protein sequence": "MKITISGTGYVGLSNGVLIAQNHEVVALDIVQAKVDMLNQKISPIVDKEIQEYLAEKPLNFRATTDKHDAYRNADYVIIATPTDYDPKTNYFNTSTVEAVIRDVTEINPNAVMIIKSTIPVGFTRDIKERLGIDNVIFSPEFLREGRALYDNLHPSRIVIGERSARAERFADLLKEGAIKQDIPTLFTDSTEAEAIKLFANTYLALRVAYFNELDSYAESQGLNSKQIIEGVCLDPRIGNHYNNPSFGYGGYCLPKDTKQLLANYESVPNNIIAAIVDANRTRKDFIADSILARKPKVVGVYRLIMKSGSDNFRASSIQGIMKRIKAKGIPVIIYEPVMQEDEFFNSRVVRDLNAFKQEADVIISNRMAEELADVADKVYTRDLFGND*"\n+ },\n+ "tblastn result": {\n+ "Coverage": "100.00%",\n+ "Identity": "100.00%",\n+ "Contig name": "AB924555",\n+ "Contig start position": 24859,\n+ "Contig end position": 26026,\n+ "Contig strand": "+",\n+ "Bit score": 790.0,\n+ "E-value": 0.0,\n+ "Nucleotide length": 1167,\n+ "Protein length": 389,\n+ "Nucleotide sequence": "ATGAAAATTACTATTTCCGGTACAGGTTATGTTGGTTTATCGAACGGTGTCCTGATCGCGCAAAACCACGAAGTGGTGGCCCTGGATATCGTACAGGCCAAAGTGGATATGCTTAACCAGAAGATCTCTCCGATTGTCGATAAAGAGATTCAGGAATATCTGGCAGAAAAACCGTTAAATTTCCGTGCCACCACGGATAAGCACGACGCGTACCGCAATGCCGACTACGTGATCATTGCCACGCCGACCGATTACGATCCCAAAACTAACTACTTTAACACCTCTACGGTGGAAGCGGTTATTCGCGATGTCACAGAGATCAACCCGAACGCGGTAATGATCATTAAATCGACCATCCCGGTGGGGTTCACCCGCGACATCAAAGAACGTTTAGGGATTGATAATGTTATTTTCTCTCCGGAGTTCCTGCGTGAAGGACGTGCGCTGTACGACAACCTACATCCGTCGCGTATTGTCATCGGTGAGCGCTCCGCGCGTGCCGAACGTTTCGCTGATCTGCTGAAAGAAGGCGCGATCAAGCAGGATATCCCGACCCTGTTTACCGACTCTACCGAAGCGGAAGCGATCAAACTGTTCGCTAACACCTATCTGGCGCTGCGCGTTGCCTATTTCAACGAGCTCGACAGCTATGCTGAAAGCCAGGGGCTGAACAGCAAGCAGATTATCGAAGGGGTATGCCTGGATCCGCGTATCGGCAACCACTATAACAACCCGTCCTTTGGCTACGGCGGCTACTGCCTGCCAAAAGATACCAAGCAGCTGCTGGCGAACTACGAATCGGTCCCGAACAATATCATCGCGGCTATCGTCGATGCCAACCGTACCCGTAAAGACTTTATCGCGGATTCTATTCTCGCTCGTAAGCCGAAAGTAGTGGGTGTGTATCGCCTGATCATGAAGAGTGGTTCGGACAACTTCCGTGCCTCTTCTATTCAGGGCATTATGAAGCGCATCAAGGCGAAAGGTATTCCGGTTATTATCTATGAACCGGTGATGCAGGAAGATGAGTTCTTCAACTCCCGCGTCGTGCGCGACCTGAATGCCTTCAAGCAAGAAGCTGATGTGATCATTTCTAACCGTATGGCGGAAGAGTTGGCGGATGTGGCGGACAAGGTCTACACCCGCGATCTGTTTGGTAACGATTAA",\n+ "Protein sequence": "MKITISGTGYVGLSNGVLIAQNHEVVALDIVQAKVDMLNQKISPIVDKEIQEYLAEKPLNFRATTDKHDAYRNADYVIIATPTDYDPKTNYFNTSTVEAVIRDVTEINPNAVMIIKSTIPVGFTRDIKERLGIDNVIFSPEFLREGRALYDNLHPSRIVIGERSARAERFADLLKEGAIKQDIPTLFTDSTEAEAIKLFANTYLALRVAYFNELDSYAESQGLNSKQIIEGVCLDPRIGNHYNNPSFGYGGYCLPKDTKQLLANYESVPNNIIAAIVDANRTRKDFIADSILARKPKVVGVYRLIMKSGSDNFRASSIQGIMKRIKAKGIPVIIYEPVMQEDEFFNSRVVRDLNAFKQEADVIISNRMAEELADVADKVYTRDLFGND*"\n+ },\n+ "Match confidence": "Very high"\n+ }\n+ ],\n+ "Other genes in locus": {},\n+ "Other genes outside locus": {}\n+ }\n+]\n' |
| b |
| diff -r 000000000000 -r bda1fd5c651d test-data/result_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_input.fasta Mon Apr 10 14:47:17 2017 -0400 |
| b |
| b'@@ -0,0 +1,435 @@\n+>input_AB924555_1_to_26026_+_strand\n+GTGAATATGAATATGGCGAATTTGAAAGCGGTTATTCCGGTCGCAGGACTAGGCATGCAT\n+ATGCTGCCGGCCACAAAGGCAATTCCAAAGGAGATGCTGCCGATCGTTGATAAGCCAATG\n+ATTCAGTACATCGTTGACGAAATCGTCGCCGCCGGGATCAAAGAGATTGTTCTGGTGACG\n+CACTCCTCGAAGAACGCGGTGGAAAACCACTTCGACACCTCCTACGAGCTGGAAGCCCTG\n+CTGGAACAGCGCGTGAAGCGCCAGCTGCTGGCGGAAGTGCAGGCCATTTGCCCGCCGGGC\n+GTGACCATCATGAACGTGCGTCAGGCGCAGCCGCTGGGTCTGGGCCACTCCATCCTCTGC\n+GCCCGCCCGGTAGTCGGCGACAACCCGTTTGTGGTGGTCCTGCCGGATATCATCCTTGAC\n+GGCGGCACCGCTGACCCGCTGCGCTATAACCTCGCCGCTATGATCGCCCGCTTTAACGAG\n+ACCGGCCGCAGCCAGGTGCTGGCGAAACGTATGCCGGGCGATCTCTCCGAATACTCCGTC\n+ATCCAGACCAAAGAGCCGATGGTGGCTGAAGGCCAGGTGGCGCGTATCGTTGAGTTTATT\n+GAAAAACCGGACGAACCGCAGACCCTGGACTCCGATCTGATGGCGGTGGGGCGCTACGTG\n+CTGTCGGCGGATATCTGGGCCGAACTGGAACGTACCGAGCCGGGCGCATGGGGCCGTATC\n+CAACTGACCGACGCCATTGCCGAACTGGCGAAGAAGCAGTCCGTCGACGCGATGCTGATG\n+ACCGGCGAAAGCTACGACTGCGGGAAGAAAATGGGCTACATGCAGGCCTTCGTCACCTAC\n+GGGATGCGTAACCTGAAAGAAGGCGCCAAATTCCGCGAAAGCATTAAAAAACTGCTGGCC\n+TGAGCGCCAGCCTGAAACCGAGCGGCAAGGCTGAAGCATTCGTCCTGCCGCTCATAACGT\n+TATGCAGAAATTATTCATAACGCGAATGTTATAACGATTGTAAAGAAACGTATGGCTTCG\n+GAGACTTCTGGTAGTTTGTCTCTGGCCTCTGTGGTGCAATGGTCGGAGTAGCGGCAATAA\n+TGCTTTATGAATAGTCACTTAGTGCGACAATTCCTAAAGCGCAGGGAAAGCGGTCAACGT\n+CAGCCAAAAATAAAACTTGACTGCGATCATGTTTACGCTTTAAACAACTCACTTGCATGC\n+ATAAAAATGTGAAATGAATTGGCATGCGAGCTGGTACAGACATTACGGATAATCCCTGAG\n+CACGGCAGTGGACATCATCGAAGGATCACAGGTATTTGAACTGGCAACTCATCTCATTTT\n+TTGGCGATAGCACCGTTTTGCTGCCCAGCGCAGCGGCGCTGTTTATTGTCCTGATGCTGC\n+GTAAAACGTCGCGGTTGCTGGCGTGGCAGTGGAGTTTGCTGTTCGGCATCACCGGCGCTA\n+TCGTCTGCGCCTCCAAACTGGCCTTTATGGGCTGGGGTCTGGGTATTCGCGAGCTGGATT\n+ACACCGGCTTCAGCGGCCACTCCGCGCTCTCCGCGGCCTTCTGGCCTATCTTCCTGTGGC\n+TGCTCAGCGCCCGTTTCTCCGTCGGTCTGCGTAAAGCGGCCGTTATTACCGGCTATGTTC\n+TGGCCGCCGTGGTGGGCTATTCGCGGCTGGTCATCCATGCGCATTCCGTCTCGGAAGTGA\n+TTGCCGGCCTGCTGCTGGGCGCTGCTGGCAGCGCTTTGTTCCTGCTGCTGCAAAAATGCA\n+CTTCTGACTGCGATTATAAGACAATACCCTGGGGTGGAATTGCATGCCTGGTAATGGTCC\n+CACTGATACTGTTGTATAGCGGCAGTAAAGCGCCGACACAGACCCTGCTGGGGCAAATCG\n+CCACCGCAATTGGGCCGCTGGATAAACCTTTTACCAGAGAGGACCTGCACAAGCAGGCCT\n+GGTAATCGCCGTTTGTTTTACAGGGGAAATTAAATTTTCGCCGGTTAATTAGACAAATAA\n+GAAAATAATCTACTATATACCCGGTAATTGATAATTCATATTTATGAAATAATGAAGTGC\n+TACTACATTGTTATTGCATATTTGCCTGGATATAGCCTTGATCAGACGTTTCTTAAATGC\n+GCTGAGACGTTACCTGATGGACATTCAATGAATATCCAGATTCAGGAAACTATTAGAAAT\n+TGTAGTTGACTACAACGCCATCATCTGATTTTTGCATGTTGATGAGCTATGGAAAAAGAC\n+GTTTTTTTACAGTCAGTTAGCTGCATATGTGATGTTGTAGCAGTACCGGGAAGATCTTTA\n+ACCCTGGAAGCCAGTGAATAATCTTAATTGGTGACCCGCTTATTTTTTGTCAGTAGAACG\n+ACAGGCGGCATTAATTGGCAGATATTCGGTAACAACACTCCCAATTGTGACCGAAATCCC\n+GTAAACTTAACGCCGCCAAAAATAATGGCCTGACCAATTATTCATCCACAGGTCGATAAA\n+AAAATTAAGCCGTTCAGGTAGTCAGTGCGCTGGTAGCTGTTAAGCCAGGGGCGGTAGCGT\n+CGCTGAAGCCGCTTGCTGCTGCACAGAGGTTCTCTTCGACGGCTGAAAAATCGTCCCGGT\n+CAGGATGATCGCCCTCAATCGATATCTATCAATTTTCTACGGATATCCTCAGAAGTTGGC\n+CAGGAACGGCTGCTGATATCGCCTGGAGATTAACTTTCCTGTCTCATCGATAGCCTGTAG\n+GGTAAAATTCGCCTACATTGTGAGCTGAGTGGATGTTATAAGGCTAACAAGCAGCTTAGG\n+GTAAATGTACTTGCCTCGCCGGTGTTGCACAGCGAAGTCAGCTGGTGCCGCGAGCGCTTT\n+CTATCTTGGTATTCCCCTCATTCTCATTGAGATACGACAGCGGGGCTGAAAATGGATCTT\n+GTACAATGATAAAAATTGCGCGCATTGCCGTGACGTTGGGTTTGCTTTCCTCACTGGGAG\n+CCCAGGCTTACGCGGCCGGGTTAGTGGTAAATGACAACGACTTGCGTAACGACCTGGCCT\n+GGCTTTCCGATCGCGGGGTCATCCATCTGAGCCTGTCGACGTGGCCGCTGAGCCAGGAAG\n+AGATCGCCCGGGCGCTGAAAAAGGCCAAACCTTCCTACTCTTCTGAGCAAGTTGTGCTGG\n+CGCGTATCAACCAGCGACTGTCTGCCTTAAAAGCGGATTTCCGGGTCACCGGCTACACTT\n+CAACCGATCAGCCGGGCACTCCGCAGGGGTTTGGTCAGACACAGCCGGCGGATAACTCGT\n+TAGGCCTGGCATTCAACAACAGCGGCGAGTGGTGGGATATCCATCTCCAGGGCAACGTTG\n+AAGGGGGAGAGCGGATTAGCAACGGATCGCGCTTCAACGCCAACGGCGCATACGGCGCGG\n+TGAAGTTCTGGAACCAGTGGCTCTCTTTTGGCCAGGTACCACAGTGGTGGGGGCCTGGCT\n+ATGAAGGTAGCCTGATTCGCGGGGATGCAATGCGACCGATGACCGGTTTCCTGATGCAGC\n+GAGCCGAGCAGGCGGCGCCAGAGACCTGGTGGCTGCGCTGGGTGGGGCCATGGCAGTATC\n+AAATCTCCGCAAGCCAGATGAATCAATATACCGCGGTACCTCATGCCAAAATTATCGGCG\n+GTCGTTTCACTTTCTCACCTTTCCAGTCACTGGAACTAGGCGCGTCGCGCATTATGCAGT\n+GGGGGGGGGAAGGGCGGCCGCAATCCTTTAGCAGCTTCTGGGATGGGTTTACTGGTCATG\n+ATAATACCGGGACTAATAATGAACCTGGTAACCAACTGGCCGGGTTTGACTTTAAGTTCA\n+AACTAGAACCGACTTTGGGCTTGCCAATAAGCTTTTA'..b'CATCGCCCTGGCGGCCCTCCAGGCCACCCGCCACGGCGACGACC\n+CGCTGATGCTGGTCCTCGCCGCCGACCATATCATCAATAACCAGCCGGTCTTCCACGACG\n+CCATCCGCGTCGCCGAGCAGTATGCCGATGAAGGCCATCTGGTCACCTTCGGTATCGTGC\n+CGAACGCCCCGGAAACCGGCTACGGCTACATCCAGCGCGGCGTGGCCCTCACCGACAGCG\n+CCCATACTCCGTACCAGGTGGCCCGCTTCGTGGAGAAGCCGGACCGCGAGCGCGCCGAGG\n+CTTACCTCGCCTCCGGGGAGTACTACTGGAACAGCGGCATGTTTATGTTCCGCGCCAAAA\n+AATACCTTTCCGAGCTGGCCAAATTCCGCCCGGATATCCTCGAAGCCTGCCAGGCCGCGG\n+TCAATGCCGCCGATAACGGCAGCGACTTCATCAGTATCCCGCATGACATTTTCTGCGAGT\n+GTCCGGACGAGTCTGTGGACTACGCGGTGATGGAGAAAACCGCCGACGCGGTGGTGGTCG\n+GTCTCGATGCCGACTGGAGCGACGTCGGCTCCTGGTCCGCCCTGTGGGAGGTCAGCCCGA\n+AAGACGGGCAGGGTAACGTCCTCAGCGGCGACGCGTGGGTGCACAACAGCGAAAACTGCT\n+ACATCAACAGCGACGAGAAGCTGGTGGCGGCCATCGGCGTGGAGAATCTGGTGATTGTCA\n+GCACCAAGGACGCCGTGCTGGTGATGAACCGCGAGCGTTCCCAGGACGTGAAGAAGGCGG\n+TCGAGTTTCTCAAGCAGAACCAGCGCAGCGAGTACAAGCGCCACCGCGAGATTTACCGTC\n+CCTGGGGCCGCTGCGACGTGGTGGTCCAGACCCCGCGCTTCAACGTCAACCGCATTACGG\n+TGAAACCGGGCGGCGCCTTCTCGATGCAGATGCATCACCACCGCGCCGAGCACTGGGTCA\n+TTCTCGCCGGCACCGGCCAGGTGACCGTCAACGGCAAGCAGTTCCTGCTGACCGAGAACC\n+AGTCCACCTTTATTCCGATTGGCGCCGAGCACAGCCTGGAAAACCCGGGCCGCATTCCGC\n+TGGAAGTGCTGGAGATCCAGTCGGGGTCGTACCTCGGCGAGGACGACATTATTCGTATTA\n+AAGACCAGTATGGTCGTTGCTAATTTTTTCGGGACAAAACGCAGAATGACACAGTTAACA\n+TGCTTTAAGGCTTATGACATCCGTGGTGAACTGGGCGAGGAGCTGAACGAGGACATCGCC\n+TACCGTATCGGCCGCGCCTACGGCGAATTTCTGAAACCCGGGAAGATAGTGGTGGGGGGC\n+GATGTGCGCCTCACCAGCGAGTCGCTGAAGCTGGCGCTGGCCCGCGGGCTGATGGACGCC\n+GGCACCGACGTGCTGGATATCGGCCTGAGCGGCACGGAAGAGATTTACTTCGCCACTTTC\n+CACCTCGGGGTGGATGGCGGTATCGAGGTGACGGCCAGCCACAACCCGATGAACTACAAC\n+GGCATGAAGCTGGTGCGCGAGAACGCGAAGCCCATCAGCGGCGACACCGGCCTGCGGGAT\n+ATCCAGCGCCTGGCGGAGGAGAACCAGTTCCCGCCGGTGGACCCGGCGCGTCGCGGGACC\n+CTGCGCCAGATTTCGGTGCTGAAGGAGTACGTCGACCACCTGATGGGCTACGTGGACCTG\n+GCGAACTTCACCCGTCCGCTGAAGCTGGTGGTGAACTCCGGCAACGGGGCGGCGGGGCAC\n+GTAATTGATGAGGTGGAGAAACGCTTCGCGGCGGCCGGGGCGCCGGTGACCTTTATCAAG\n+GTGCATCACCAGCCGGACGGCCATTTCCCGAACGGTATCCCGAACCCGCTGCTGCCGGAG\n+TGCCGCCAGGACACCGCCTACGCGGTGCGTGCGCATCAGGCGGACATGGGGATCGCCTTT\n+GACGGCGACTTCGACCGCTGCTTCCTGTTCGATGACGAGGCGTCGTTTATCGAGGGGTAC\n+TACATTGTCGGCCTGCTGGCGGAAGCGTTCCTGCAGAAGCAGCCGGGGGCGAAAATCATT\n+CACGACCCGCGTCTGACATGGAACACGGTGGACATCGTGACCCGCAGCGGCGGCCAGCCG\n+GTGATGTCGAAGACCGGGCATGCGTTCATCAAGGAGCGGATGCGCCAGGAAGACGCCATC\n+TACGGCGGGGAGATGAGCGCGCACCATTACTTCCGCGACTTTGCCTACTGCGACAGCGGG\n+ATGATCCCGTGGCTGCTGGTGGCGGAGCTGCTGTGCCTGAAGAACAGCTCGCTGAAATCG\n+CTGGTGGCGGACCGCCAGGCGGCGTTCCCGGCGTCGGGGGAGATCAACCGCAAGCTGGGA\n+AATGCAGCGGAGGCGATAGCGCGCATCCGGGCGCAGTATGAGCCGGCGGCCGCACACATC\n+GACACAACGGACGGTATCAGTATTGAATACCCTGAGTGGCGCTTTAACCTGCGCACGTCC\n+AATACCGAGCCGGTGGTGCGTCTGAACGTTGAGTCCAGAGCGGATACTGCGTTAATGAAT\n+GCAAAAACCGAAGAGATTTTAGCTCTTCTCAAGTAATGCATTATCCATAATGGAAGCCAT\n+AGGGTCAGATTTTAATCGTATTTTTGACCTTATGGCTTATTCTTGACATCCCACTGGTCA\n+AAGCGTAAAACCGCCCACAGAATTATTTAATTTCGTGGCTATCCGCCATTATCCAGTTAA\n+CTGATTAAAGTGTAATCTCATGAAAATTACTATTTCCGGTACAGGTTATGTTGGTTTATC\n+GAACGGTGTCCTGATCGCGCAAAACCACGAAGTGGTGGCCCTGGATATCGTACAGGCCAA\n+AGTGGATATGCTTAACCAGAAGATCTCTCCGATTGTCGATAAAGAGATTCAGGAATATCT\n+GGCAGAAAAACCGTTAAATTTCCGTGCCACCACGGATAAGCACGACGCGTACCGCAATGC\n+CGACTACGTGATCATTGCCACGCCGACCGATTACGATCCCAAAACTAACTACTTTAACAC\n+CTCTACGGTGGAAGCGGTTATTCGCGATGTCACAGAGATCAACCCGAACGCGGTAATGAT\n+CATTAAATCGACCATCCCGGTGGGGTTCACCCGCGACATCAAAGAACGTTTAGGGATTGA\n+TAATGTTATTTTCTCTCCGGAGTTCCTGCGTGAAGGACGTGCGCTGTACGACAACCTACA\n+TCCGTCGCGTATTGTCATCGGTGAGCGCTCCGCGCGTGCCGAACGTTTCGCTGATCTGCT\n+GAAAGAAGGCGCGATCAAGCAGGATATCCCGACCCTGTTTACCGACTCTACCGAAGCGGA\n+AGCGATCAAACTGTTCGCTAACACCTATCTGGCGCTGCGCGTTGCCTATTTCAACGAGCT\n+CGACAGCTATGCTGAAAGCCAGGGGCTGAACAGCAAGCAGATTATCGAAGGGGTATGCCT\n+GGATCCGCGTATCGGCAACCACTATAACAACCCGTCCTTTGGCTACGGCGGCTACTGCCT\n+GCCAAAAGATACCAAGCAGCTGCTGGCGAACTACGAATCGGTCCCGAACAATATCATCGC\n+GGCTATCGTCGATGCCAACCGTACCCGTAAAGACTTTATCGCGGATTCTATTCTCGCTCG\n+TAAGCCGAAAGTAGTGGGTGTGTATCGCCTGATCATGAAGAGTGGTTCGGACAACTTCCG\n+TGCCTCTTCTATTCAGGGCATTATGAAGCGCATCAAGGCGAAAGGTATTCCGGTTATTAT\n+CTATGAACCGGTGATGCAGGAAGATGAGTTCTTCAACTCCCGCGTCGTGCGCGACCTGAA\n+TGCCTTCAAGCAAGAAGCTGATGTGATCATTTCTAACCGTATGGCGGAAGAGTTGGCGGA\n+TGTGGCGGACAAGGTCTACACCCGCGATCTGTTTGGTAACGATTAA\n' |
| b |
| diff -r 000000000000 -r bda1fd5c651d test-data/result_table.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_table.txt Mon Apr 10 14:47:17 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Assembly Best match locus Match confidence Problems Coverage Identity Length discrepancy Expected genes in locus Expected genes in locus, details Missing expected genes Other genes in locus Other genes in locus, details Expected genes outside locus Expected genes outside locus, details Other genes outside locus Other genes outside locus, details +input KL13 Perfect 100.00% 100.00% 0 bp 19 / 19 (100%) KL13_01_galF,100.0%;KL13_02_cpsACP,100.0%;KL13_03_wzi,100.0%;KL13_04_wza,100.0%;KL13_05_wzb,100.0%;KL13_06_wzc,100.0%;KL13_07_wcuD,100.0%;KL13_08_wclX,100.0%;KL13_09_wzy,100.0%;KL13_10_wcuF,100.0%;KL13_11_wzx,100.0%;KL13_12_wcuL,100.0%;KL13_13_wcoW,100.0%;KL13_14,100.0%;KL13_15_wcaJ,100.0%;KL13_16_gnd,100.0%;KL13_17_manC,100.0%;KL13_18_manB,100.0%;KL13_19_ugd,100.0% 0 0 / 19 (0%) 0 |