| Next changeset 1:eccc7495c3d9 (2022-10-14) |
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Commit message:
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1 |
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added:
macro.xml plasmidfinder.xml test-data/contigs.fasta test-data/data.fastq.gz test-data/plasmidfinder_db.loc test-data/test-db/.gitignore test-data/test-db/Inc18.comp.b test-data/test-db/Inc18.fsa test-data/test-db/Inc18.length.b test-data/test-db/Inc18.name test-data/test-db/Inc18.seq.b test-data/test-db/Rep3.comp.b test-data/test-db/Rep3.fsa test-data/test-db/Rep3.length.b test-data/test-db/Rep3.name test-data/test-db/Rep3.seq.b test-data/test-db/Rep_trans.comp.b test-data/test-db/Rep_trans.fsa test-data/test-db/Rep_trans.length.b test-data/test-db/Rep_trans.name test-data/test-db/Rep_trans.seq.b test-data/test-db/config test-data/test_1/Hit_in_genome_seq_test1.fsa test-data/test_1/Plasmid_seqs_test1.fsa test-data/test_1/data_test1.json test-data/test_1/logfile_test1.log test-data/test_1/results_tab_test1.tsv test-data/test_1/results_test1.txt test-data/test_2/data_test2.json test-data/test_2/logfile_test2.log test-data/test_2/results_tab_test2.tsv test-data/test_2/results_test2.txt test-data/test_3/Hit_in_genome_seq_test3.fsa test-data/test_3/Plasmid_seqs_test3.fsa test-data/test_3/results_tab_test3.tsv tool-data/plasmidfinder.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 2b6e795b22a9 macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Mon Sep 19 08:47:42 2022 +0000 |
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| @@ -0,0 +1,23 @@ + +<macros> + <token name="@TOOL_VERSION@">2.1.6</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token> + + <xml name="xrefs"> + <xrefs> + <xref type='bio.tools'>PlasmidFinder</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">plasmidfinder</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1007/978-1-4939-9877-7_20</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 2b6e795b22a9 plasmidfinder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plasmidfinder.xml Mon Sep 19 08:47:42 2022 +0000 |
| [ |
| b'@@ -0,0 +1,149 @@\n+<tool id="plasmidfinder" name="PlasmidFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>\n+ Plasmid identification in bacteria.\n+ </description>\n+ <macros>\n+ <import>macro.xml</import>\n+ </macros>\n+ <expand macro=\'xrefs\'/>\n+ <expand macro="requirements" />\n+ <command detect_errors="aggressive"><![CDATA[\n+ mkdir output_dir &&\n+ mkdir temp_dir &&\n+ plasmidfinder.py\n+ -i \'$input.input_file\'\n+ -p \'$input.database_name.fields.path\'\n+ -l \'$options.min_cov\'\n+ -t \'$options.threshold\'\n+ #if $input.input_file.ext == \'fasta\' or $input.input_file.ext == \'fasta.gz\'\n+ -mp blastn\n+ #else if $input.input_file.ext == \'fastqsanger.gz\' or $input.input_file.ext == \'fastqsanger\'\n+ -mp kma\n+ #end if\n+ -x\n+ -o output_dir\n+ -tmp temp_dir\n+ #*======================================\n+ LOG file\n+ ======================================*#\n+ | tee \'$log_file\'\n+ ]]>\n+ </command>\n+ <inputs>\n+ <section name="input" title="Input parameters" expanded="true">\n+ <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/>\n+ <param name="database_name" type="select" label="PlasmidFinder database">\n+ <options from_data_table="plasmidfinder_db">\n+ <validator message="No PlasmidFinder database is available" type="no_options"/>\n+ </options>\n+ </param>\n+ </section>\n+ <section name="options" title="Options">\n+ <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help="Choose a minimum coverage value (default: 0.6)"/>\n+ <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help="Choose a minimum identity value (default: 0.95)"/>\n+ </section>\n+ <section name="output_files" title="Output file selection">\n+ <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">\n+ <option value="data_json">JSON file result</option>\n+ <option value="hit_fasta" selected="true">Hits in genome</option>\n+ <option value="plasmid_fasta" selected="true">Plasmid hits</option>\n+ <option value="result_tsv" selected="true">Plasmid results</option>\n+ <option value="result_txt" selected="true">Raw results</option>\n+ <option value="logfile">Log file</option>\n+ </param>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="json_file" format="json" from_work_dir="output_dir/data.json" label="${tool.name} on ${on_string}: data.json">\n+ <filter> "data_json" in output_files[\'output_selection\'] </filter>\n+ </data>\n+ <data name="hit_file" format="fasta" from_work_dir="output_dir/Hit_in_genome_seq.fsa" label="${tool.name} on ${on_string}: hit_in_genome.fasta">\n+ <filter> "hit_fasta" in output_files[\'output_selection\'] </filter>\n+ </data>\n+ <data name="plasmid_file" format="fasta" from_work_dir="output_dir/Plasmid_seqs.fsa" label="${tool.name} on ${on_string}: plasmid.fasta">\n+ <filter> "plasmid_fasta" in output_files[\'output_selection\'] </filter>\n+ </data>\n+ <data name="result_file" format="tabular" from_work_dir="output_dir/results_tab.tsv" label="${tool.name} on ${on_string}: results.tsv">\n+ <filter> "result_tsv" in output_files[\'output_selection\'] </filter>\n+ </data>\n+ <data name="raw_file" format="txt" from_work_dir="output_dir/results.txt" label="${tool.name} on ${on_string}: raw_result.txt">\n+ <filter> "result_txt" in output_files[\'output_selection\'] </filter>\n+ </d'..b'sta"/>\n+ <param name="input_type" value="genome"/>\n+ <param name="database_name" value="test-plasmindfinder-db"/>\n+ </section>\n+ <section name="output_files">\n+ <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/>\n+ </section>\n+ <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/>\n+ <output name="hit_file" value="test_1/Hit_in_genome_seq_test1.fsa" ftype="fasta"/>\n+ <output name="plasmid_file" value="test_1/Plasmid_seqs_test1.fsa" ftype="fasta"/>\n+ <output name="result_file" value="test_1/results_tab_test1.tsv"/>\n+ <output name="raw_file" value="test_1/results_test1.txt" lines_diff="2"/>\n+ <output name="log_file" value="test_1/logfile_test1.log" lines_diff="7"/>\n+ </test>\n+ <!--test_2 with default value and for fastq file -->\n+ <test expect_num_outputs="4">\n+ <section name="input">\n+ <param name="input_file" value="data.fastq.gz"/>\n+ <param name="input_type" value="raw"/>\n+ <param name="database_name" value="test-plasmindfinder-db"/>\n+ </section>\n+ <section name="output_files">\n+ <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/>\n+ </section>\n+ <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/>\n+ <output name="result_file" value="test_2/results_tab_test2.tsv"/>\n+ <output name="raw_file" value="test_2/results_test2.txt" lines_diff="2"/>\n+ <output name="log_file" value="test_2/logfile_test2.log" lines_diff="7"/>\n+ </test>\n+ <!--test_3 with default value and for fastq file -->\n+ <test expect_num_outputs="3">\n+ <section name="input">\n+ <param name="input_file" value="contigs.fasta"/>\n+ <param name="input_type" value="genome"/>\n+ <param name="database_name" value="test-plasmindfinder-db"/>\n+ </section>\n+ <section name="options">\n+ <param name="min_cov" value="0.2" />\n+ <param name="threshold" value="0.6"/>\n+ </section>\n+ <section name="output_files">\n+ <param name="output_selection" value="hit_fasta,plasmid_fasta,result_tsv"/>\n+ </section>\n+ <output name="hit_file" value="test_3/Hit_in_genome_seq_test3.fsa" ftype="fasta"/>\n+ <output name="plasmid_file" value="test_3/Plasmid_seqs_test3.fsa" ftype="fasta"/>\n+ <output name="result_file" value="test_3/results_tab_test3.tsv"/>\n+ </test>\n+ </tests>\n+ <help>< with hundreds sequences.\n+ **Input**\n+ It can analyse raw data using a k-mer approach based on KMA or a blastn for genome assembly.\n+ A database is need obtained from the plasmidfinder database.\n+ **Options**\n+ You can modify the coverage value (% of matching sequence on the total target sequence)\n+ You can modify the identity threshold (% of shared nucleotide on the match)\n+ **Output**\n+ Some output files are availables\n+ - A fasta file with all available hits detected in the genome\n+ - A fasta file with all plasmid sequences from the database\n+ - A summary of the analysis in tabular format\n+ - A Raw result file in text format\n+ - A JSON file could be use for other boinformatic analaysis\n+ - A log file with analysis parameters\n+\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 2b6e795b22a9 test-data/contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fasta Mon Sep 19 08:47:42 2022 +0000 |
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| b'@@ -0,0 +1,603 @@\n+>contig00001 len=5513 cov=11.7 corr=0 origname=NODE_1_length_5513_cov_11.741181_pilon sw=shovill-spades/1.1.0 date=20220302\n+CAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTAC\n+CATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAA\n+GCCACTTCTCCTCATCCAACGCGTCAGTTTTTGACAGAATCGTTAGTTGATGGCGAAAGG\n+TCGCAAAGTAAGAGCTTCTCGAGCTGCGCAAGGATAGGTCGAATTTTCTCATTTTCCGCC\n+AGCAGTCCACTTCGATTTAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTATCAAGATA\n+ATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAA\n+ACTCTGCAGGTTGGATACGCCAATCATTTTTATCGAAGCGCGCATAAATTTGAGCAGATT\n+TGTCGTCACAGGTTGCGCCGCCAAAACGTCGGCTACAGTAACTTTTCCCAGCCTCAATCT\n+CATCTCTCTTTTTGCGTTCTGCTTCAATATCTGGTTGAACGGCGTCGCGTCGTAACCCAG\n+CTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCC\n+GAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCGACAGCTTGGTTTT\n+TAGTGAGTTGTTCCATTCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATATCTGACTT\n+TTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAAGCGG\n+CTCACCTTTAGCATCAACAGGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTA\n+GCGAACTGCGATGGGCATACTGTAACCATAAGGCCACGTATTTTGCAAGCTATTTAACTG\n+GCGGCGATTGCGTACCCGACGACCAAAATTAGGGTCAACGCTACCTGTAGGAAGTGTCCG\n+CATAAAGTGCACCGCATGGAAATGAAGACGGCCATTAGCTGTACCATACTCAGGCACACA\n+AAAATACTGATAGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCTCGGCAGCAAGAAC\n+CATACGACCAATATCACGAAAATAGTCACGCAAAGCATTGGGATTATCATAAAACGCCTC\n+TAATCGGTCGTCAGCCAACGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGC\n+CTGTCGCATTGCATTCATCAAACGCTGAATAGCAAAGCCTCTACGCGATTTCATAGTGGA\n+GGCCTCCAGCAATCTTGAACACTCATCCTTAATACCTTTCTTTTTGGGGTAATTATACTC\n+ATCGCGAATATCCTTAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACTGCGTAACCGT\n+CTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTCTATAGTGTTATT\n+AATATCAAGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCATTAACTTCTCAGT\n+AACAGATACAAACTCATCACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATACATATC\n+ACCATTATCGAACTCAACGCCCTGCATACGAAAAGACAGAATCTCTTCCAAGAGCTTGAT\n+GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGGGGATTGAGAAAGAGTAGAAATGCC\n+ACAAGCCTCAATAGCAGGTTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAGCGTG\n+ACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAA\n+AACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAAT\n+ACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAAT\n+ACCATGAAAAATATCAACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTT\n+TGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGATGAACTAA\n+GTCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTGATTTGGTCATTGGTAAAATACTG\n+ACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCTT\n+GGAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGCAGTAGACTCCTTCTGTTGATA\n+AGCAAGCATCTCATTTTGTGCATATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCGA\n+CTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGATT\n+GTCCAGTTGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCGGCGTCAACCATACCAGC\n+AGAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAAGCTCAGGAAATGCAGCAGCAAG\n+ATAATCACGAGTATCCTTTCCTTTATCAGCGGCAGACTTGCCACCAAGTCCAACCAAATC\n+AAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTT\n+ACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGGAAC\n+ATTAGAGCCTTGAATGGCAGATTTAATACCAGCATCACCCATGCCTACAGTATTGTTATC\n+GGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAACAA\n+TTTAGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAACAT\n+AAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAA\n+ACCAATCCGCGGCATTTAGTAGCGGTAAAGTTAGACCAAACCATGAAACCAACATAAACA\n+TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTCACACAGTCCTTGACGGTATAATAA\n+CCACCATCATGGCGACCATCCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGA\n+ACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATCAAAAGCA\n+ATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAGATGTATCCATCTGAATG\n+CAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAACGTTGAC\n+GATGTAGCTTTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGA\n+ACCAGCTTATCAGAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATT\n+AAACTCCTAAGCAGAAAACCTACCGCGCTTCGCTTGGTCAACCCCTCAGCGGCAAAAATT\n+AAAATTTTTACCGCTTCGGCGTTATAACCTCACACTCAATCTTTTATCACGAAGTCATGA\n+TTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGTCACATTAAATTTAACCTGACTAT\n+TCCACTGCAACAACTGAACGGACTGGAAACACTGGTCATAATCATGGTGGCGAATAAGTA\n+CGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAAGCCTTCAAGAAGGT\n+GATAAGCAGGAGAAACATACGAAGGCGCATAACGATACCACTGACCCTCAGCAATCTTAA\n+ACTTCTTAGAC'..b'44_length_887_cov_2.006579_pilon sw=shovill-spades/1.1.0 date=20220302\n+AATCGATATCGATGCGTCAAAATTTGGACGACGCCATGAAACATCTTTGTCGATCCTCGG\n+TGATGCAAACACAGCTTTGCAAAGACTTGTCGAGTTAGGGGATGCTCGCCCTGCTGATAG\n+CTGGTACCTAGCAAATCAAGAAAATAAAGAAAAATGGGTAAATTGGTTGAAATCTTTTGA\n+AGATCGAGAGGAAGAACCGATTCGTCCAGAGGCTGTCTATAAAGAAATCAATCGTATTGC\n+TGAAGACGATGCGATTTTCGTCACAGATGTCGGTAACACGACTATCCATTCTATTCGTTT\n+ATTGAATATGAACGGTAAACAAAAACATACGACATCTGGATGGTTCGCAACTATGGGTAA\n+TGGTGTGCCAGGAGGAATTGCCGCACAACTAAGCTACCCAGAAAAACAAGTATTTACCTT\n+AAGTGGTGATGGCGGGTTTGCTATGGTCATGCAAGATATCATTACACAAGTCAAATATCA\n+GCTTCCAATTATTAATGTTGTCTTTTCGAATGATTCTTTTGGTTTCATCGAAGCAGAACA\n+AGAAGATACGGAACAAAAGAAATTTGGTGTATTTTTAGAAGATGCAGATTTCGGTAAAGT\n+TGGAGAAGCGCTCGGGGCAAATAGCTTTACAGTCACAGAATACTCGCAACTTCGATTTGC\n+CTTTGATGCAGCTGCAAAATCAGATCGTCCTGTAGTAATCGATGTGAAGATCAATAACAA\n+GCGCCCATTGCCAGTAGAAGATCTGCATTTAGATCCAAGAAAATATTCTGAAGAAGAAAT\n+CCAAGCATTCAAAGAAAAATATGAAGTCCATGATTTGCCAGTATTGAATGAATTATATGA\n+AAAGAGGTTGTGACAACTGCGCTATGCTTCGAGTATTAAGATAAAAT\n+>contig00013 len=886 cov=2.2 corr=0 origname=NODE_146_length_886_cov_2.193676_pilon sw=shovill-spades/1.1.0 date=20220302\n+ATCGACAATGTAGGTATTCGCCGTAAAATAGGTGTGGCAGCCACGACAGTGGTAGCGTTG\n+TTTCGCTAAAGCAAGATAAGTCAGTTGGTTCGCACATTTATTAAGTTGAATGAGCGATTT\n+TTTCTTTCCGTTCTTAACGATCATGCCTTCATGATTCATCTGTTTACACAAAGGACAGCG\n+ACGAATTTCTTTACTTAACGTCGCAGAAACAACAAGACTCTTGATATTCTTAATGCTCTT\n+CGATTCCACATTTGTGATGAAAATGTTTTTATCTTTGATTCCAAGTAGTAGTTTGATATG\n+ATGAAGATCAGGCATACAGAACGCTCCTTTGATTGTGTTGTGGTGATTCAATTCTAACGG\n+AGCTTCTGTATGTTTTGTTTTTTCATGCTCAAAAGGGACCGATAGAATGATTTTCTATCA\n+GTCCTAGAAATTATAGAGCCTTTTTTATTTGGTCTTGAAGAAGAAAAGTAAGCGCCCCAT\n+AGAACAGTACCTGTACGTCAAATAACCCGACCTATAGAATAGAATCGGGAATGTTTGGCG\n+TTTTTAGTTACGAGAAAAATGTTGTTGTACATCCTTGTTCCAAGGCAACAGTTGATCTAA\n+AGTTTCTGCTGAAAGTACGGGAAGATTTGGTATCTTATCAAATAGAAACTCTAGATACTT\n+TACAGGATTCAATCCGTTAAGTTCTGCTGTTTTATATACACTCAGAATGATTCCTGAAGT\n+TCGTGCTCCTTCAAGACTTGTGGAATGCAACCAATTTTTCCGTCCTATCACCAGCTCTTT\n+GATATTTCGCTCCGCACGATTATTTGTGAGTTCTAAACGACCATCTTCAAAAATAGGTTC\n+AAAACCACTTCGTAGTTTACACGCATATTGAACGGCTGCATCCAAC\n+>contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302\n+GGGGCTACATGCCAACGCTAATTTTAGAATCAGATCATGGTTATCAAGTTTATTTTGTAC\n+TAAAGACACCAGGCTATGTCACAAAGAAAAGCAATTTCAAGGTGATCGATGTAGCAAAAA\n+AAATTTCAAAAACAATTCGTCTACAGTTGGCTGAAAAATTGTCCGGAGTGGATCTAGGAT\n+GTAACCACTTCGGAATTGCTCGATTCCCACAAGAAAATAATATTGTTTTTAAAGAAATGA\n+ACTATCAGTATTCTTTTGCTGACTGGATTCAATGGTCGATGAAGCTTGAATCAGATCAAA\n+AAACAAAAGAAGATCGAGAACGAAAACTAATTGTCTTTCCTGAGAAAAAAGAAATTCGTC\n+AAGTAGATGAACCGTGGTTCGATATGTTACTTCATAAAGCAAACATCGTCGGCGGAGAAG\n+GACGTCTTGGTCGAAATAATGTGATTTTCACGCTTTCTTTAGCTTATTACTCTTCAGGTT\n+ATGCATTGGATACTTGCGAATACAATATGTTCACATTCAACGAACGGTTACAGGAACCGC\n+TATCTGAAGCAGAATTAGTAAAGATTGTACGTAGTGCTTATTCTGGTAATTATCAAGCAG\n+CAAGCAGAGAATTCATTATTGAATTGTGCCAGCAATGGGTTTCACCAACCTTAAAAAATA\n+ATGATCTGTTCATTCAACGACGTGGCTGGTGGAAATTTAAAAAGCCACGAGATCAAAGAA\n+AATATAGTCATAAAAATGAATGGAAAGAAGATCTATTGGCTTATCTAAGCGAAAAAAGTC\n+TTGCTAGTGAGCCTTATTTGAACCTGTCAAAAAAAGAATTGGCTTCACAACTAACG\n+>contig00015 len=834 cov=2.2 corr=0 origname=NODE_175_length_834_cov_2.244696_pilon sw=shovill-spades/1.1.0 date=20220302\n+TAGAAAATGACAATGGTTTAGTGTCTATTAAAGGTACGGGGAAAAGAACTATAGTTGAGG\n+TTTCATCTACGTATCCAACTACGATGATTCTATCTTTATTAATTAGTTCAATAACTTTTA\n+TATTCTTATTTACACGTTATTTAATAAGATGCTGCGGTGAAATGAAAATAGATTAGATAG\n+ATATTATAAATATGTTGATTCTATTTTCATAGCAATGGAGAAAATACATTAGCAATATAT\n+AAAAGAAGGTATCAAGAGTCACAGTGAATTTATTCCGAAAAGTGAAAAGAGCAAATATAA\n+AATTTAATGAAAATATAGAACTAAATAGGAAAACGTAGACGTAATTTTCTACGTTTTCCT\n+TTTCATATATATTAAATATTACGGAAAATTATATAAACTAATTTAGTGTTTTGTTTGTAA\n+TTCCTAATTTTGCTCCACTTTTAGATAATTTTTAGGTCTATTTAACTCATCAGACATTCT\n+ATGCTCATTTTTCTCCAAATTTGTTTCAACTCTTTCGTACTTAATTTTGCGTATTTGAAA\n+ATTCTTCTTTTAGAGTACTTTTATTACGATACTAGTATGATATATATCTATAGCAAACAG\n+TTAAAATCTTCCTAAAATAAGCGAATAGCATTCCTAAAACCTATAAAATTTTTAGATGAA\n+GCGACAAGTGGACAATTAATAAACTACTTGAACATGAAATTATGGATCACCTTTCAAATT\n+TAGAAAATGGAATTCTTATACTTATTGCGCAACATTTATTGATTGCAAAATTATGTGACA\n+AAAAAAACTAGTAGAAGAAAGAATAATGGCTTGATAATAAAGTACTACCTATTA\n' |
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| diff -r 000000000000 -r 2b6e795b22a9 test-data/data.fastq.gz |
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| Binary file test-data/data.fastq.gz has changed |
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| diff -r 000000000000 -r 2b6e795b22a9 test-data/plasmidfinder_db.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder_db.loc Mon Sep 19 08:47:42 2022 +0000 |
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| @@ -0,0 +1,1 @@ +test-plasmindfinder-db Test Database ${__HERE__}/test-db |
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| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/.gitignore Mon Sep 19 08:47:42 2022 +0000 |
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| @@ -0,0 +1,2 @@ +*.b +*.name |
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| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.comp.b |
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| Binary file test-data/test-db/Inc18.comp.b has changed |
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| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/Inc18.fsa Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>rep2_2_repR(pEF1)_DQ198088 +atgttgagcgaaatttattcagctattcttaaaaacggcttacgtacatacaaatatcgaaacagcaccatgaaacctgcaggtcatattgattccagtaggagtggtgctatctttgcgtaccttagcaagcaattaatgaatgttgggcgtggtatggtcattacttcggaagaagctattttagagaacgaaaagaaactaacgcattggacacctaatacctatcgctttggtacttatgcggatgattatcgaacagtggttaaaggtcattctgagaaaaacttaagtcaaatcaacacatttgtagttgatatcgattcaaaagagaaccatcaaggcgaaattattttagcctgtttagatcaagtgggctacatgccaacgctaattttagaatcagatcatggttatcaagtttattttgtactaaagacaccaggctatgtcacaaagaaaagcaatttcaaggtgatcgatgtagcaaaaaaaatttcaaaaacaattcgtctacagttggctgaaaaattgtccggagtggatctaggatgtaaccacttcggaattgctcgattcccacaagaaaataatattgtttttaaagaaatgaactatcagtattcttttgctgactggattcaatggtcgatgaagcttgaatcagatcaaaaaacaaaagaagatcgagaacgaaaactaattgtctttcctgagaaaaaagaaattcgtcaagtagatgaaccgtggttcgatatgttacttcataaagcaaacatcgtcggcggagaaggacgtcttggtcgaaataatgtgattttcacgctttctttagcttattactcttcaggttatgcattggatacttgcgaatacaatatgttcacattcaacgaacggttacaggaaccgctatctgaagcagaattagtaaagattgtacgtagtgcttattctggtaattatcaagcagcaagcagagaattcattattgaattgtgccagcaatgggtttcaccaaccttaaaaaataatgatctgttcattcaacgacgtggctggtggaaatttaaaaagccacgagatcaaagaaaatatagtcataaaaatgaatggaaagaagatctattggcttatctaagcgaaaaaagtcttgctagtgagccttatttgaacctgtcaaaaaaagaattggcttcacaactaacgatgcccaagcgaacacttgataagatcttaaatgagttacgagaggagaataaagtcttctacaaggtaacacgaggaagaaatggcggaatgatcattgcttcagtcaaaacgttgttcgcgagagttattcaactaagtaaagaaaagagactagattattcaacaaggatcacagaggtatttggactcaacgagagcttagtagaagagacatttagacaattatcaacccccttgaaccctcttaaagaagtgaatctttttgaagtagatacaggttga |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.length.b |
| b |
| Binary file test-data/test-db/Inc18.length.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.name --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/Inc18.name Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +rep2_2_repR(pEF1)_DQ198088 +rep11a_1_repA(pB82)_AB178871 +rep14a_2_ORF1(pKQ10)_EFU01917 |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.seq.b |
| b |
| Binary file test-data/test-db/Inc18.seq.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.comp.b |
| b |
| Binary file test-data/test-db/Rep3.comp.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/Rep3.fsa Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>rep11a_1_repA(pB82)_AB178871 +atggctaatgagattgtaaaataccaccatgaattaaatacaattcctttaagaaaatttacaccggttgaaatgaatttgtttttttccatcgtgtctagaatgcgtgaaaaaggggataagacagttcgttttacgtttgaccaactaaaagatttaagtaactacaaagcaactgcaaatgtacgatttgtagaagatttaaaagcaacttatgaaaaaatcttatctttacgctttggtcgtagaagtgagtctgggctttcttacgatatgtttgtaatgtttacagaatttaaaatcaacggggacgtagaaaatccttacgtagatatacgaatttacgaaaaagcactgcctttgttaaataatttagacgagtgggtacgctattctttacaacaattcaacgagctacaaagtggctatgcaaagactatgtttcgtctgttaaagcaatacagaaccaaaggtttcgcatatttctccaaagaagactttcttgaattattagatattcctaaaagttataagcaacctgatatagataaacgagttataaaacctatacgtcaagaactaactgcaatcttcaaaggactaacaatcaaaaagaaatacggaaaaggacggggaaaacctgttattggctatcaatttacgttcaaacctgagatcaaaaaagcagacgactttaacaaacatgcaccaaccaaagaagaccaaaataaagcattggctttagctgataaacaaaaagaatacgaagaacccgctacaacaattaacgaaaaaatcaaacagaagaaacgagaacttgaactcctccaacaaatcaaacaactagaaaaagagaaaaaagctcttgaaaaacaaacagagtccgcactttcggaaaaagagaaaaaaagtttattatctgatttagataatttattccagtag |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.length.b |
| b |
| Binary file test-data/test-db/Rep3.length.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.name --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/Rep3.name Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +rep11a_1_repA(pB82)_AB178871 |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.seq.b |
| b |
| Binary file test-data/test-db/Rep3.seq.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.comp.b |
| b |
| Binary file test-data/test-db/Rep_trans.comp.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/Rep_trans.fsa Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>rep14a_2_ORF1(pKQ10)_EFU01917 +gtgcgactgtacaacaaaaagctagagcaggaacgaaaaaaagtaatcgtgccaaaagaaatcgatacgtggtggcggttagaaatgcagctaagacgtggcaaagcaacggattggcatgcgatggttcaggaaagcttagatagttttgcaagcccgcattttttgccgattgatataaaacctattgataaaatagttattgaaggtttgatagctgagccttctaattggtcgataattgctagacatacaaaatataaatatcggaatttgctgaagcaagaaagtcaaaatgatgagttaacgaaccatttacgagagacttttaaggaatctgcagacgaattaaaaaaagaattggatacgtggcttttggggttggatgtgacagagaagtga |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.length.b |
| b |
| Binary file test-data/test-db/Rep_trans.length.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.name --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/Rep_trans.name Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +rep14a_2_ORF1(pKQ10)_EFU01917 |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.seq.b |
| b |
| Binary file test-data/test-db/Rep_trans.seq.b has changed |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/config --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/config Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# Database configuration file - Describes the content of the database +# Each db consist of 1 file(s) with the following extensions: fsa +# Other important files are: notes.txt +#db_prefix name description +Inc18 Gram Positive Inc18 +Rep3 Gram Positive Rep3 +Rep_trans Gram Positive Rep_trans |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/Hit_in_genome_seq_test1.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/Hit_in_genome_seq_test1.fsa Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,25 @@ +>rep11a:WARNING ID:99.89% COV:100.0% Best_match:contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180 +ATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTT +ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT +AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA +AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT +GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA +ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT +TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA +AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA +TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT +GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA +CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT +ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA +GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA +ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA +CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA +GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG +>rep14a:WARNING ID:99.5% COV:100.0% Best_match:contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488 +GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA +ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT +GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA +AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA +ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT +GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA +TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/Plasmid_seqs_test1.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/Plasmid_seqs_test1.fsa Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,25 @@ +>contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180 +ATGGCTAATGAGATTGTAAAATACCACCATGAATTAAATACAATTCCTTTAAGAAAATTT +ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT +AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA +AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT +GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA +ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT +TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA +AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA +TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT +GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA +CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT +ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA +GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA +ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA +CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA +GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG +>contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488 +GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA +ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT +GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA +AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA +ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT +GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA +TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/data_test1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/data_test1.json Mon Sep 19 08:47:42 2022 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat"], "method": "blast", "file_format": "fasta"}, "run_info": {"date": "09.09.2022", "time": "08:52:55"}, "results": {"Gram Positive": {"Inc18": "No hit found", "Rep3": {"contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180": {"plasmid": "rep11a", "identity": 99.89, "HSP_length": 945, "template_length": 945, "position_in_ref": "1..945", "contig_name": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "308..1252", "note": "repA(pB82)", "accession": "AB178871", "coverage": 100.0, "hit_id": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180"}}, "Rep_trans": {"contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488": {"plasmid": "rep14a", "identity": 99.5, "HSP_length": 402, "template_length": 402, "position_in_ref": "1..402", "contig_name": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "1703..2104", "note": "ORF1(pKQ10)", "accession": "EFU01917", "coverage": 100.0, "hit_id": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488"}}}}}} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/logfile_test1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/logfile_test1.log Mon Sep 19 08:47:42 2022 +0000 |
| [ |
| b"@@ -0,0 +1,57 @@\n+Found: rep2_2_repR(pEF1)_DQ198088\n+Saving: contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228\n+Found: rep11a_1_repA(pB82)_AB178871\n+Saving: contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180\n+Found: rep14a_2_ORF1(pKQ10)_EFU01917\n+Saving: contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488\n+{'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found',\n+ 'Rep3': {'contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180': {'HSP_length': 945,\n+ 'accession': 'AB178871',\n+ 'contig_name': 'contig00003 '\n+ 'len=3227 '\n+ 'cov=2.2 '\n+ 'corr=0 '\n+ 'origname=NODE_3_length_3227_cov_2.232903_pilon '\n+ 'sw=shovill-spades/1.1.0 '\n+ 'date=20220302',\n+ 'coverage': 100.0,\n+ 'hit_id': 'contig00003 '\n+ 'len=3227 '\n+ "..b" 'coverage': 100.0,\n+ 'hit_id': 'contig00008 '\n+ 'len=2292 '\n+ 'cov=2.6 '\n+ 'corr=0 '\n+ 'origname=NODE_11_length_2292_cov_2.631409_pilon '\n+ 'sw=shovill-spades/1.1.0 '\n+ 'date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488',\n+ 'identity': 99.5,\n+ 'note': 'ORF1(pKQ10)',\n+ 'plasmid': 'rep14a',\n+ 'position_in_ref': '1..402',\n+ 'positions_in_contig': '1703..2104',\n+ 'template_length': 402}}}},\n+ 'run_info': {'date': '09.09.2022', 'time': '08:52:55'},\n+ 'user_input': {'file_format': 'fasta',\n+ 'filename(s)': ['/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat'],\n+ 'method': 'blast'}}}\n" |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/results_tab_test1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/results_tab_test1.tsv Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +Database Plasmid Identity Query / Template length Contig Position in contig Note Accession number +Rep3 rep11a 99.89 945 / 945 contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302 308..1252 repA(pB82) AB178871 +Rep_trans rep14a 99.5 402 / 402 contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302 1703..2104 ORF1(pKQ10) EFU01917 |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/results_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/results_test1.txt Mon Sep 19 08:47:42 2022 +0000 |
| b |
| b'@@ -0,0 +1,127 @@\n+plasmidfinder Results\n+\n+Organism(s): Gram Positive\n+\n+****************************************************************************************\n+Inc18\n+****************************************************************************************************************\n+Plasmid Identity Query / Template length Contig Position in contig Note Accession number\n+****************************************************************************************************************\n+- - - No hit found - - -\n+================================================================================================================\n+\n+****************************************************************************************\n+Rep3\n+********************************************************************************************************************************************************************************************************************************\n+Plasmid Identity Query / Template length Contig Position in contig Note Accession number\n+********************************************************************************************************************************************************************************************************************************\n+rep11a 99.89 945 / 945 contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302 308..1252 repA(pB82) AB178871\n+================================================================================================================================================================================================================================\n+\n+****************************************************************************************\n+Rep_trans\n+**********************************************************************************************************************************************************************************************************************************\n+Plasmid Identity Query / Template length Contig Position in contig Note Accession number\n+**********************************************************************************************************************************************************************************************************************************\n+rep14a 99.5 402 / 402 contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302 1703..2104 ORF1(pKQ10) EFU01917\n+==================================================================================================================================================================================================================================\n+\n+\n+\n+\n+Extended Output:\n+\n+# rep11a_AB178871\n+template: \tATGGCTAATGAGATTGTAAAATACCACCATGAATTAAATACAATTCCTTTAAGAAAATTT\n+ \t|||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||\n+query: \tATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTT\n+\n+template: \tACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT\n+\n+template: \tAAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tAAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA\n+\n+template: \tAATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT\n+ \t||||||||||||||||||||||||||||||||||||'..b'|||||||||||||||||||||||||\n+query: \tGGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA\n+\n+template: \tATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT\n+\n+template: \tTTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tTTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA\n+\n+template: \tAGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tAGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA\n+\n+template: \tTATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tTATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT\n+\n+template: \tGATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA\n+\n+template: \tCTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tCTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT\n+\n+template: \tACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA\n+\n+template: \tGACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA\n+\n+template: \tACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA\n+\n+template: \tCAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tCAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA\n+\n+template: \tGAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG\n+ \t|||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG\n+\n+# rep14a_EFU01917\n+template: \tGTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA\n+\n+template: \tATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT\n+\n+template: \tGCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA\n+\n+template: \tAAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA\n+ \t|||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||\n+query: \tAAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA\n+\n+template: \tATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT\n+ \t||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT\n+\n+template: \tGAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA\n+ \t||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||\n+query: \tGAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA\n+\n+template: \tTTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA\n+ \t||||||||||||||||||||||||||||||||||||||||||\n+query: \tTTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA\n+\n' |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/data_test2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/data_test2.json Mon Sep 19 08:47:42 2022 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmpj3aqa6lu/files/3/2/3/dataset_32342c91-595d-40c3-b39a-60aa67724edc.dat"], "method": "kma", "file_format": "fastq"}, "run_info": {"date": "09.09.2022", "time": "08:53:07"}, "results": {"Gram Positive": {"Inc18": "No hit found", "Rep3": "No hit found", "Rep_trans": "No hit found"}}}} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/logfile_test2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/logfile_test2.log Mon Sep 19 08:47:42 2022 +0000 |
| [ |
| @@ -0,0 +1,7 @@ +{'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found', + 'Rep3': 'No hit found', + 'Rep_trans': 'No hit found'}}, + 'run_info': {'date': '09.09.2022', 'time': '08:53:07'}, + 'user_input': {'file_format': 'fastq', + 'filename(s)': ['/tmp/tmpj3aqa6lu/files/3/2/3/dataset_32342c91-595d-40c3-b39a-60aa67724edc.dat'], + 'method': 'kma'}}} |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/results_tab_test2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/results_tab_test2.tsv Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Database Plasmid Identity Query / Template length Contig Position in contig Note Accession number |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/results_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/results_test2.txt Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,33 @@ +plasmidfinder Results + +Organism(s): Gram Positive + +**************************************************************************************** +Inc18 +**************************************************************************************************************** +Plasmid Identity Query / Template length Contig Position in contig Note Accession number +**************************************************************************************************************** +- - - No hit found - - - +================================================================================================================ + +**************************************************************************************** +Rep3 +**************************************************************************************************************** +Plasmid Identity Query / Template length Contig Position in contig Note Accession number +**************************************************************************************************************** +- - - No hit found - - - +================================================================================================================ + +**************************************************************************************** +Rep_trans +**************************************************************************************************************** +Plasmid Identity Query / Template length Contig Position in contig Note Accession number +**************************************************************************************************************** +- - - No hit found - - - +================================================================================================================ + + + + +Extended Output: + |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_3/Hit_in_genome_seq_test3.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3/Hit_in_genome_seq_test3.fsa Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,59 @@ +>rep2:WARNING ID:100.0% COV:55.89% Best_match:contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------GGGCTACATGCCAACGCTAATTTTAGAATCAGATCATGGTTATCAA +GTTTATTTTGTACTAAAGACACCAGGCTATGTCACAAAGAAAAGCAATTTCAAGGTGATC +GATGTAGCAAAAAAAATTTCAAAAACAATTCGTCTACAGTTGGCTGAAAAATTGTCCGGA +GTGGATCTAGGATGTAACCACTTCGGAATTGCTCGATTCCCACAAGAAAATAATATTGTT +TTTAAAGAAATGAACTATCAGTATTCTTTTGCTGACTGGATTCAATGGTCGATGAAGCTT +GAATCAGATCAAAAAACAAAAGAAGATCGAGAACGAAAACTAATTGTCTTTCCTGAGAAA +AAAGAAATTCGTCAAGTAGATGAACCGTGGTTCGATATGTTACTTCATAAAGCAAACATC +GTCGGCGGAGAAGGACGTCTTGGTCGAAATAATGTGATTTTCACGCTTTCTTTAGCTTAT +TACTCTTCAGGTTATGCATTGGATACTTGCGAATACAATATGTTCACATTCAACGAACGG +TTACAGGAACCGCTATCTGAAGCAGAATTAGTAAAGATTGTACGTAGTGCTTATTCTGGT +AATTATCAAGCAGCAAGCAGAGAATTCATTATTGAATTGTGCCAGCAATGGGTTTCACCA +ACCTTAAAAAATAATGATCTGTTCATTCAACGACGTGGCTGGTGGAAATTTAAAAAGCCA +CGAGATCAAAGAAAATATAGTCATAAAAATGAATGGAAAGAAGATCTATTGGCTTATCTA +AGCGAAAAAAGTCTTGCTAGTGAGCCTTATTTGAACCTGTCAAAAAAAGAATTGGCTTCA +CAACTAACG--------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------ +>rep11a:WARNING ID:99.89% COV:100.0% Best_match:contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180 +ATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTT +ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT +AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA +AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT +GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA +ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT +TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA +AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA +TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT +GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA +CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT +ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA +GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA +ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA +CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA +GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG +>rep14a:WARNING ID:99.5% COV:100.0% Best_match:contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488 +GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA +ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT +GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA +AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA +ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT +GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA +TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA +>rep14a:WARNING ID:78.5% COV:97.01% Best_match:contig00009 len=2060 cov=9.4 corr=0 origname=NODE_14_length_2060_cov_9.400414_pilon sw=shovill-spades/1.1.0 date=20220302:1478..1872:rep14a_2_ORF1(pKQ10)_EFU01917:76.156716 +ATTCGGATGTATAATAAAAAACTGGAACAAGAGAA-GAAAAGAAA-AATTGTGCCAAAAG +AAATCGTGAGTTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACAGATTGGC +ATGCGATGGTTCGGGAAAGTTTAGATAGCTTTGCAAGTCCTCATTACTTGCCTGGA-GAT +GTAAAACCTGTTGATAGAATTATGATAAAAGGGCTGA-ATCAAGATCATTCAGAGTGGGC +GTATATTAGC-AGAAATTTGAAATATAGATTGCGCAAATTGTTGAAAGAAGAAAGCCAAA +ATGATGAATTGACGAATCATTTGCGAGAAACCTTTGCAGAATCGGCAGACGATTTAAAAA +AAGAATTAGACACATGGCTTCTAGGGCTAGACGTAACAGAGGAGTGA |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_3/Plasmid_seqs_test3.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3/Plasmid_seqs_test3.fsa Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,59 @@ +>contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228 +atgttgagcgaaatttattcagctattcttaaaaacggcttacgtacatacaaatatcga +aacagcaccatgaaacctgcaggtcatattgattccagtaggagtggtgctatctttgcg +taccttagcaagcaattaatgaatgttgggcgtggtatggtcattacttcggaagaagct +attttagagaacgaaaagaaactaacgcattggacacctaatacctatcgctttggtact +tatgcggatgattatcgaacagtggttaaaggtcattctgagaaaaacttaagtcaaatc +aacacatttgtagttgatatcgattcaaaagagaaccatcaaggcgaaattattttagcc +tgtttagatcaagtGGGCTACATGCCAACGCTAATTTTAGAATCAGATCATGGTTATCAA +GTTTATTTTGTACTAAAGACACCAGGCTATGTCACAAAGAAAAGCAATTTCAAGGTGATC +GATGTAGCAAAAAAAATTTCAAAAACAATTCGTCTACAGTTGGCTGAAAAATTGTCCGGA +GTGGATCTAGGATGTAACCACTTCGGAATTGCTCGATTCCCACAAGAAAATAATATTGTT +TTTAAAGAAATGAACTATCAGTATTCTTTTGCTGACTGGATTCAATGGTCGATGAAGCTT +GAATCAGATCAAAAAACAAAAGAAGATCGAGAACGAAAACTAATTGTCTTTCCTGAGAAA +AAAGAAATTCGTCAAGTAGATGAACCGTGGTTCGATATGTTACTTCATAAAGCAAACATC +GTCGGCGGAGAAGGACGTCTTGGTCGAAATAATGTGATTTTCACGCTTTCTTTAGCTTAT +TACTCTTCAGGTTATGCATTGGATACTTGCGAATACAATATGTTCACATTCAACGAACGG +TTACAGGAACCGCTATCTGAAGCAGAATTAGTAAAGATTGTACGTAGTGCTTATTCTGGT +AATTATCAAGCAGCAAGCAGAGAATTCATTATTGAATTGTGCCAGCAATGGGTTTCACCA +ACCTTAAAAAATAATGATCTGTTCATTCAACGACGTGGCTGGTGGAAATTTAAAAAGCCA +CGAGATCAAAGAAAATATAGTCATAAAAATGAATGGAAAGAAGATCTATTGGCTTATCTA +AGCGAAAAAAGTCTTGCTAGTGAGCCTTATTTGAACCTGTCAAAAAAAGAATTGGCTTCA +CAACTAACGatgcccaagcgaacacttgataagatcttaaatgagttacgagaggagaat +aaagtcttctacaaggtaacacgaggaagaaatggcggaatgatcattgcttcagtcaaa +acgttgttcgcgagagttattcaactaagtaaagaaaagagactagattattcaacaagg +atcacagaggtatttggactcaacgagagcttagtagaagagacatttagacaattatca +acccccttgaaccctcttaaagaagtgaatctttttgaagtagatacaggttga +>contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180 +ATGGCTAATGAGATTGTAAAATACCACCATGAATTAAATACAATTCCTTTAAGAAAATTT +ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT +AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA +AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT +GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA +ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT +TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA +AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA +TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT +GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA +CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT +ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA +GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA +ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA +CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA +GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG +>contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488 +GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA +ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT +GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA +AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA +ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT +GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA +TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA +>contig00009 len=2060 cov=9.4 corr=0 origname=NODE_14_length_2060_cov_9.400414_pilon sw=shovill-spades/1.1.0 date=20220302:1478..1872:rep14a_2_ORF1(pKQ10)_EFU01917:76.156716 +gtgcgacTGTACAACAAAAAGCTAGAGCA-G-GAACGAAAAAAAGTAATCGTGCCAAAAG +AAATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGC +ATGCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCC-GATTGAT +ATAAAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCT-GAGCCTTCTAATTGGTC +G-ATAATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAA +ATGATGAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAA +AAGAATTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 test-data/test_3/results_tab_test3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3/results_tab_test3.tsv Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Database Plasmid Identity Query / Template length Contig Position in contig Note Accession number +Inc18 rep2 100.0 835 / 1494 contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302 2..836 repR(pEF1) DQ198088 +Rep3 rep11a 99.89 945 / 945 contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302 308..1252 repA(pB82) AB178871 +Rep_trans rep14a 99.5 402 / 402 contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302 1703..2104 ORF1(pKQ10) EFU01917 +Rep_trans rep14a 78.5 400 / 402 contig00009 len=2060 cov=9.4 corr=0 origname=NODE_14_length_2060_cov_9.400414_pilon sw=shovill-spades/1.1.0 date=20220302 1478..1872 ORF1(pKQ10) EFU01917 |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 tool-data/plasmidfinder.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.loc.sample Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#value name path +test-db-2022 "Test Database" ${__HERE__}/test-db |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of plasmid database to plasmidfinder --> + <table name="plasmidfinder_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/plasmidfinder_db.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 2b6e795b22a9 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Sep 19 08:47:42 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of plasmid database to plasmidfinder --> + <table name="plasmidfinder_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/plasmidfinder_db.loc" /> + </table> +</tables> |