| Next changeset 1:28587613264f (2021-07-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1" |
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added:
macros.xml ncbi_acc_download.xml test-data/CP011064.fa test-data/CP021680.fa test-data/accessions_1.tsv |
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| diff -r 000000000000 -r 1c58de56d587 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 04 07:01:37 2019 -0500 |
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| @@ -0,0 +1,3 @@ +<macros> + <token name="@TOOL_VERSION@">0.2.5</token> +</macros> |
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| diff -r 000000000000 -r 1c58de56d587 ncbi_acc_download.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ncbi_acc_download.xml Wed Dec 04 07:01:37 2019 -0500 |
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| b'@@ -0,0 +1,313 @@\n+<tool id="ncbi_acc_download" name="NCBI Accession Download" version="@TOOL_VERSION@+galaxy0">\n+ <description>Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">ncbi-acc-download</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $query_source.select == "accession_file":\n+ { grep -v "^[ \\t]*$" $query_source.accession_file > accessions ||\n+ { echo "No accession numbers in input. Aborting." 1>&2; exit 1; } } &&\n+ #else if $query_source.select == "accession_list":\n+ echo \'$query_source.accession_list\' | sed -r \'s/(\\,|__cn__)/\\n/g\' | grep -v "^[ \\t]*$" > accessions &&\n+ #end if\n+ mkdir outdir &&\n+ cd outdir &&\n+ ignore_errors=$ignore_failed &&\n+ while read accession; do\n+ echo "Downloading accession number: " \\$accession " ..." >> ../error.log &&\n+ ncbi-acc-download\n+ --molecule \'${molecule.select}\'\n+ --format \'${molecule.format}\'\n+ #if $molecule.format != \'featuretable\' and $molecule.format != \'gff3\':\n+ --extended-validation all\n+ #end if\n+ \\${accession};\n+ failure=\\$?;\n+ if [ \\$failure -ne 0 ]; then\n+ echo " failed." >> ../error.log;\n+ if [ \\$ignore_errors -ne 0 ]; then\n+ echo \\$accession >> ../failed.txt;\n+ else\n+ exit 1;\n+ fi;\n+ else\n+ echo " done." >> ../error.log;\n+ fi;\n+ sleep 2;\n+ done < ../accessions 2> >(tee -a ../error.log >&2);\n+ ]]></command>\n+ <inputs>\n+ <conditional name="query_source">\n+ <param name="select" type="select" label="Select source for IDs">\n+ <option value="accession_file">File containing Accessions (one per line)</option>\n+ <option value="accession_list">Direct Entry</option>\n+ </param>\n+ <when value="accession_file">\n+ <param label="Accession File" name="accession_file" type="data" format="txt,tabular"/>\n+ </when>\n+ <when value="accession_list">\n+ <param label="ID List" name="accession_list" type="text" area="true" help="Newline/Comma separated list of IDs">\n+ <validator type="expression" message="ID list cannot be empty">value.strip()</validator>\n+ </param>\n+ </when>\n+ </conditional>\n+ <conditional name="molecule">\n+ <param name="select" type="select" label="Molecule Type">\n+ <option value="nucleotide" selected="true">Nucleotide</option>\n+ <option value="protein">Protein</option>\n+ </param>\n+ <when value="nucleotide">\n+ <param name="format" type="select" label="File Format">\n+ <option value="fasta" selected="true">FASTA</option>\n+ <option value="genbank">GenBank</option>\n+ <option value="featuretable">Feature Table</option>\n+ <option value="gff3">GFF3</option>\n+ </param>\n+ </when>\n+ <when value="protein">\n+ <param name="format" type="select" label="File Format">\n+ <option value="fasta" selected="true">FASTA</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ <param name="ignore_failed" type="select" display="radio"\n+ label="How to handle download failures">\n+ <option value="0">Abort with error on first failure</option>\n+ <option value="1">Add accession to failed list and continue</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <collection name="output" type="list" label="${tool.'..b' </output_collection>\n+ <output name="failed_accessions">\n+ <assert_contents>\n+ <has_line line="CP0XXXXX" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="molecule">\n+ <param name="select" value="nucleotide"/>\n+ <param name="format" value="fasta"/>\n+ </conditional>\n+ <conditional name="query_source">\n+ <param name="select" value="accession_list" />\n+ <param name="accession_list" value="CP0XXXXX"/>\n+ </conditional>\n+ <param name="ignore_failed" value="1" />\n+ <output name="failed_accessions">\n+ <assert_contents>\n+ <has_line line="CP0XXXXX" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_failure="true">\n+ <conditional name="molecule">\n+ <param name="select" value="nucleotide"/>\n+ <param name="format" value="fasta"/>\n+ </conditional>\n+ <conditional name="query_source">\n+ <param name="select" value="accession_list" />\n+ <param name="accession_list" value="CP011064,CP0XXXXX,CP021680"/>\n+ </conditional>\n+ <param name="ignore_failed" value="0" />\n+ </test>\n+ <test>\n+ <conditional name="molecule">\n+ <param name="select" value="nucleotide"/>\n+ <param name="format" value="fasta"/>\n+ </conditional>\n+ <conditional name="query_source">\n+ <param name="select" value="accession_list" />\n+ <param name="accession_list" value="CP011064 CP021680"/>\n+ </conditional>\n+ <output_collection name="output" type="list">\n+ <element name="CP011064" ftype="fasta">\n+ <assert_contents>\n+ <has_line line=">CP011064.1 Escherichia coli str. Sanji plasmid pSJ_94, complete sequence" />\n+ </assert_contents>\n+ </element>\n+ <element name="CP021680" ftype="fasta">\n+ <assert_contents>\n+ <has_line line=">CP021680.1 Escherichia coli strain AR_0162 plasmid tig00002623, complete sequence" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ <test>\n+ <conditional name="molecule">\n+ <param name="select" value="protein"/>\n+ <param name="format" value="fasta"/>\n+ </conditional>\n+ <conditional name="query_source">\n+ <param name="select" value="accession_list" />\n+ <param name="accession_list" value="NP_003192"/>\n+ </conditional>\n+ <output_collection name="output" type="list">\n+ <element name="NP_003192" ftype="fasta">\n+ <assert_contents>\n+ <has_line line=">NP_003192.1 transcription factor A, mitochondrial isoform 1 precursor [Homo sapiens]" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+Given a file containing a list of NCBI accession numbers or a direct entry of accession numbers in the tool text input box, this tool will download the corresponding sequence records via the NCBI API. \n+\n+**Limitations**\n+- For protein sequence downloads, only fasta format is supported\n+- To avoid rate-limits imposed by the NCBI API, records are downloaded sequentially with a delay between requests. This may make it impractical to use this tool to download many (>100) records.\n+\n+**Output**\n+A collection of sequence records in the desired format.\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 1c58de56d587 test-data/CP011064.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CP011064.fa Wed Dec 04 07:01:37 2019 -0500 |
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| b'@@ -0,0 +1,1356 @@\n+>CP011064.1 Escherichia coli str. Sanji plasmid pSJ_94, complete sequence\n+AGATGTCAGGCATATGGATATGTTCAGCCTATGTTATTTTCTCTCTTTCCCCGTGCAGATCCGGTTTCTG\n+GTGGTTCCGGATCCGCGGATCCTTCGCTGCCGCCCGCTGGTCCGCTTTCACAGGATGTGGTGTCCCGCTC\n+CGCTGACATGACACTGTATGTTGTGTTTCTTCCCGTGTTCCCGAGCCAGTCATCAGCGGCAGAAAAGATC\n+GCTTCGCTTATTCACTGATCCTGATTCACTTCCGGAAAATCCTGAATCCGATAAAAATCGGATCATAGAA\n+AAACAGTCATCCTGTAATTTATCATGGTTACTACATTGCAGGTTATTATTGTCATGATTACTTTTCAGGT\n+CAGTTATTGATGGTGGTGTTAATAATAGCTGGATAACAATATTCCGTTGCCGGAGGCATGTTATAGCGTA\n+ATACTGGTGTATACTTAATGGTGTACAGAGAGTATGTAAGATGAGGTGCATTATGAAGCAGCGCATTACA\n+GTCACCGTCGACAGTGACAGCTATCAGTTGCTCAAGGCATATGATGTCAATATCTCCGGGCTGGTAAGCA\n+CCACCCTGCAGAATGAAGCCCGTCGTCTGCGTGCCGAACGCTGGCAGGCAGAAAATCAGGAAGGGATGGC\n+TGAGGTCGCCCGGTTTATTGAAATGAACGGCTCTTTTGCCGACGAGAACAGGGACTGGTGAAATGCAGTT\n+TAAGGTTTACACCTATAAAAGAGAGAGCCGTTATCGTCTGTTTGTGGATGTCCAGAGTGACATTATTGAC\n+ACGCCTGGGCGACGGATGGTGATCCCCCTGGCCAGTGCACGTCTGTTGTCAGATAAGGTCTCCCGTGAGC\n+TTTACCCGGTGGTGCATGTCGGGGATGAAAGCTGGCGCATGATGACCACCGATATGGCCAGTGTGCCGGT\n+CTCCGTTATCGGGGAGGAAGTGGCTGATCTCAGCCACCGAGAAAATGACATCAAAAATGCCATTAACCTG\n+ATGTTCTGGGGAATATAAATGTCAGGCTCCGTTATACACAGCCAGTCTGCAGCCATGGTACCGGCAGTGT\n+ATTCTGCCGGACAGTCTGCACAACTTCCTGTTGCCATTGATTATCCGGCAGCTCTGGCACTCCGCCAGAT\n+GTCGATGGTTCATGATGAACTGCCGAAATATCTGCTGGCTCCCGAGGTGAGTGCCCTGCTTCATTATGTC\n+CCGGATCTGCGCCGCAAGATGCTGCTGGCCACTCTGTGGAACACCGGCGCGCGTATTAATGAAGCACTAG\n+CGCTGACGCGGGGGGATTTTTCGCTCACGCCTCCGTATCCGTTTGTGCAGCTTGCGACCCTGAAACAACG\n+GACCGAAAAAGCTGCCAGGACGGCGGGGAGAATGCCCGCCGGTCAGCAGACTCACCGGCTGGTTCCGCTC\n+TCTGACTCCTGGTACGTCAGCCAGCTGCAGACGATGGTGGCAACACTGAAAATACCCATGGAGCGGCGTA\n+ACCGTCGCACAGGAAGGACAGAGAAAGCGCGGATCTGGGAAGTGACGGACAGAACGGTCAGGACCTGGAT\n+TGGGGAGGCGGTTGCCGCCGCTGCTGCTGACGGTGTGACGTTCTCTGTTCCGGTCACACCACATACGTTC\n+CGCCATTCCTATGCGATGCACATGCTGTATGCCGGTATACCGCTGAAAGTTCTGCAAAGCCTGATGGGAC\n+ATAAGTCCATCAGTTCAACGGAAGTCTACACGAAGGTTTTTGCGCTGGATGTGGCTGCCCGGCACCGGGT\n+GCAGTTTGCGATGCCGGAGTCTGATGCGGTTGCGATGCTGAAACAATTATCCTGAGAATAAATGCCTTGG\n+CCTTTATATGGAAATGTGGAACTGAGTGGATATGCTGTTTTTGTCTGTTAAACAGAGAAGCTGGCTGTTA\n+TCCACTGAGAAGCGAACGAGACAGTCGGGAAAATCTCCCATTATCGTAGAGATCCGCATTATTAATCTCA\n+GGAGCCTGTGTAGCGTTTATAGGAAGTAGTGTTCTGTCATGATGCCTGCAAGCGGTAACGAAAACGATTT\n+GAATATGCCTTCAGGAACAATAGAAATCTTCGTGCGGTGTTACGTTGAAGTGGAGCGGATTATGTCAGCA\n+ATGGACAGAACAACCTAATGAACACAGAACCATGATGTTTGGTCTGTCCTTTTACAGCCAGTAGTGCTCG\n+CCGCAGTCGAGCGACAGGGCGAAGCCCTCGAGTGAGCGAGGAAGCACCAGGGAACAGCACTTATATATTC\n+TGCTTACACACGATGCCTGAAAAAACTTCCCTTGGGGTTATCCACTTATCCACGGGGATATTTTTATAAT\n+TATTTTTTTTATAGTTTTTAGATCTTCTTTTTTAGAGCGCCTTGTAGGCCTTTATCCATGCTGGTTCTAG\n+AGAAGGTGTTGTGACAAATTGCCCTTAACCCTGTGACAAATTGCCCTCAGAAGAAGCTGTTTTTTCGCAA\n+AGTTATCCCTGCTTATTGACTCTTTTTTATTTAGTGTGACAATCTAAAAACTTGTCACACTTCACATGGA\n+TCTGTCATGGCGGAAACAGCGGTTATCAATCACAAGAAACGTAAAAATAGCCCGCGAATCGTCCAGTCAA\n+ACGACCTCACTGAGGCGGCATATAGTCTCTCCCGGGATCAAAAACGTATGCTGTATCTGTTCGTTGACCA\n+GATCAGAAAATCTGATGGCACCCTACAGGAACATGACGGTATCTGCGAGATCCATGTTGCTAAATATGCT\n+GAAATATTCGGATTGACCTCTGCGGAAGCCAGTAAGGATATACGGCAGGCATTGAAGAGTTTCGCGGGGA\n+AGGAAGTGGTTTTTTATCGCCCTGAAGAGGATGCCGGCGATGAAAAAGGCTATGAATCTTTTCCCTGGTT\n+TATCAAACGTGCGCACAGTCCATCCAGAGGGCTTTACAGTGTACATATCAACCCATATCTCATTCCCTTC\n+TTTATCGGGTTACAGAACCGGTTTACGCAGTTTCGGCTTAGTGAAACAAAAGAAATCACCAATCCGTATG\n+CCATGCGTTTATACGAATCCCTGTGTCAGTATCGTAAGCCGGATGGCTCAGGCATCGTCTCTCTGAAAAT\n+CGACTGGATCATAGAGCGTTACCAGCTGCCTCAAAGTTACCAGCGTATGCCTGACTTCCGCCGCCGCTTC\n+CTGCAGGTCTGTGTTAATGAGATCAACAGCAGAACTCCAATGCGCCTCTCATACATTGAGAAAAAGAAAG\n+GCCGCCAGACGACTCATATCGTATTTTCCTTCCGCGATATCACTTCCATGACGACAGGATAGTCTGAGGG\n+TTATCTGTCACAGATTTGAGGGTGGTTCGTCACATTTATTCTGACCTACTGAGGGTAATTTGTCACAGTT\n+TTGCTGTTTCCTTCAGCCTGCATGGATTTTCTCATACTTTTTGAACTGTAATTTTTAAGGAAGCCAAATT\n+TGAGGGCAGTTTGTCACAGTTGATTTCCTTCTCTTTCCCTTCGTCATGTGACCTGATATCGGGGGTTAGT\n+TCGTCATCATTGATGAGGGTTGATTATCACAGTTTATTACTCTGAATTGGCTATCCGCGTGTGTACCTCT\n+ACCTGGAGTTTTTCCCACGGTGGATATTTCTTCTTGCGCTGAGCGTAAGAGCTATCTGACAGAACAGTTC\n+TTCTTTGCTTCCTCGCCAGTTCGCTCGCTATGCTCGGTTACACGGCTGCGGCGAGCGCTAGTGATAATAA\n+GTGACTGAGGTATGTGCTCTTCTTATCTCCTTTTGTAGTGTTGCTCTTATTTTAAACAACTTTGCGGTTT\n+TTTGATGACTTTGCGA'..b'GCGTCTTATGAGCCTGCTGTCACCCTTTGACG\n+TGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAG\n+CAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGG\n+AAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAAC\n+ACTATCAATAAGTTGGAGTCATTACCGCGCTTCCTGGGGGGTTAATGGCTGATGACGATAAAATCATATA\n+TCGAATGATTTATTTCTCTGCCTGTAAATATCAGGCCAGGATTTATTATGCGATTAATGATAAATATCAT\n+ATCATCTGCGGGTTTCCCTCCACGCAGGTCCGGTTTCCGGCGAAACCGGAGCCTCATTTTTCGGCCTGAA\n+GTTTTGTCGTTGACTACTTTTTACCGGCTTGTGCCCAGTTGAGAAGCCGCTGACTTAGTTTCTGAATCTC\n+CGAAGATGGCTTTCCGGAATAAAATAGATGTTGCCCCGTGCCCGTGAGCAGGCCACGTATAGCCTGTTAC\n+GGGATGATGGTGGAAGTGCTGCCAGCTTCTGTTGGATGAGGCGCATCCAGTGGTTGGCCCCCATCACGAT\n+GCAGACGTCCTGAAAGTGGTCGAGTCCTTTACTGCCCCCCCAGTTCATTGAGTGGCATCCGTAACGGTGA\n+TGTTCGCGATAGAAGAGCTTGATCATCGTGTTGTCCGCGTGCAGGGCCGCTGAACGCGCTTCATCCGTGA\n+CGATTTCAATCTGGGTGGTATGTGTTCCATGAGCCGAAATGCGAATGTTCAGTTGTCCGGTAATGAACTC\n+ACACACTGTAGCTGAACAGCGCCATGTCCGGCTGAGCGTCTCACAATCCACCATGATACCCGCAGCCCTG\n+AAGCGAGCCTCGTATCGGGTTATGTCTTCATGCAGCGTAGCATTGACGTTACCGTCGCGGCTTGTGTCAA\n+AGGTATGCTGATAAAAATCCCCGCAGCACAGCACTGAGATTTCCGCGCGGCATAGCTCCAGCAGAAAATT\n+AAAGTCATGGCCGGCAAAGTCCTGGACTTCATCAACGAACAACTCATCGTAGTAACGGGCAAGTCGGGTA\n+CGGATATCTGGCAGCAACCCCCGGGCTGTCAGCAGGTGTGCGAGCCGCCGGTGATACAGCCGTCCGGCGG\n+GATCCTGATAATGCCGGATATTCGTGCGCGGTATTCTGGAAGGGGGCTGGTTGAAGCTCAGACCACGCGA\n+TGACAGTTGCTCCTGCAGGAAAGGGCGAAAACAGAAACCGTGCAGAAACTCAAACCAGGTCATCACACGG\n+ATCCCGTACGGTATGTAGCCAAAGCGTCTGATAATCTGCGCCCGCAGATGTGCTTCATTATTTACGGTGA\n+AGGTCAGGATCAGCGTCCGCCGGTCCTCTCTTAACCGACGTATCAGCAGCGTGGTTTTACCCGAGCCGGC\n+AACCGCAAATATCACTCTCTTATCCATGCCAGTGCCTCCTGGATATAATCAGGAACGGTCAGCTTTTCGG\n+CGTGCAACTGTAACAGCTGGAATGCTGCTTCTGCCTTATTGGCCAGCATGTAATCCTGAACCGTGAGTGT\n+CCGGCGGGTTCCGCGGAAAAGCGCATCACACAGGTCGGCATTATCCTGATACAGGCAGATTTCAAATGTG\n+GAGCGGCTGTTGTCGTGGTCAGCAAATACCCGGGAGCGGGAACAAAGCACGTCAGCATAGCGTTCATCGC\n+AATTTTGCTGATAGTTGCCGTCATTGTCGCGAAGGGCCGCGACACGATTTTCCAGAAGACGGGCCAGTTC\n+AAGATAACGACGGAAACTCGTTCCGCCGATAGCGATGATGTGAACCCCGTCATCCTCCGGTGCCCTGCCA\n+TACAGGCGGTGATAAAAGGCCTCGATCAGAATAAACTCAGCATCCCCCTCCACGAGCAGCACGCGTCTGG\n+CCAGCGCAAATTCCAGCACGTTATTATCCGGTGCTTTCATGAAGAAGGCGGCAGTCTCAGCGGAAAGTTC\n+ATTCATCAGTACCGGCCGGGTAGCTCCGAGGAGAATAGCCTTACGTAGGTCGAGGCGGGAGGAGATATGG\n+CTACTGTGTGTGGCAATAAACACCTGCGTCTGCCGTTCCGTGGCAAGCTGATTAACCAGCCTCTTCATAC\n+TGACATGGCTGAGATGATTCTCCGGCTCCTCAAGCAACAGCGCGTGGATCTCTCCCCCCTGCTGCTGATG\n+CCGCTGCAGCGCAAACTCCGTTTTGATGAAACACTGTCTTCCTTTTCCGCGGTGACGAATGGAAATACCG\n+TCCTCAGTAATGTCCAGGTTCGCCTCAAGACCTGATTTAGCGCCGGAACGCACGCCAAACTGATACGTTT\n+TCAGCGTGTCGTTTATGGCGGACAGATGCCGGGCGCAGAAGTGCATTTTCTGTTGCCGGTAACTGTTTTC\n+AAGCCGGTACCGATCGGCCACCGGCACATTGACGCTGTAAACTGTGCGCGTATACTCCTGTGCGGCATGC\n+TCGTTATCAATGCGTGCACTGTCTAAGAACAGATGGCGCAGATAGCGTCTGAAGCCTGCGAAATGACCAC\n+CGGAGAATGTGCTGAACTGCACGGAATAGTATTCATAGGGAAAATTATCAGGATCCTGCTGCAAAACATG\n+GTGTATATCCTGACCGTATTCCTCCATCATGGGAGCAATGCGCATTCTGAGACCATCCGCATCGATACCC\n+GCCAGATTTTGCCTGCCGTTCAGGTCAGGCTCTCCCCCATTACTCAGGAAAACGTCAGCGGTCAGCACGG\n+GTAACTGATCGGCACGGCGCTCACCTTCCTGAAAATGCCTGACTGCTGACTGTGACAGGAGCGATTCCAC\n+CCCCAGCGCCTCAACCCGATGCCTGCTGTCACTCAGCACAAGGTCAAGAGCCAGCAGAATAGTGCTTTTC\n+CCGGACTCATTGTCCCCAACCAGAATGTTACGATCGTTGCTGAAGCGCAGGTCCAGTTCCGGAAACTTTT\n+TGAAGTTTTGCAGCATAAGCCGCGTGATCAGTGGCATTTTTTTATTCCTTTATATACCGCTGCCTGAAAG\n+AGCGGCCGGCCGCGCCTGACCGCCTGTTTTGTTTTACAGCGTTATCTTACCCAGTCTTCCAGCACAAGAC\n+CCGGTACCCGCTCAAACTCTCTCACATTATTCGTCACCAGAATGGCACAGGCAGCGATGGCGTGTCCGGC\n+TATCGCCGTGTCGTTCGGACCGATCGGCGTGCCGGCGAGACGCAGTGCCACCTTAATCTCCGTGGTCGCA\n+TCCACCGCGGCGCGGTCCCACGGCAGGACGGCATCGAGCCTCTCACAGAACGCGTCAACCAGTTGCACGT\n+GGCGTGGCGAGGCCTTCGGACCGGTGGCACCGAAGCGCATCTCGGAGTAGGTGATGGCCGAGACCACGAT\n+ACGGTGACCGCGCAGCACCGACTGCTCCAGGTGCTTAAGCAATGCTTCAGGTTGCTCGCGCATGATGAAC\n+GAGCAGATGTTCGTGTCGAGCATATAGATCTTGTTCACAGGTTAACTCGTCCTTCGTCGCTGACAACGTC\n+CTCGCGCTCCGTCATAAAGTCCGGATCGGCCTTTTCTAGCTCCAGGAATGAGCCCCAGGTCGGCCGGACG\n+GGGCGCAGAATGATGCTGTCCCCTTCCCGGACGATCTCCAGCTCGCTCACCCCCTCAAAATCCAGATCGC\n+GTGGAAGGCGGATAGCACGGTTGTTGCCATTTTTAAAAATGGATACGGTTCTCATGATTCTCTCCCGGGT\n+AAGTGTGGATATGTGATGCATATCCGGAATGATGTTCATTGCACCGGGTGTGTGCATATGTTTAGTATAG\n+GC\n+\n' 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| diff -r 000000000000 -r 1c58de56d587 test-data/CP021680.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CP021680.fa Wed Dec 04 07:01:37 2019 -0500 |
| b |
| b'@@ -0,0 +1,336 @@\n+>CP021680.1 Escherichia coli strain AR_0162 plasmid tig00002623, complete sequence\n+TTCTTGTCGCCTTTGCCGCCGTATTCCCGGATGTCGCCGACAAAAATTTTAAACTACTTCAGCAACAAAT\n+CTTCACGAATGCCAGCTGGTTCTACATCCTTGCTGTGGCCCTGATTTTACTGAGTGTCACGTTCCTTGGA\n+CTCTCACGCTACGGTGATATCAAGCTGGGCCCGGACCATGCGCAGCCTGATTTCAGCTACCACTCCTGGT\n+TTGCGATGCTTTTTTCGGCAGGGATGGGGATCGGCCTGATGTTCTTTGGCGTTGCCGAACCTGTAATGCA\n+TTATCTTTCGCCACCCGTTGGCACTCCAGAAACCGTTGCGGCAGCTAAGGAAGCAATGCGTCTGACCTTT\n+TTCCACTGGGGACTGCACGCATGGGCAATTTATGCCATTGTGGCGCTGATTCTGGCGTTCTTCAGTTACC\n+GTCACGGTCTGCCTTTAACTCTGCGCTCCGCACTCTATCCCATTATTGGCGATCGCATATACGGACCTGT\n+AGGACATGCGGTTGATATTTTCGCTGTTATAGGCACGGTCTTTGGCGTTGCGACATCACTGGGTTACGGT\n+GTTTTGCAGGTGAATGCCGGTTTGAACCATCTTTTCGGGGTGCCCATCAATGAAACGGTGCAGGTAATTC\n+TGATCGTGGTCATCACGGGGTTAGCGACGATTTCAGTGGTGTCCGGTCTGGATAAGGGAATACGTATCCT\n+GTCTGAACTCAATCTGGGTCTGGCTTTGTTGCTCCTGGCGCTGGTCCTGTGTCTGGGACCAACCGTGCTT\n+CTGCTGAAGTCATTTGTGGAAAATACGGGCGGTTATCTTTCGGAACTGGTGAGTAAAACGTTCAACCTTT\n+ACGCGTATGAGCCCAAGTCGAGCAACTGGCTGGGGGGCTGGACATTACTGTACTGGGGATGGTGGCTTTC\n+ATGGTCGCCGTTTGTGGGGATGTTCATCGCACGGGTCTCCCGCGGGCGAACCATTCGCGAGTTTGTCACC\n+GGCGTGCTGTTTGTTCCCGCGGGTTTTACGCTAATGTGGATGACGGTGTTTGGTAACAGCGCGATCTATC\n+TCATTATGAACCAGGGGGCCACAGACCTCGCCAATACTGTTCAGCAGGATGTGGCGCTGGCCCTGTTTAA\n+TTTCCTGGAGCATTTCCCGTTCTCTTCTGTGCTGTCATTCATTGCAATGGCGATGGTCATCGTCTTCTTT\n+GTAACGTCTGCTGATTCGGGGGCAATGGTTGTGGATACTCTGGCATCAGGTGGAGTGGCAAACACACCCG\n+TCTGGCAGCGAATATTCTGGGCCTCGCTCATGGGCATTGTTGCAATTGCGCTTCTCCTTGCCGGAGGGCT\n+AAGTGCGCTGCAAACGGTGACAATAGCGAGTGCATTGCCCTTCTCAGTGATCTTACTAATATCTATATAC\n+GGACTTTTAAAAGCTTTGCGCCGGGATTTGACCAAGCGTGAAAGCCTGAGCATGGCGACAATTGCTCCTA\n+CGGCTGCACGTAACCCAATTCCTTGGCAGAGAAGGTTACGCAATATCGCGTATCTGCCGAAGCGATCTCT\n+TGTGAAACGTTTTATGGACGACGTTATCCAGCCTGCCATGACGCTGGTTCAGGAGGAACTGAACAAGCAG\n+GGGACGATAAGCCACATTAGTGATGCAGTCGACGATCGTATTCGTCTTGAAGTCGATTTGGGCAACGAGC\n+TGAATTTTATATATGAAGTGAGGCTTCGCGGGTATATCTCACCGACCTTCGCGCTCGCCGCAATGGATAA\n+TGATGAGCAGCAGACTGAACAACATCGATATTATCGCGCTGAGGTTTATCTCAAAGAAGGCGGTCAAAAT\n+TATGATGTGATGGGCTGGAACCAGGAACAGCTGATTAATGACATACTGGACCAGTACGAAAAACACCTGC\n+ACTTCCTGCACCTGGTTCGTTAATAGCAACATGCCGTCCTGGGGGCGGCAATTATTATCCCGGCCGCAAT\n+ATGAGGGAATGCAGAATGATTTCACGCTGGAAATGGATGCTGAAGCAGACAATTAAAAAACTATGGTTCA\n+GGGCAACGTTATTCGCAATTGTCGCGATAATAACGGCCCTTTTATCAATTCTTTTTAAATCAATGATACC\n+TGAGTCGGTTTCCGTGAAGGTTGGTGCGGAAGCAGTCGATAACATTCTGAACATACTGGCATCGAGTATG\n+CTGGCAGTGACCACATTTTCGCTGAGTATCATGGTCACAGCCTACGGTTCAGCCACTACTAATGTGACTC\n+CCAGAGCTACGCGTTTAGTTGTTGAAGACGTCACCACACAAAATGTACTGGCCACCTTCATCGGTTCTTT\n+TCTCTTCAGTCTGGTAGGGATTATTGCCCTCAATATGGGAGCTTATGGAGAAAGGGGGAGAGTCATTTTA\n+TTCATTGTCACACTGGTTGTCATTGCCTTAATCCTCATCACATTGCTTCGCTGGATACAGCATTTGACCT\n+CTCTGGGGAGGGTTGGTGAGACAACGGCACAAGTAGAACAGGCGGCCATCGAAACATTTATTGCGAGAGC\n+AAGAAATCCCTGTCTCGGTGGATATCCATGGCTTGAGAACAATGAACAGCCGAAAGGAACGGTTGCAGTT\n+TATCCGAAGAAGATTGGCTATGTTGAATATATTGATATGGTGAAACTTAGCAAGCTGCTGACCAATGATC\n+CCCGTCATGTATACCTCGTGGCGCAGCCAGGCAGTTTCATACATCCGTCCATGCCAGTTTTGTACCTGAG\n+TCAGGGCCAGGAGTCGTCAATCAACACCGATTTACTTGAGACGATTATTGTCTCGGATGCACGTTCATTT\n+GCTCAGGATCCTCGATTTTGTCTTAGCGTCATGGCCGAAATAGCCTGCCGGGCCCTTTCCCCTGCAGTGA\n+ACGATCCTGGAACCGCCATTGATGTCATTGGCAGAGGTGTTCGTATACTTTCCACTTACGCGCAGAATAA\n+ATCTGATGAAATAGAAGTGAAATATCCTTCAGTACATGTTGCACCACTTCAGAATAACGATCTACTGGAA\n+GACTTTTTCTCACCTGTCGCGCGCGATGGTGCCAGTATGAGGGAGATTCAGATAAGAGTCCTTAAAGGAC\n+TGTCGATGCTGAGTAAAGGTTGGCCTGAGATATTTGCTGAAGCCGCACATACCCTGGCATTTGAAACATT\n+AGAGCATGCAACTCGTGCTGACCATATAGATTCTGATAGATATCTAATAAAATCAACTTATTATAATTTA\n+TTTAGTGGCGAATATTCTAATAAAAAAACATAGCTGCAGAGCAAGCAATTCGGTTGTTGGCAAGTCAAGG\n+GCAAAGCATTCGCGTGAGAATGGGCGTATGCTTTGTGCCAAAAGCAAACGTTGCTAATTCTGCACTGTTC\n+AGCGATGGCGCAGTAGAGACAGGCACTGCCACTGTCCAGTCGGCAAAAGCGAACACTTTGCCACTGCGGG\n+GATAAACTGATTGAAGCTCTCGCGCAAAATCACTTATTCTTTTGCGTTAATAAAATGTAGGAGATGGGTC\n+ATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGA\n+GGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCG\n+CATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCC\n+ACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATACTTCCACGCAGATTATGCCGCTTCAGTTGCG\n+CCTGATAA'..b'ACAGTATCAGAT\n+TGACAGTATGGGCATGCATGATGATGTTTTTATTGCTGACAATGTTTTTCCTGCCGCCCCCGTATATCGG\n+GTTGCCAGTCTGGTGGTTCTGCCTTCAGAAACGAATCTTTTGGTATGGTGCTGGCAGAAGCATCGGCATT\n+TTCTGTGCCTGTAGTGGCCACTCAGATTGGTGGAATCCCTGAGGTTATTCAGAACAACCAGACCGGGACA\n+TTGTTACCAGCAAGTAATAAGCACGCATGGATGTGCGCCCTGAATGATTTTTTAATGACCCTGGGCGTTT\n+TTATCAGATGGCTCGCCTGGCAAAACAGGATATAGAAGAGCGGTTTGATATTAATAAAACTGCGTTAAAA\n+TACTCACATTAGCGAAGCAAAGTACAATATGTTTCTATAAGTAACTTATCATTTATCGGTTTCCTTAAAA\n+GGATTATTTTTTCCTCAGATTCCTACCGGGGAGTGGAACACAGAAATTTCGGTTCATGTACATTTTGCGA\n+TGTTCTATAAATCCGGTTGTCAGTATTCGATATTATATGAACTGCGTTCCTTGCCGTGCATTGAGGATTC\n+TGGCATACACCCCACGTTGCCAGCAGAATTCATCGCCCTTATTTGCATAAGGGGGGCGCGCCTGGACCGT\n+GGACAATATATTCTTGAGCATTATCGCTTTGTGCAAAATTTGCCAGAAAAATATTCTAATTTTTGTTTCC\n+ACAAAATCGGTATCATTAGTCCATTCATCGGGAAGATGGAGAGAATTTTGATATCCAGTGTTCTCCCAGT\n+GGTTTTGACCGGGAAGGAGAGTTGATGTTGTCATTGTTTACAATAAAACAGTTATTGCCCGGTTAACATT\n+TTCAGTCATTCTGACTCAAATGGACACATTGCTTTTATTGGCGGATTACAGGGAGCCCTAAAAATACCGG\n+ACTGATGTTATTCGGTGCGCAACCCGGGCTGTTATGGGATTTTCCCAAACGGATTATTTTGAAGCTTTTG\n+TGCGTTGATGAAAGCTTGCAATATCTCTGAGTGTCTGGCAGTCAGTGAGCACAGTCATGTTTTCCGGCAA\n+TTGAGATACTGGTATCAGAAACGCAAAACCTTTGTTGCGGTCTATAGTGATTTCTGGGAGTCTGTAGCAG\n+GAAAAACCTGTGGTGACTGGTACAGATTACCAACCCAGGTGATTCGAAAGCCGCTAAGCGATATAGCCAG\n+TAAAAAACGCTCTGAGTACCGAAAACGATACGCTTTGCTGGATTATATCCATGAAACTACTATCAGCTCT\n+TTGGATGCATATCCTGTACACTCAGAACATCAGAATTTAAATTAAGGTTTGATGTATTCTCTGAATAAAA\n+CAGTAATGATAATTTTGGTAGAGGCATTCGCACTAAATAATGAAAAAATATAAATCTGAGTTTATTCCTG\n+AATTTAAGAAAAATTACCTTTCCCCTGTTTACTGGTCTACATGGTTCCTTTTGGGAATGATTGCAGGTAT\n+TTCAATGTTTCCCCCTTCATTCAGAGATCCTGTCTTGGCAAAAATAGGGCGTTGGGCGGGCAGATTGAGC\n+AAAAAAGCTCGTCGCAGGGCGACGATTAATTTATCGCTTTGTTTCCCAGAAAAGAGTGATACAGAACGGG\n+AAATAATTGTCGACAAAATGTTTATCACAGCATTGCAATCCATAGTGATGATGGCAGAACTGGCAATTCG\n+TGGTCCGGAAAAGTTCCAGAAACGAGTGTTCTGGAAAGGCCTCGAAATTCTTGAGGAAATTCGACACAAT\n+AATAGAAATGTGATTTTTCTGGTTCCCCATGGCTGGAGCGTGGATATTCCTGCAATGTTGCTGGCAGCTC\n+AGGGAAAAAAAATGGCCGCCATGTTTCATCAGCAACGAAATCCAGTGATTGATTATGTCTGGAATTCAGT\n+ACGGCGTAAATTCGGGGGGCGCTTACATGCCCGGGAGGATGGGATAAAACCATTTATTCAGTCAGTACGC\n+CAGGGATACTGGGGATATTACCTCCCAGATCAGGATCATGGTCCTGAATACAGTGAATTTGCTGATTTTT\n+TTGCGACCTATAAAGCGACATTACCAATCATTGGACGTCTGATGAACATCAGTCAGGCTATGATTATACC\n+ACTTTTCCCGGTTTATGATGAAAAAAAACATCTACTGACTATTGAAATTCGGCCACCAATGGATGCTTGC\n+ATTGCCAGCGCGGACAATAAAACGATTGCCCGACAAATGAACAAAACAGTGGAAATTTTGGTGGGGCCAC\n+ATCCGGAACAGTATGTCTGGGTTTTAAAATTGTTAAAAACACGCAAATCAAACGAAGCGGACCCGTACCC\n+TTGAAATTATAAAGTACAAGTATTTCCACTAGTTGTTTGTAAGCGTACAGCCTGAACCGTCTGGTCAGAA\n+TCTGACGAATTAGACAAAGTGGTGTCCACCAAATAAGTAGTGGGAACCAATGAGGTAGCCTGAGTTTAAC\n+GGACACTCCTTCCTGAAATAGAATGGCATCAGAAGGAGCTAATAATGAGCAGAAAAACCCAACGTTACTC\n+TAAAGAGTTCAAAGCCGAAGCTGTCAGAACGGTTCTTGAAAATCAACTTTCGATCAGTGAAGGCGCTTCC\n+CGATTATCTCTTCCTGAAGGCACTTTAGGACAATGGGTTACCGCCGCCAGAAAAGGGCTCGGTACTCCTG\n+GTTCCCGCACGGTGGCTGAACTGGAATCTGAAATTCTGCAACTGCGTAAGGCGTTAAATGAAGCTCGCCT\n+TGAGCGAGATATATTAAATTGCACAGGAGTCGCTGAAAAATACGCGTTAATCGAACAATGGCGACAACAA\n+TTTCCCATTGAAGCGATGTGTCAGGTATTTGGTGTATCCAGGAGCGGTTATTACAACTGGGTACAGCATG\n+AACCCTCAGACAGAAAACAAAGTGATGAGCGGCTAAAACTGGAGATTAAGGTGGCACATATCCGCACTCG\n+CGAAACATATGGAACCCGGCGGCTCCAGACGGAGCTGGCAGAGAATGGCATCATCGTTGGTCGTGACCGA\n+CTGGCACGTCTTCGTAAGGAGCTAAGGCTACGCTGTAAGCAGAAACGCAAGTTCAGAGCGACTACGAACT\n+CGAACCACAATCTGCCAGTTGCGCCAAATCTGCTGAACCAGACGTTCGCTCCTACAGCACCAAATCAGGT\n+CTGGGTGGCGGACCTGACGTATGTTGCCACACAGGAGGGATGGTTGTACCTCGCTGGCATCAAAGATGTT\n+TATACGTGCGAAATTGTCGGCTACGCCATGGGAGAGCGCATGACAAAAGAGCTGACAGGTAAAGCCCTGT\n+TTATGGCGCTCAGGAGCCAGCGCCCACCTGCCGGGCTAATCCACCACTCTGATCGAGGTTCACAGTACTG\n+CGCATACGATTACCGGGTCATACAGGAGCAGTTTGGTCTGAAAACATCAATGTCGCGTAAAGGTAACTGT\n+TACGACAACGCTCCGATGGAAAGCTTCTGGGGAACGCTGAAAAATGAGAGCCTGAGCCACTATCGTTTTA\n+ATAACCGGGATGAAGCCATCTCAGTAATACGGGAATACATTGAGATTTTCTACAATCGTCAGCGTCGTCA\n+CTCTCGTCTGGGGAATATCTCCCCGGCAGCCTTCAGGGAAAAATATCATCAGATGGCTGCTTAAAAAAAG\n+AACAAATGGTAGTGTCCGCTATTGCCAGTACACCTCAACATTCCACCATGCATTACGATTAACGCCGCAT\n+AGCCAGTTGAACTTTGCTACTTTGTGAGAGGTAGTACCTTCTATCCAGTGCGAATTTAATTAATGGAATA\n+AATGATTATGAGTGAAAATGATACAATCCCAAAGAAGTCTACAAGTCAGATTAACAAAGCGGTATTCTTT\n+ACATCTGCTTTGCTAATTTTCC\n+\n' |
| b |
| diff -r 000000000000 -r 1c58de56d587 test-data/accessions_1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/accessions_1.tsv Wed Dec 04 07:01:37 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +CP011064 +CP021680 |