Mercurial > repos > iuc > plasmidfinder
changeset 0:2b6e795b22a9 draft
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Mon Sep 19 08:47:42 2022 +0000 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plasmidfinder.xml Mon Sep 19 08:47:42 2022 +0000 @@ -0,0 +1,149 @@ +<tool id="plasmidfinder" name="PlasmidFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description> + Plasmid identification in bacteria. + </description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro='xrefs'/> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + mkdir output_dir && + mkdir temp_dir && + plasmidfinder.py + -i '$input.input_file' + -p '$input.database_name.fields.path' + -l '$options.min_cov' + -t '$options.threshold' + #if $input.input_file.ext == 'fasta' or $input.input_file.ext == 'fasta.gz' + -mp blastn + #else if $input.input_file.ext == 'fastqsanger.gz' or $input.input_file.ext == 'fastqsanger' + -mp kma + #end if + -x + -o output_dir + -tmp temp_dir + #*====================================== + LOG file + ======================================*# + | tee '$log_file' + ]]> + </command> + <inputs> + <section name="input" title="Input parameters" expanded="true"> + <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"/> + <param name="database_name" type="select" label="PlasmidFinder database"> + <options from_data_table="plasmidfinder_db"> + <validator message="No PlasmidFinder database is available" type="no_options"/> + </options> + </param> + </section> + <section name="options" title="Options"> + <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)"/> + <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help="Choose a minimum identity value (default: 0.95)"/> + </section> + <section name="output_files" title="Output file selection"> + <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection"> + <option value="data_json">JSON file result</option> + <option value="hit_fasta" selected="true">Hits in genome</option> + <option value="plasmid_fasta" selected="true">Plasmid hits</option> + <option value="result_tsv" selected="true">Plasmid results</option> + <option value="result_txt" selected="true">Raw results</option> + <option value="logfile">Log file</option> + </param> + </section> + </inputs> + <outputs> + <data name="json_file" format="json" from_work_dir="output_dir/data.json" label="${tool.name} on ${on_string}: data.json"> + <filter> "data_json" in output_files['output_selection'] </filter> + </data> + <data name="hit_file" format="fasta" from_work_dir="output_dir/Hit_in_genome_seq.fsa" label="${tool.name} on ${on_string}: hit_in_genome.fasta"> + <filter> "hit_fasta" in output_files['output_selection'] </filter> + </data> + <data name="plasmid_file" format="fasta" from_work_dir="output_dir/Plasmid_seqs.fsa" label="${tool.name} on ${on_string}: plasmid.fasta"> + <filter> "plasmid_fasta" in output_files['output_selection'] </filter> + </data> + <data name="result_file" format="tabular" from_work_dir="output_dir/results_tab.tsv" label="${tool.name} on ${on_string}: results.tsv"> + <filter> "result_tsv" in output_files['output_selection'] </filter> + </data> + <data name="raw_file" format="txt" from_work_dir="output_dir/results.txt" label="${tool.name} on ${on_string}: raw_result.txt"> + <filter> "result_txt" in output_files['output_selection'] </filter> + </data> + <data name="log_file" format="txt" from_work_dir="output_dir" label="${tool.name} on ${on_string}: log file"> + <filter> "logfile" in output_files['output_selection'] </filter> + </data> + </outputs> + <tests> + <!--test_1 with default value and all output files for contigs --> + <test expect_num_outputs="6"> + <section name="input"> + <param name="input_file" value="contigs.fasta"/> + <param name="input_type" value="genome"/> + <param name="database_name" value="test-plasmindfinder-db"/> + </section> + <section name="output_files"> + <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/> + </section> + <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/> + <output name="hit_file" value="test_1/Hit_in_genome_seq_test1.fsa" ftype="fasta"/> + <output name="plasmid_file" value="test_1/Plasmid_seqs_test1.fsa" ftype="fasta"/> + <output name="result_file" value="test_1/results_tab_test1.tsv"/> + <output name="raw_file" value="test_1/results_test1.txt" lines_diff="2"/> + <output name="log_file" value="test_1/logfile_test1.log" lines_diff="7"/> + </test> + <!--test_2 with default value and for fastq file --> + <test expect_num_outputs="4"> + <section name="input"> + <param name="input_file" value="data.fastq.gz"/> + <param name="input_type" value="raw"/> + <param name="database_name" value="test-plasmindfinder-db"/> + </section> + <section name="output_files"> + <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/> + </section> + <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/> + <output name="result_file" value="test_2/results_tab_test2.tsv"/> + <output name="raw_file" value="test_2/results_test2.txt" lines_diff="2"/> + <output name="log_file" value="test_2/logfile_test2.log" lines_diff="7"/> + </test> + <!--test_3 with default value and for fastq file --> + <test expect_num_outputs="3"> + <section name="input"> + <param name="input_file" value="contigs.fasta"/> + <param name="input_type" value="genome"/> + <param name="database_name" value="test-plasmindfinder-db"/> + </section> + <section name="options"> + <param name="min_cov" value="0.2" /> + <param name="threshold" value="0.6"/> + </section> + <section name="output_files"> + <param name="output_selection" value="hit_fasta,plasmid_fasta,result_tsv"/> + </section> + <output name="hit_file" value="test_3/Hit_in_genome_seq_test3.fsa" ftype="fasta"/> + <output name="plasmid_file" value="test_3/Plasmid_seqs_test3.fsa" ftype="fasta"/> + <output name="result_file" value="test_3/results_tab_test3.tsv"/> + </test> + </tests> + <help>< with hundreds sequences. + **Input** + It can analyse raw data using a k-mer approach based on KMA or a blastn for genome assembly. + A database is need obtained from the plasmidfinder database. + **Options** + You can modify the coverage value (% of matching sequence on the total target sequence) + You can modify the identity threshold (% of shared nucleotide on the match) + **Output** + Some output files are availables + - A fasta file with all available hits detected in the genome + - A fasta file with all plasmid sequences from the database + - A summary of the analysis in tabular format + - A Raw result file in text format + - A JSON file could be use for other boinformatic analaysis + - A log file with analysis parameters + + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fasta Mon Sep 19 08:47:42 2022 +0000 @@ -0,0 +1,603 @@ +>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 +CAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTAC +CATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAA +GCCACTTCTCCTCATCCAACGCGTCAGTTTTTGACAGAATCGTTAGTTGATGGCGAAAGG +TCGCAAAGTAAGAGCTTCTCGAGCTGCGCAAGGATAGGTCGAATTTTCTCATTTTCCGCC +AGCAGTCCACTTCGATTTAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTATCAAGATA +ATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAA +ACTCTGCAGGTTGGATACGCCAATCATTTTTATCGAAGCGCGCATAAATTTGAGCAGATT +TGTCGTCACAGGTTGCGCCGCCAAAACGTCGGCTACAGTAACTTTTCCCAGCCTCAATCT +CATCTCTCTTTTTGCGTTCTGCTTCAATATCTGGTTGAACGGCGTCGCGTCGTAACCCAG +CTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCC +GAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCGACAGCTTGGTTTT +TAGTGAGTTGTTCCATTCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATATCTGACTT +TTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAAGCGG +CTCACCTTTAGCATCAACAGGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTA +GCGAACTGCGATGGGCATACTGTAACCATAAGGCCACGTATTTTGCAAGCTATTTAACTG +GCGGCGATTGCGTACCCGACGACCAAAATTAGGGTCAACGCTACCTGTAGGAAGTGTCCG +CATAAAGTGCACCGCATGGAAATGAAGACGGCCATTAGCTGTACCATACTCAGGCACACA +AAAATACTGATAGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCTCGGCAGCAAGAAC +CATACGACCAATATCACGAAAATAGTCACGCAAAGCATTGGGATTATCATAAAACGCCTC +TAATCGGTCGTCAGCCAACGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGC +CTGTCGCATTGCATTCATCAAACGCTGAATAGCAAAGCCTCTACGCGATTTCATAGTGGA +GGCCTCCAGCAATCTTGAACACTCATCCTTAATACCTTTCTTTTTGGGGTAATTATACTC +ATCGCGAATATCCTTAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACTGCGTAACCGT +CTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTCTATAGTGTTATT +AATATCAAGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCATTAACTTCTCAGT +AACAGATACAAACTCATCACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATACATATC +ACCATTATCGAACTCAACGCCCTGCATACGAAAAGACAGAATCTCTTCCAAGAGCTTGAT +GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGGGGATTGAGAAAGAGTAGAAATGCC +ACAAGCCTCAATAGCAGGTTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAGCGTG +ACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAA +AACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAAT +ACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAAT +ACCATGAAAAATATCAACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTT +TGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGATGAACTAA +GTCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTGATTTGGTCATTGGTAAAATACTG +ACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCTT +GGAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGCAGTAGACTCCTTCTGTTGATA +AGCAAGCATCTCATTTTGTGCATATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCGA +CTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGATT +GTCCAGTTGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCGGCGTCAACCATACCAGC +AGAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAAGCTCAGGAAATGCAGCAGCAAG +ATAATCACGAGTATCCTTTCCTTTATCAGCGGCAGACTTGCCACCAAGTCCAACCAAATC +AAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTT +ACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGGAAC +ATTAGAGCCTTGAATGGCAGATTTAATACCAGCATCACCCATGCCTACAGTATTGTTATC +GGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAACAA +TTTAGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAACAT +AAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAA +ACCAATCCGCGGCATTTAGTAGCGGTAAAGTTAGACCAAACCATGAAACCAACATAAACA +TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTCACACAGTCCTTGACGGTATAATAA +CCACCATCATGGCGACCATCCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGA +ACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATCAAAAGCA +ATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAGATGTATCCATCTGAATG +CAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAACGTTGAC +GATGTAGCTTTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGA +ACCAGCTTATCAGAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATT +AAACTCCTAAGCAGAAAACCTACCGCGCTTCGCTTGGTCAACCCCTCAGCGGCAAAAATT +AAAATTTTTACCGCTTCGGCGTTATAACCTCACACTCAATCTTTTATCACGAAGTCATGA +TTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGTCACATTAAATTTAACCTGACTAT +TCCACTGCAACAACTGAACGGACTGGAAACACTGGTCATAATCATGGTGGCGAATAAGTA +CGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAAGCCTTCAAGAAGGT +GATAAGCAGGAGAAACATACGAAGGCGCATAACGATACCACTGACCCTCAGCAATCTTAA +ACTTCTTAGACGAATCACCAGAACGGAAAACATCCTTCATAGAAATTTCACGCGGCGGCA +AGTTGCCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGT +TAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACA +TAGTGCCATGCTCAGGAACAAAGAAACGCGGCACAGAATGTTTATAGGTCTGTTGAACAC +GACCAGAAAACTGGCCTAACGACGTTTGGTCAGTTCCATCAACATCATAGCCAGATGCCC +AGAGATTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAGAGGTTTTACCTC +CAAATGAAGAAATAACATCATGGTAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTAT +GCAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCA +TTTGGCGAGAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAAATGTTTTTGAGATGGC +AGCAACGGAAACCATAACGAGCATCATCTTGATTAAGCTCATTAGGGTTAGCCTCGGTAC +GGTCAGGCATCCACGGCGCTTTAAAATAGTTGTTATAGATATTCAAATAACCCTGAAACA +AATGCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGCCAAGAAAAGCGGCATGGTCAA +TATAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCATTAACACCATCCTTCATGAACT +TAATCCACTGTTCACCATAAACGTGACGATGAGGGACATAAAAAGTAAAAATGTCTACAG +TAGAGTCAATAGCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCGCCAACGGCGTCCA +TCTCGAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAGACGACCAATCT +GACCAGCAAGGAAGCCAAGATGGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTTGAA +TATTAGACATAATTTATCCTCAAGTAAGGGGCCGAAGCCCCTGCAATTAAAATTGTTGAC +CACCTACATACCAAAGACGAGCGCCTTTACGCTTGCCTTTAGTACCTCGCAACGGCTGCG +GACGACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAGACATTACATCACTCCTTCTGC +ACGTAATTTTTGACGCACGTTTTCTTCTGCGTCAGTAAGAACGTCAGTGTTTCCTGCGCG +TACACGCAAGGTAAACGCGAACAATTCAGCGGCTTTAACCGGACGCTCGACGCCATTAAT +AATGTTTTCCGTAAATTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAATGTTGACGGG +ATGAACATAATAAGCAATGACGGCAGCAATAAACTCAACAGGAGCAGGAAAGCGAGGGTA +TCCTACAAAGTCCAGCGTACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCG +GTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAAAATCGAAATCATCTTCGGTTAAATC +CAAAACGGCAGAAGCCTGAATGAGCTTAATAGAGGCCAAAGCGGTCTGGAAACGTACGGA +TTGTTCAGTAACTTGACTCATGATTTCTTACCTATTAGTGGTTGAACAGCATCGGACTCA +GATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGT +GACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAAGCCACTT +>contig00002 len=3532 cov=5.1 corr=0 origname=NODE_2_length_3532_cov_5.072834_pilon sw=shovill-spades/1.1.0 date=20220302 +CGGACTACCGTCCCGAAATACTCATATAAATGCCAAAAACCATTTGCTGTCAAAACGGCG +TAACAATTTCCTACTGTCAGTTTCTTTTTAATTTCTGCTTTACTGGAACCATATTTATGT +TGAGCATATTGGTCCCACTCTGCAAACTCATTTCCCTTGATCATCTGATTGAATGTATTG +TCAGAAACAAAATAATAATCCTCTTGATCTTTTTCCCCAGGTCTTGGTGATCGATTCGTG +TAAGTAATGATCTTTTGTTCCGGCTGAAAAATAGCTTCTGCGAGTGAAGTTTTTCCAGAA +CCAGAAGGACCGATAAATACATAGCAATAATTCATTGTCATTTCTCCTTTGATGATTGAA +CAAGTGAAAAAGCTTTGGAAAATATTTCCAAAGCTTTTAAAAGTAACTTTGCTTTTTTGT +ATATTATACCAGCAAGCCAGTCACAATAGCACTTAAAAAGCTGACTAAAGTCGCTGTTAG +CAAAATTTTCAATCCGTGTTTTGCGACAAGATTTCCTTTTTCTTCATTTAATCCCTTCAT +CGCACCAGAAATGATCCCGATAGAAGAGAAGTTGGCAAATGAAACGAGGAAGACAGATAT +AATTGCTGTTGTACGCTCAGTAAAATGGAAAGATTTTCTGTAGTTGCTTCTTTCCGTTTC +TTTGTGAATTTTTACCAGTCATTTTTTACTGGATTGTTATTTTTTATAAAATATGATAAA +ATTTTGGTAGCGCTTTATAAGCGCGTTGCTTTTTCAAGAATAAACTCTCATTATTTTTTT +AACTGGCTGCTCGAAAGAGCAGTCTTTTTTATTATTTATCCGTCTCTTTTACAAACAATT +CTTCGTTAGGACTGTTGTAATAATTTGAATTTAATTTAAGTTCTCCGTTGGAATTGTTTT +TTCCAATTACGGATAATAGCATGGGGCTAAAACCTAATATTCCTAGAGAAATAGAACCCA +GTACCAACACAGTTTTTTTTAACATAGGTTATACCTCCACTTTTTTTAACGCTACCACTT +GTATACACATTTTAAATACTAGCCTTCAGTTTATCAAATGTTTAAATTGAACGGATATAA +ATCAAAATTAAATTTTCAAAAGTTGTTCTAAAAAATTTTTCTTTTTTGGAAGTTACTCTA +ACTTTTTTTGCTTGTGGTGCTTGGTATGTTTTCTTCGCCGACCGTTTAGGTTCTTGACCA +TTTTCTCTTATAAGTGGGATTTTTACCACGTTGAGAGAAAATGGTCAAGAACCTGGGAGG +CGGAGAATGCCCTTAATACCAAGCACCGCAAGCCTTTCCCATACTTTATTCGATGATCCC +ACGATGATCTCATAATGATTCTACAATGACCCTACGATGATCAAAATTCTCAAAAAAAAT +AAACGAAATTTCAAACGATTTTTTTGAAATTTTGTTAAAATCACATTTGTTTTTTTATGA +CTTTTTCAACAAAATCGATTAGAATTTATTTTGTTTTTCCACCAAAAATTGAGTGAGATT +TCAACCTATTTTAAGCAATAAGTCACCATATAGTTTGATAGTTTACAACTATAAACATTG +ATTGTTTACAGTTGTAAACTATTTTTTCTTTCTCATAAAAATTTGAGTGATCTCCCCATC +AGGTAGTACAACTTTTTCCTCTACTATCCGAACTAACTTCTAGAAAATTTTAGAGATTGG +TTCTATTAGATTTCCAAATTTGCCACCACTTTTTTTCAATAAGTGGTTGTGTATTGTCTG +CTTTTTTTTCAGAAAAGGCAGTTGATTCGGTTGTTGGAGTTTCTTCTGTATAAGTTAAAT +GGAGCTGTTCTTGTAGGTTCTCAATTTGTTGGTTCGCTTGTAGAGTGAGTTGTTGTTGCT +GGTCGAGTAATTTTTGCATTTGTTTTATTTGATTATCTTTTTCTTGTAGCTGTATATCTT +TTCGATTTAACTGTTTTTCTAGGAAAGAAAGGAGTTTTAATTCGGAAACTTGGTTGGTGT +TTTTATGGTTTTTGGTTTTTGATTTTTCGCCAACTAGTTTTCGATTTAAGTTTGCGTTAT +CGACTAAAAACATTGATTTTATAGCTTTTTGACCGGTTTCGTTAATCACAAACTTGTTTC +CGTTTTTTGCAAACCAAAGTTTTCGATTTTTGTCAGAAACTTTTTTGTTAATTGCTGTTT +TACTAACTCCTAATTCTTCCGCAAGTTCTTTGATTGTTTTATCTGCCATAAATACTCCTT +AAGCTTAATCGAATAAGTTTTGTAAATTTCCTAGTAAATCTTGTTTGAGTTTGTTTGAAA +GTTCTCGTTTTTCTGCCTGTTTTTCTTCAGTTTGTTGTTGTTGTTTAAAATCAGCTTCAT +GAGTGCCTAAGGGAAGATTTAGTATTCGATCTTTAGCGCGCCATTTTTCTTCTCGTGTTA +ATTCTCCATTGTGATCAATATTAAATAATTTGGTTCTGTTGCAAAGTTTTAAATAAAGAA +TAAAATCCCTTACGGTATCTATGATTTAAGCTGGGATTCCCAATAATACCTTGATTTCAG +TACAGACCGAAAACCCGAAGAGAGTGCCTTCTTTTCGGGTTTTCTTATATAATCCTCGAA +TGGCTTCCATGCCTTTAATCGTGGTAGAGGCAGTGCGTAAACTTCGATAGAATTTATTGC +GTCTCTTTACTGGACGATGGTCTTGTTCAATCAAATTATTCAGGTATTTAATGGTACGAT +GTTCTGTCCCTTGATAAAAGCCGTATTCTTTTAGTTTCTTAAAGGCACTTGTAATAGAGG +GGGCTTTATCTGTGACTACAACCTTCGGTTCATCAAACTGCTTCACTAACCGCTTAAGAA +AAGCATAGGCTGCTTGTGTGTCCCGTTTTTTACGTAACCAAATATCCAAGGTTAAACCAT +CTGCATCGATGGCTCGATACAAATAATGCCATTTTCCTTTAATTTTGATGTACGTTTCAT +CCATTTTCCATGAATAAAAGGATTTTTTATTTTTCTTTTTCCAAATTTGATAGAGTAGTT +TGCCATATTCTTGCACCCAACGATAAATCGTCGTATGAGAAACGTTAATGCCACGATCAT +ATAAGATTTCTTGAACTTCACGATAGCTAAGGTTATAACGAAGATAGTAGCCCACGGCTA +CAATAATCACATCCTGCTGAAATTGCTTTCCTTTAAAATGATTCATCGTCATTCCTCCTG +CTATCTTTTTCTATTATTCTACCTTATTTGATAGTAGATTTAAAACTTTGCAACAGAACC +GATAATCTTATACGTGGGGAATTTCATTTCCTTTCTGAAAAAGATATGAACATAATCCCC +TCGTTTAAAGATTCAGGTTATATTCCTGATACGAAGGCTATGCTTATTTACGATGAAACA +GGGCAATTAGAAAATTATTTATCAGAGATAAGTGGTGCAAGACCAAATAGACTTACTGAA +GAAAATGCTAATTTTTTGTTGTGTAATTTCTCTAATCTATGGTTGATGGGAATCAACGTT +CTAAAAAGAGGAGAATATGCTCGTTCATTAGAACTCTTATCACAACTTCAAA +>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 +GATGGGCGACTTCTGCCTAATTCTGTTAAAGAAAAAAGAAGTGGTTTTTAGGCGGGAAAA +TTAGCCCCCCTCTTTTTATATCTCTTTTTAAACCTCTTTTTAAACCTCTTTACCGTAAGC +TGTGTCCTTACTCTACCAATGGATACAGAATGTTATGAAGGACATTTTGTCTGTTTATGA +AGGACATTTTGTCTGTTTATGAAGGACATTTTGTCTGTTTATGAAGGACATTTTGTCTGT +TTGAACGTCAAATATGAATGTCTTGACATTTAAAAAATGTCATTCATAATTGGATTGAGG +TGATTATATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAG +AAAATTTACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAA +AGGGGATAAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGC +AACTGCAAATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTT +ACGCTTTGGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGA +ATTTAAAATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGC +ACTGCCTTTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGA +GCTACAAAGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGG +TTTCGCATATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAA +GCAACCTGATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTT +CAAAGGACTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTA +TCAATTTACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAAC +CAAAGAAGACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACC +CGCTACAACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACA +AATCAAACAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTC +GGAAAAAGAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAGCAACCTAG +GAGGCAACCAGTATGCAACCACAAGAAACCTTTACAATAAAGGAATTGTCAGATCTTTTT +AAGATGAGTAGGCAAGCAATATCGAAACATATCCAAAAATTAGATTCTTCCATGATAGCT +AAAAATGAGCGTGGTTATAAGGTTGTATTGCGTTCTGGAGTATTGCAACTTGCTCGCAAC +TTAGACAATCAAAGGTTGCTAGATAAGTTGCATAAACATGAACAAAACAACGATAAAAAT +GCTTATATACCAAACAAAAACGTGGTTGCAAACAAGTTGCTAGATCAGTTGCGTGAAGAA +AATGAATTTTTACGAGAACAACTTGCCCTCAAAGAGCAAAATAATTCTCATATACAAAAA +CTACTCGACCAGCAACAACAACTCACCCTGCAAGCCAACCAACAAATCGAAAAACTTCAG +GAGCAACTGCAGTTGACTTATACGGAAGAGTCTTCAGAGAATAGTTCAACGACTCTTTCT +GAAGCAACAGAAACAATGGACGAACAAACAAAGAATTGGAAAAAATGGTGGCAGCTATGG +AAATGAAGAAGGAAATACTTATGACAAAAAAACACTTGCTATTCGGTTCTATCCTACTAG +GAATATTAAGCTTTAGCCCAATGTTATTATCAGTGGCCAACAAAGGAAATAAAAAAGGGG +AACTAAAACTCAATCCTAATTACTACAACAGTCAAAATGAGGAAGTATTTGTAGAAAAAC +TTGATAAATAAGAAAAGACTGCTCGTACGAGCAGTCTTTCTGAAAGAGATTATCCTATTA +TTAACCTTAGAAAAGAATAATAAATGAATATGAGATATGTAAAAAGCATAACAAACACAA +ACAAAAATAACAAGTATTTAAAAAATGACCGATCAATATTCACAAAGAATTAGAAAGAAA +CAACCGCAGAAAACCAAGCCTTAAAAAGAGCTTTTAACCTAGACCAATAAAAATTCACAA +AATCAGCGCCTGGATCCCTTGGTACAGGCGTTACTTGGTAGTATACACATTATGTCTACT +AGCTGTTTAAATAACTGATCTTATAATTTTATTTAAACGATTATGAATTCAAAACTACTT +TTTATGACGTTAATCATTGTTATATAATAAAATGTTATATAATAAAATTACTAAGATTAT +TTAATATAACAAGCAATTTTAAAAAAACGAAAAGGAAAAACAATCATGAAAAAGAAAGTA +TTAAAACATTGTGTTATTCTAGGAATATTAGGAACTTGTCTAGCTGGCATCGGTACAGGA +ATAAAAGTTGATGCAGCTACTTACTATGGAAATGGTCTTTATTGTAACAAAGAAAAATGT +TGGGTAGATTGGAATCAAGCTAAAGGAGAAATTGGAAAAATTATTGTTAATGGTTGGGTT +AATCATGGTCCATGGGCACCTAGAAGGTAGTGGTAGGGAGGTTATTATAATGGATTTTAC +TAAAGAAGAAAAACTTTTAAATGCAATTAGTAAAGTATACAATGAAGCAACTATAGATGA +CTATCCTGACTTAAAAGAAAAGCTCTTTCTTTATTCTAAAGAAATCAGTGAGGGAAAAAG +TGTTGGTGAAGTTAGTATGAAATTAAGTAGTTTTCTTGGAAGATATATTTTAAAACATAA +ATTTGGATTACCTAAATCTTTAATAGAATTACAAGAAATTGTTAGTAAGGAATCTCAAGT +ATATAGAGGATGGGCTTCTATTGGTATTTGGAGTTAATTCTTTGGAATAAAATGAAAATG +GGACTGAAGAATCAATTCTGATTCATCAGTCCCATAAATTATAGAGCCGAAAAATTATCA +TATTTATAGATTTATTAATAGTAAATGGCATAAGAATCTTTGAACAACGAAAAAAATGTA +GCTCTACCTAATTATTGATTTGCAACAATTTCACCGAAGGTGAAACAAGCGAAACTTTAC +AAAAAGTGGCTAGCATTTGCTAGTCTTTTTTGTATTGTGGAGAGTGG +>contig00004 len=3138 cov=2.3 corr=1 origname=NODE_4_length_3138_cov_2.261375_pilon sw=shovill-spades/1.1.0 date=20220302 +TTTTTTTCCGATATAATTTGCTGGTAAATCTATCACAGCCAATGAGAGTCCGGGATTGCT +TTCTTCCTGATAATCTTTCCGTTGGTATAAAATCTTTTCGCCTAGATATACAGTAATCCA +TTGATGGTTTCCTTTGATTAGTAAATTTGCTTCGTCCAACGGTTTTTCAAGTGTCGTTTC +CATAATGAATGTTTCGTCTTTATCCACGGTAGGAATCGTACGAGTGTACTTGCTGTCAAA +CTTAAAATCAGGATCATCTTTTGTATAGAAAACCCACGAATCTTTTATTTCTTTCATTTG +ATTGCTGTCCGCAGGAGAAAAAATAAAATAAAAGAAATAAGCAATTCCTGTTAAAAATAA +CAATGATAATATAATGATTATGCTCCACTTTATACGTAAATAAAAAGATTCTTTTTTATT +ATATATGTTATTAAAAAAAGACATAAAGGTATTCCTTTGAGAGTATAAAATATTTTGTGT +AAATGAAAAAATCCATACAAAAAAGGAAGTCCCTTCTGTAGAATAAAGTTAACGACAACC +AATTCACAGAAAAGAGGACTTCCCTATGAATGATTTTACTACAGAAATTGTGCAAACTCT +AGTCACTAAAGGCGATTTAAATGAATTATTCCGTTCGCACTTAGAAAAAGCGATAAACAC +ACTCCTACGGACTGAATTAACGGCTTTTTTAGATTACGAAAAATATGATCGCACTGGTTT +TAATTCAGGTAATTCGAGAAACGGTTCTTACTTTCGATCAATCAAAACCGAATATGGTGA +ATTAACATTGGAAATACCTAGAGATCGTAATGGTGAGTTTAAACAACAAACTTTACCAGC +CTACAAAAGAACAAACGATACATTGGAAACCACTATTATCCATTTATTCGAAAAAGGTGT +TACGATGTCTGAAATTGCTGATTTGATCGAAAAAATGTACGGTCATCACTATACTCCACA +AACCATGTCCAACATGACTAAAGTTCTGACTGAAGAAGTAAATGCCTTTAAATCCAGAGC +CTTAAATGATAAGTATGTCGCTATTTTTATGGACGTTACTTACATTCCACTAAAACGTCA +AACTGTATCCAAAGAAGCGATTTATATTGCCATTGGTATACGAGAAGACGGCACTAAAGA +AGTACTGAGTTATGCGATTGCTCCAACTGAATCAACATACGTTTGGAATGAGCTGCTACA +GGATATTAACTCCAGAGGAGTTCAAGAAGTCTTGCTTTTTATTACGGACGGCTTAAAAGG +CATGAAAGATACTATCCATCAAATTTATCCTAAAGCAAAATATCAGCATTGTTGTATCCA +TGTATCTCGTAACATCGCTCATAAAGTACGTGTCAAAGACCGAAAAGAAATCTGTGATGA +CTTTAAGGCTGTTTATCAAGCTAACTCAAAAGAAGAAGCGAATACCTTCTTATCCGGCAT +GATTGAGAAATGGAAGAAAAACTATCCTAAAGTGACGCAGTCACTCATAGAAAACCAAGA +CTTATTAACTTTTTATGATTTTCCACCTAGCATTCGTAGAACCATTTACTCAACCAATCT +AATCGAGTCTTTCAATAAGCAAATTAAAAGATACAGCCGTAGAAAAGAGCAGTTTCAAAA +TGAAGAATCACTAGAACGCTTTCTAGTCAGCATTTTTGATACATACAATCAAAAATTTCT +AAACAGAAGCCATAAAGGTTTTCAACAGGTAACCGATACATTAGTTTCAATGTTTACTGA +GTAACTAATTATTTTGCAGGAGGACAATTTATTTACACAAAATTATTGACGCTCCCTAAC +AAAATCCCACCTACTTTATCTTATAACTTGTTTTTTTGCATAAAAACTAAATAAAGAGTG +CGGCATTTCGCACTTTTTTATTATATATTATTTGTCAAATTAAGCGAGACAAAACTTTCC +ATTTACGTAACTCAAAAAAACTTCTAATGGTGTTTGGTAATTTAGTGATTTTCTAGGGAT +ATGGTTTCTTTTGGACGCAACGGATGAGATGAATCCTTGATTGACTTGGTGGAAGTCCAT +TTCTTTTGGTAGTCCATCTTTTCGGAGGAGTCCGTTTGAATGTTCATTTAATCCCCGTTG +GGAAGGCGTTCCTGGGTCTGCGAAATAAATATCAATATCATTCGTATTACTAATACTTTT +CCAATTAGAGAATTCTTTTCCACAATCAAAGGTAATTGATTTGAAAAGATTTTTGGGTAC +GGATTGAAGCCATTCATTAATCGAATTTTCAATATCAACTGCCTTACGGCCTTCTGGTTT +CAAGGCGATAATGGCTTTTGAAAGTCGCTCAACGAGTGTGATGACGGCACTTTTATGGTG +GATGCCGACAATCGTATCACCCTCTAAATGTCCAAATTCTTCTTCGAAAACGACATAATC +TTTTTTACGTTCAGAAATATTTCTTTTGAATGCCTGTTTTCCACGTTTTTCCTTATAACC +ATTTGGTTTTCGTTTTCCTTGCATCGGTAAATGTAAAACATTGAATTCTCCCGTCTTAAA +CCGGCGATAGAGGGTACTTACTGAACAAGAGAAGGTTCGCTCTGCACGGCCAATAATGAC +GTCTGGGGTCCAACCTTCAGTTGATCTTTTTGCAATGTATTCTTTTTCCTCAGCAGGAAA +AATGATTTCGGTTCTCCCACAACGTCGCTTATTTTCTTTGTATTGTTCAAAGTATTCAAG +TGCTGTTCCACCACATTTGAGAAAGTTATAGACATTGTAAATTGTTTGGCGTCCACGTTT +AAGCTGCTTCGCAACGATAGCAACCGGAGTTTCTTGATGAAAATATGCTTCTATCATTAC +AAGCTCGTTTGGTGTAAGATGGGTATAAGTCATTTATGTTCACTCTCCTTGTATGCTTTA +GCGGGTATTACAATTGGAGTGTAACATAAATGGCTTTTTTATTTGTCTCGCTTAATTATA +CAAACGGCGTTGTTAAATAAATAGGAACAAAAAAATTAAATTATTTAATACACACATTAG +GGATCATTCATTGAAGGATTAGAAGACAACGAGGATGGCGAAAAATATGATTACAATAGA +AAAGTCGTTCTAAACCAATCAGTTCCTAGTATCACACAACGCAAGCCAGTCGATTTGGTG +AGATTAGAGGAGTGAAAG +>contig00005 len=3026 cov=4.4 corr=0 origname=NODE_5_length_3026_cov_4.409452_pilon sw=shovill-spades/1.1.0 date=20220302 +AATGATTTTTCCGGTGTAATCGTGATTGCTGTATTTAGCATAACTTCGCCGACTCTTGTC +GCATTTGGCTTGGCTTGTAGTAGGCGATCTTCTCCAATCAACTCTTCTACGAAATCGTTT +GCAGGATGACGTAAAATATTTTCTGGTGTATCAAATTGGATCACACGGCCTTCACTCATG +ATGGCGATACGGCTTGCTAGTTTAACAGAATTAGGCAGAAGTCGCCCATCCTCTATAGGT +GGGTGATGAATGCCGTTCGGTATGAGGGTTACCGTTGGTAACTCGAAGACCGACAACTAA +GGCGTATTGCCTTTTTATTTTGTTCCATGTTACAATCAGTCTATACAAGAAATGAGTTGA +TATAACATGGAATTAGATACAAATAATCATTCAGTATTTCTTCTTTATTACCACCTTGTT +TTAGTAACGAAATATCGTAGACAAGTGATTGATGATGAAATATCTGATTATGCCAAAACT +ACTTTTGAAAGAATTTCAGAATCGTATCACATTACTTTAGTGGAGTGGAATCATGATAAA +GACCACGTTCATATTATGTTCAAAGCTCAACCTAAAACAGAATTGACAAAATTCATCAAT +GCCTATAAAAGTGCCAGCTCAAGATTGATAAAACGTGACTTTCCAAGAGTCAAACAATTT +CTTTGGAAAGAAATGTTCTGGTCTAAAAGTTTTTGTCTTCTGACAACTGGTGGCGCACCA +ATTGATGTGATTAAGAAGTATATCCAAAATCAAGGAAACAATCATAAATAGAAAGTAGGT +GAACTTTATGGAACAACTAAAAGCATACAAATTCAGAATCTATCCAACAGAGGAACAAGA +AATCTTCTTTGCCAAATCTTTTGGTTGTGTCCGTAAGGTCTACAATCTAATGCTTGATGA +CCGAAAAAAGGCGTATGAAGAAGTTAAAAATGATTCTTCTAAAAAAATGACTTTTCCGAC +ACCAGCTAAATACAAGAAAGAATTTCCGTTTTTGAAAGAAATTGATAGCCTTGCTTTAGC +CAATGCCCAACTTAATTTAGATAAAGCATACAAGAATTTTTTTCGGGATAAATCCGTTGG +ATTTCCACGTTTCAAAAGTAAGAAAAATCCTGTTCAGAGTTATACAACGAATAATCAAAA +TGGTACAGTTGCTTTGATTGATAGTAAATTCATCAAAGTTCCTAAATTGAAGTCATTAGT +AAGAATTAAGCTTCATAGACAACCAAAAGGGATTATCAAATCTGCTACAATATCACGTCA +TTCTAGCGGTAAATACTATATTTCTTTGTTGTGTAAAGAAGAAATTATCGAATTACCTAA +AACTAATTCCACAATTGGTATTGACTTAGGTATTATGGACTTTGCGATTCTTTCTGATGG +ACAAAAAATTGATAATAATAAATTCACGTCCAAAATGGAAAAGAAACTAAAGCGTGAACA +ACGCAAATTGTCTAGGCGTGCTTTATTGGCTAAAAATAAAGGTACCAATCTATTTGAAGC +TAAAAATTATCAAAAACAAAAACGCAAAGTAGCTAGATTGCATGAAAAAGTAATGAATCA +ACGTACTGATTTTCTGAATAAGTTGAGTACAGAAATGATCAAAAATCACGATATTATCTG +TATTGAAGACTTAAACACAAAAGGTATGTTGCGAAATCATAAATTAGCTAAAAGTATTTC +TGATGTTTCTTGGTCAAAGTTTGTGACTAAATTACAATACAAGGCTGACTGGTATGGACG +AAAAATCATCAAAGTAGATAAATGGTTTCCGTCTAGTCAGATTTGTTCAGAGTGCGGACA +TAAAGATGGCAAGAAATCTCTTGAAATTCGAGAATGGACTTGTCCTGTTTGTCATACTCA +TCATGATCGTGATATCAATGCTAGTATCAATATTCTGACCGAAGGTCTAAGACTACATTC +TATGGGATTGGCTTAGATCCAATCATCAAGAACCGTAGGAACTACGGGGATAGCTTGGTA +AATAAGAGACACCGCTGTTAGTAAAGAAATACGCTATCAAGTATGCTCTATTCCCAAGAA +GCTCCCACTTCAAGCGTTAAGAACCGTCAGGTTTAGCTAAGTGGTGAGTAGTTCACACAG +GTTCGCGCATTTTTCAAAACTGCCAATCCAAAACCTTGCTTCCTACGGTCGCCAAAAAGG +TGTGATCGCTACGCTCTCACATTGTACTGCGCAGTCGCCTAAAGGCTCCTTTGCTAAAAA +CATGTTGGTAAAGAGGCCTTTGAGCGGTTCTGAATGCTTATCTAAGCCGTTTTAAGACAG +TCTTGGATAAAAATCCTTATCTAGCTTTAAAGCGCCTTACAGGCGGTCAGGGCAAGCCCT +AACAACCCTAAAATAAGCGATACTTAAAAACACCACACAAGTTTAATTTTTTAAGATATA +ATAACTTGTCGCCTATCCGACAGTCTTGCGACTGGAAGGAGGTGTATCTAATGTTTGAAT +TGTTCATTTGCCCCCTTCTTATAGAAGTTTGTGTCTCTTTATTCAGTTATTGGTTGAATA +ACCGAAACAAGAAGTAAAATCAATAAAGGCGACATCAACCTGAAAAAAAGCCCCAGAGAA +TCCGACCTCTCTGGGGATTTCGTGTGTTTCGTGTTCACTTATTTGCAATCAAATTATAAC +AGAAATAAATATTTATTTCAAAAATATCCTACAAAAGTCTAAAATCCGTAATTATTTCTT +ATATGCAACATTTACAAATAAAGTCGCTCTGAGAGCTCGTATTTTTCGATTTAAGACGTT +TTATTTAGTTTTTGGTGTATTTCATTGGTCCAAGCTAAAAAACTCTTAGAAGCGATTTTA +GAGCCATTTAAACCCACTTAATTATATTCTCCATGAAATTCGCTCCATGCGTCAAAAGCT +GCGTCTGAAATTCCGCCGTCTTCGTTCACTAGTTGCATTAATTTTTCCAACGATCGTTTT +CTTTCGGGTGTCATATTTTTATATTCCAACAATTTTTCGTCTGTTAAATTTGGTTATCGA +TTACACGTGCAGCACTCCCCCCCGAA +>contig00006 len=2973 cov=2.6 corr=1 origname=NODE_6_length_2973_cov_2.590302_pilon sw=shovill-spades/1.1.0 date=20220302 +TACAGTCATCCATCATGTATTCGATGGAGATGCTTATTTTCCACCTGTTGACTGGTCTGA +TTGGTCACTGATCAATACTAGTCAAGGAGAAATGGATGAAAAAAATCGTTATCCGCATCA +ATTTGAAACGTATCAGCGTAATGAGAATCCTGTAAAAAGCGGGACAGGCGAATTGACGAT +ATAAAAAGATTCCCGAATCCAATGCTTCTTCCACAATAAACTGGATCGTTGGTTTATCCA +CGATTGGAAGCATTTCTTTTGCCATGGCTTTTGTTGCCGGCAAAAAACGTGTTCCTAGCC +CAGCGGCAGGAATGACTGCTTTTTTGACCTTCACTTGCTGTTCCTCCTCGTAAAATATCA +TTTTTCTAATAGTTTTTATTCAAAATGTTTCTAGATTATAAAATTTATTGAATAACACAT +TCCTAACGGAATTTGTTTCGATATTGTGTGATTTCTCAGAGTACAATGGATGTATGGAAA +GGATCCAACGGGAATTTGCTATTTCCTCCTGTAGCGTTTGTCTACCCTGTTTAGTCTGTT +ACCCGAACCACTGTTATCACTACCAACTCATTAGCTGTTTCGATAATGGACTAGACTTTC +AAATAGTAGTTTGGAAGGCAGCTTCTAGCTCTTTTATCACCGTATTCTATTAGGCGAGGT +TGTGGCTATACAGTGAGTTTCTGGGAAATCCCACAGTATCGAAGCATTTTCCAAAATTTA +TATCGAAAGGAGGTCCTTCTTCCATGAAATTATTTGTCGGTATTGACGTTAGCTCTGAAA +AACTAGATGTTTGTTTTTTAACAGACGACAATCAATTGTCTATCTTATCTGAAATCTCTG +TTGCCAATGACATCGAAGGTGCTTCATTCATACGAGAAACAATTCTTGAATTCAATGACA +GCTACCACTTTGATCAAATTGTGATTGGCATGGAGTCAACGTCCATGTACAGCTTCCATC +CTTCCATGTTTTTTCATGAAGATGAGAAACTAAAGAAGCTCAACACACTTGTAACGATTG +AAAATCCTTTTCGGGTGAAACAATTTAGTCGCATGTTTGATGAGAATAAAACTGATCGAA +ACGATGCATTAAGAATCGCTGATTTCTTGCGTATTCAACGATTCACAACTTCCCCTATCA +AAGAAGAGAAATACATGGCCTTACAGCGTTTAACACGTACTCGCTATCAACTTATTAAGC +AATTGATTCGTACAAAGCAACATTTTCTTGAAAATCTAACGTACAAATGTAATACGCTTG +CTCGAGAAATGCGAGACGAATCGACGAGTCTTTTTAGTGCAACCCTCATTTCACTCATGA +CGGAAGATTTCACATTGGATGAACTTGCTGAGCTTCCTTTAGAAGCTTTCTGTGATTTAC +TTCAAGAAAAAGGAAAAGGCCGTTTCAAGCAACCAGAAAAAATCGCTAAAGCAATTCAAC +GTGCAATTACCATGAGTTACCGCCTAGGTGCTCTTGCACAAGAATCAATTAATGTTGTTT +TAAGTGTTCTCGTACGAGAAATACGAGCACTTGAAAAAAATATCAAAGAATTAGATAAAG +CCATCGAACAAGTAATTGTTGTCATTCCAGAATATCAATGCTTAACCAGTATTCCAGGCG +TTGGTAAAGTCTATGCTGCCGGTTTAATCGCTGAAATTGGTCAAATCGAAAGATTTGAAG +ATCAGACAAAATTGGCAAAATACGCTGGATTAAGTTGGAAAGTGAACCAATCTGGAAACT +ATCAGTCGCAAAATACACCTCTGACAAAACAAGGAAATCGATATTTTAGATACTACTTAG +TTGAAGCTGCCAACTCTGTAAAAAATTATCTTCCTGAATACAAAGCTTTTTATCAAAGTA +AATATAAGGAGGTTCCAAAGCATCAACACAAACGTGCACTCGTCCTAACCGCAAGAAAAT +TTACGCGTCTGGTGGATACGCTACTACGTAAACACCAACTCTATACGCCACCAAGGAGTG +TGATAGAGAAATAACAATCCGTTATTGACGCAAATCCTTGAATCAACCCGAAAAAAATTT +GATTTTGATCGGGTCTAGTTTCGTGCGCTTCAAAACATATTACTCAATAAAGAAAATCTT +AAATTTCATCTTGACTTATCACCATTAGACTAAATAAATTCCTTACTCAATGCCTAAGGT +AATACTACCTTTTTATTAATCGTCGTGACTCCTTCTAAGCCTTTATCTGTAAAATTTATT +CCTCCAGTTTTTATTCTTCTTTATCCGCTACAAATTCAATGATTTCAAAGCTGACAATAT +AATCACTCAAATATGACCAAGTATCTTCAACAGATAATTCGTCTCCATTATCATTCATAA +GCGTCATTTTAAACCATTCATTACCTTCATCATCTTCAGGTAGCAAGCCGAATCCAATTG +GATTATCAGTCAATGTTTGATCGTATAAATCATCCTCGTCTAATGCTAAAACATCTAATC +CTTTACAATTTCCGCCCCTTCTAAACGTCACAAATCCTTTGTAATCCCAACGTTGGAAAG +AAACCTTAATAGTATGTGTGCCCAATCGTATATTCGGATCATAATTTTTCATTTGTCATT +CCTCCATTACGTAAATTTCATTTTCTCTATGCTTTATATTAATTTTTTCACTTTATTCAG +GACTTGTTCATATTTTATCGTTTTTCGTTTACTTAAAAATACATAAAAAATTTCGACTCG +TTTATGGCGTCCGAAACGAGAAACCCTAGACAGCGGTAAATGCTCGATTGATCCAATAAT +CAACGTCCTCGCAAGTATCTACATGTACTGCAGCACACGACACAATTTCTTGTGCGTCCT +CCCCATTACGAGAAGACCTACTCCTTATTCCATGAGTTTGCGTCAAAGTCTAGATCCCTT +AGTAGCTGCTCATGATTAATCTAGACGCTATTCTAACTTGTCTAACTTCTAAATTCCCTC +TTGTTTACTCTGCGCTTATTATTTACACAAATT +>contig00007 len=2947 cov=4.2 corr=0 origname=NODE_7_length_2947_cov_4.215957_pilon sw=shovill-spades/1.1.0 date=20220302 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAATTAAAAAAAAAGCAGAAGAAGGCATACGAGATAAGATGTAGTGACAGGAGTTC +AGACGTGTGCAATTCCGATCTACGATCAGTATAATCAATTCCGGAGATAAAAACATAATA +GCCATATAATAATACCAAACACAAAAATACAGTAAATAAAGATACCAAAAGAAGATAAAA +AAAACAAGAAGAACAAAAAAAAACTGTTCCTTGCATTCTAAAACCTTAAATACCAGAAAA +CAGCTTTTTCAAAGTTGTTTTCAAAGTTGGCGTATAACATAGTATCGACGGAGCCGATTT +TGAAACCACAATTATGATAGAATTTACAAGCTATAAGGTTATTGTCCTGGGTTTCAAGCA +TTAGTCCATGCAAGTTTTTATGCTTTGCCCATTCTATAGATATATTGATAAGCGCGCTGC +CTATGCCTTGCCCCCTGAAATCCTTACATACGGCGATATCTTCTATATAAAAGATAACCC +GTGGTGCTAGTTAATTTTTTCCTAGAGGAAAATGTCTAAACATGTTGGTAAATCAACAAA +AAAACGCATATAGTAGTCTCAAAACTCCCAAGAAATGGGCTCTATAATTTATGGGACTGA +TGAATCAGAATTGATTCTTCAGCCCCATTTTCATTTTAGGTATTAAAAAACATATCGTTC +TCTAGTATGATTAAATCACCACAAAATAAACAACTGAGAGGACGATACGCTATATGAATG +ATTCTATCAAAAAAATGCTGAGAATAACAGAGAAAGATTTGATGATTACAGAGGTCTCTT +ACGAGACCCTTCAGAAGAAAAAGACGTTGGTCGTCGATGCTGTTCTCTCGCCTACTCCTC +GTGCTTGTAGAAGTTGTGGTTCTACTGTGGTAGATGGAAACGGGAAAGCAATTATAGTGA +AAAATGGAAAAAAGGAAACGATTGTCCGTTTTGAACAATACAATCATATGCCTTTGGTTA +TGCGCCTAAAAAAGCAACGCTATACCTGTAAAAACTGTCGCACCCATTGGACGGCTCAAA +GTTATTTTGTCCAACCCAGACATTCAATCGCAAATCATGTTAGATATAAAATTGCTTCTT +TACTGACTGAAAAAGTATCTTTATCTTTTATTGCGAAAAGCTGTCAGGTATCTTTGACCA +CCGTTATTCGTACATTGAAAGAGTTTAAAAGCTATTTACCAAAGCAATCTAAGAAGATCC +TCCCCAGAGTATTGATGGTTGACGAATTTCGTTCGCATGCTTCCATAGAAGATAAGATGA +GCTTTATTTGCGCGGATGGCGAAACAGGAAAATTAATAGATGTTTTGCCTACGCGTAAAT +TACCTCGATTAACAAGCTATTTCTTAGGTTGTACCAATCCAGAAGAAGTAGAATTCTTGG +TGACAGACATGAACGCCGCCTACTTCCAGCTCACCAAACGTGTTCTGCCAAATGCGAAAG +TCGTGATTGATCGGTTTCATATTGTCAAACACATGAATCAAGCGTTCAATGAGTTGCGTA +TCCGTGAAATGAATGAACTTCGTAAAGCCGGACAGAAAAGCCAGGCAGAAAAACTGAAAA +AGAACTGGCGCTTTTTGCTAAAAAATCGTGCAAACATCAACCATTATGAATACAAAACAT +GGAAAAGTTTCCGAGCACCAAAATACCCATTTCTTACTGAAGCAATGATGATTGATCGAT +TGCTTGAGTTTTCTCCGCCCCTAAAGGAGGCGTATCCCTTTTTTCATGAATTAGTTGAAG +CCTTTCGAGACAAAGACCCTGACTTATTTTTCTCCTTATTGGCAGAACTTCCCGAAACGT +TAGATGACAGCTTTCGGGAAAAGCTTCAAAACCTTCTGACCTATGAAGAAGGCATCACCA +ACGCAATGATCTATCCTTATTCCAATGGAAAAATAGAAGCGAAGAATACCCACATAAAGA +CAATGAAACGAGTATCCTACGGATTTAAATCATTTGAGAACATGAGAATTAGAATCTTTT +TGATCAATCAATTAATCAATGTAAGATAACAAAAAATCTGAGCCAGAATGTGGTTCATTC +TGACTCAGATTTGATTTTGCACAACTCATCAGTCCTTATTGACAAAGAGCCTATTTAATT +AACTTATAATATAGCAGACAAAATTTTATAAACAAAGAAACCTTTTATCTCTTTTCTTCT +AGAAAGGATAAAAGGCTTTTTTGTTTTTCCTATTTGCTTCTCATAGCTAGTCAGCCAAGA +TTTCTATCGTATCCCCAACGCAATCCGTGCATAACGGCTCATCTTATCTGTCGTCCATGC +TGGATACCAGACTAGTTTGACTTCTGCTTTCGTTACTTCTGGCACTTCTTTTAATGCGTC +ATGGATAGATTCTGTTAAAATATCTGCTAATGGACAGCCCATAGTTGTTAGAGTCATCTT +AATGACTGTTTCTCCATTTTCAGGATTGAATTCTATATCATAAATCAAGCCTAAATTGAC +GATGTCGATTCCTAATTCAGGATCAATCACCATTTCCAAGGCAGCAAGAATACGTTCTTT +GATTAGTTCTATTTCTTGTCCAGACCGTTCTTGGTTTGCTTCGCTCATCGTACGACACTC +CTTAACACGATTTTTATTTATCATACTCTTTTTTTAGCTGCTTGTAAATGAGAATTTAGA +AGTAAGATTCTCGTTTAAATTTATAAAAATGTTCTTATTAGATGTAATAGATTAAATTTA +TTCTAAAATAAACCTGATTCCTCATTTTTTTTGTGAACGATTTTTTATTTCTGGCAATAC +GCCAGTTGTTCGATACATTTTTTGTTCGTTTTCATTTGCAAACCGGCCAAATACTGAATG +AGTTGGTAAAATATTGATAAATGCATCGTCGTCGATTTCATGAACGATCTGATCAAGATC +ATACATT +>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 +CTGATGAATTGAAGATCTCGGGGATCCTACGCGTGAAATCTTCTTCTACAATGAATCTCT +TATCTCCAGGAATCGCTTATAGCGATCAATTAACGACTCAAATCGTCAACGAAAACAAAG +AATCAGAAATCGTCAAAGCTCAAAGAGACAGTGGTGTAAATGTCTTAACTACTGAAAAAG +TTGACGAAAATGCCAAACAAACATTGCTTAGTTATTTAGGTGGAGACAGCTTGCCTTCAA +GTATCATGATTTATCCGAACAATTTTGAAGACAAAGAAAAGATCTTGGATTATCTAGATG +ATTACAATAAAGGCAAATCAGATGAAGATAAAATCATTTATACTGATTTAGCTGGAACGA +TGACTGAACTGACTGGCGGATTGATGGATGCTATCACTTATGTCCTTATTGCTTTTGCAG +GGATCTCTTTAGTAACAAGTATGATCATGATCAGTATCATTACTTATACATCTGTGATTG +AACGGACAAAAGAAATCGGTGTACTAAAAGCTTTAGGTGCACGTAAAAAAGACATCACTC +GCGTATTTGACGTAGAAACGTGTATTTTAGGTATTTCTTCTGGGATATTAGGTGTGTTTA +TTGCATGGCTAGCTACGTTCCCTATCAATAGCATCTTATACAACATGACGGATCTAAAAA +ATGTTGCTCAACTAAATCCTGTCCATGCGATTATTCTAGTGATCGTCTCTACTATATTGA +CGATGCTTGGCGGTCATCTTCCTGCACGAATGGCAGGGCGGAGGAAAACTGACCGATCTA +GTGGGTTATAGTGCCAATCTTGCAAGAATCGATTTCGGAGTCATCCCTACTTTAGCTAGT +AATTGTGCTCCATGGACACCTCTTGCTGTCATGTATAAGGAGAATGGACAAGCAGAAGGG +AAAACAGAACACTTTTACAGACAAGCTGCTTTTTTTATAACAGATCCCCAATTAGTGATT +GATTCCCCTGTTCCATATTTCATTGCCGGGTTAGCAGATACACTAGCAAAATGGTATGAA +TCTGAGCTCATCTTAGAACAAGATTTTTTGCAAGATGAATCATTTTTGAAGCTAGCACAA +GATACTGCGAAGATCTGCAAAGAAGAGATTTTGAATCATACTGCTAAAGCAATCCAAGAT +ATGGCACAAAGAAAACTGACATCGGAGTTCAAACAGCTTTCAGAGATTATCTTTGCTGTT +GCTGGTTTAGTTGGAGGATTAGGAGATAAATACGCAAGAAATGTGGCAGCACATGCTATG +CATGACGCTATCAGTAAATATATTCCGGAAAGCCATCGTTTTCTACATGGAGAAAAAGTA +GCGTATGGGATTTTCTATCAACTGGCACTAGAAGGTCGCTGGGAAAAAATAGACGAGTTA +TATCCTTTGTATCGGGAATTAGAAATATGGAGAAGATATTGCGTATATCGAAATACTTAA +ATTTCATGAAGGAAAAGGTCGTATTGATTTTAATCCGAATAAGATAGGCCAGTTTTTAGC +TAGTTCCATGAAAGGATTCATTCATGACCTATTTTTAGATCCGCATTTTTCCCGGGCGGA +TATTGCCTGCGATATTGTAGATGTGCCGGATGACTTTATTACTCAGTATCGTATTGTAGA +CCCGATTTCTTTTAAGCCAATCTACGGCCGTTCTGGCAAGCTAGAAACAGCGTACTGGGG +CAGTCGTGCCAGTGAGCGCCAAGTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAA +AAAAGTAATCGTGCCAAAAGAAATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACG +TGGCAAAGCAACGGATTGGCATGCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCC +GCATTTTTTGCCGATTGATATAAAACCTATTGATAAAATAGTTATTGATGGTTTGATAGC +TGAGCCTTCTAATTGGTCGATAATTGCTAGACATACAAAATATAAATATCGGAATTTGCT +GAAGCAAGAAAGTCAAAATGATGAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATC +TGCAGACGAATTAAAAAAAGAATTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAA +GTGATACCGAATAAGAAAAGTCAGATGAGTGAGAGTAAATTTACGTCAATGTTTAATGAC +GTGGATTTACGATAAGCGATTATTTTGCGTGAAGCAAAATAAAGCGTAAAAGGAGTTGAG +AGCGTGACACGCTTTCGGCTCCTTTTTTCGTTGTCACTTGTGACAGCGAATACCCTCGGA +GAGCATTTGGAA +>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 +TTTACGATAAGCGATTATTTTGCGTGAAGCAAAATAAAGCGTAAAAGGAGTTGAGAGCGT +GACACGCTTTCGGCTCCTTTTTTCGTTGTCACTTGTGACAGCGAATACCCTCGGAGAGCA +TTTGGAATTGTGACAGCCATGTCACAATTAGGAAAATATTACTCTTTGTCAAAGAGTAAC +AGAAAGGTTTACACTCTTTTTATTGGCGACAGCGCGAAGGAGGGGTTTAACTTGGGGTTT +AGTATTTCGTTCAAAAAGGGAACAAAAAATACAAGCATTTCTCATAATAATCGTGAGTTA +ACTGATAGCCAAAAAATCAATGGTTTGTCTGGTAGAAAATAATTAGCAGATTTACAAGTG +GGAAATAAAAAGCTGAAAGAAGAAAATTGCATTTCAAACTACATTTTCTACAATAGCTCT +AAAATGGCATATTTTGCGTTCTGAGCGGTTTTAGCGTTTATTTCGTTTAGTTATCGGCAC +AATCGGTGAAACACGTTAGAGGAGCGAAAATGGAGCCTGTAAGGCGACTGGTAGCGGAAC +GGTCGTGTTAGATTGTGTAGCCGATAGCTGAACGAAATAAATGCTGGCAGCGCCATTCTA +TTTCGGCAGGAGGAGGCTCAAGGGGTTCGGGGAATGAAATTCCCTGAGGTCTTTTTATTT +TTTCTAGAGGAGTGCTATAATCAAAGAAAATGAGAAAAAAGAGTAAAAAAATAGTCGAGC +AGTGTTGACGCACTCTCGACCTTTACGGAAACTAATCACACTAGCTCCGTAACTTCTTAA +TCATTATACGAATATTTTTAGGTTTCTTCAAGACTAGAGATTTTTTGGTAATGAATTTTT +AAGAGTTACGTGAACTTTTGAAAATTCTTTCCAGAAGTCTCTTTTTTCTTTGAGGAGGAA +CTAAATTTGAGTAAAAAAGGCACGATCATAAATGAGTGGGAAAAATTAACAGCCCCCTCT +AACAGGCGGTTAAGTGTTGACGATAAGGTACACCCCCTAAAATTAAGTTGGTCAATCGAT +CGAATTACAATCGTCGGAAAACTGAAAGAAAATATTTATTATCACACTCCAAATGATGTG +TTGATTTTAGATTTTGAACAGCTTATGCGCCTAAATGAAGGTAACGGTTATTTAAGATCT +GTTAGTAATAATGGTTGGCAGTTGTTAGACCAACATGAAGAGAATATTGCTTATATTGAA +ATTTTAAAATGGCAAGAGGGGAAAGGGCGTATAGACTTCAATCCGAATAAGATTAGTCAA +TTCTTAGCTAGTTCCATGAAAAATTTTATTCATGATTTGTTTATCGAACCTCACTTTTCA +CGTGCAGATATTGCTTGCGACATTATCGATGTACCTGATGAGTTTATTACACAATATCGG +GTAGTTGATCCAGTTTCTTTTAAGCCTATTTATGGACGGAATGGAAAATTAGAGACGGCA +TATTGGGGATCTCGCTCTTCTGAACGTCAAATTCGGATGTATAATAAAAAACTGGAACAA +GAGAAGAAAAGAAAAATTGTGCCAAAAGAAATCGTGAGTTGGTGGCGGTTAGAAATGCAG +CTAAGACGTGGCAAAGCAACAGATTGGCATGCGATGGTTCGGGAAAGTTTAGATAGCTTT +GCAAGTCCTCATTACTTGCCTGGAGATGTAAAACCTGTTGATAGAATTATGATAAAAGGG +CTGAATCAAGATCATTCAGAGTGGGCGTATATTAGCAGAAATTTGAAATATAGATTGCGC +AAATTGTTGAAAGAAGAAAGCCAAAATGATGAATTGACGAATCATTTGCGAGAAACCTTT +GCAGAATCGGCAGACGATTTAAAAAAAGAATTAGACACATGGCTTCTAGGGCTAGACGTA +ACAGAGGAGTGATACCGAATAAGAAAAGTCAGATGAGTGAGAGTAAATTTACGTCAATGT +TTAATGACGTGAGTTTACGATAAGCGATTATTTTGCGTGAAGCAAAATAAAGCGTAAAAG +GAGTTGAGAGCGTGACACGCTTTCGGCTCCTTTTTTCGTTGTCACTTGTGACAGCGAATA +CCCTCGGAGAGCATTTGGAA +>contig00010 len=1718 cov=2.0 corr=0 origname=NODE_18_length_1718_cov_2.041483_pilon sw=shovill-spades/1.1.0 date=20220302 +TATACTTAAAAATATAGGAATCCCCTTACATTTTTTAGGAAATAAATGCTAAAAATATGC +AAAAAAAGGGACTGAGACAAAAGTCTTGTCGCAGTCCCTTATTCCAAATAAAGGCTCTAT +ACTTTTTGATGTTGGTGAACTTCACCAACATCTTTTTTGTATAAAAAAATATAGAAAAGA +CACCCTGAAATCCTTTAGAATTAATTTGGCTACCAATTCATAGGAGGATTCAAGATGTCT +CATACTCAGCTTATCAAAGATACCCTAAATATTCTAGACCTAAATATCTATTTCGAGGAA +AATTGTTTAACTAAAGAAAAATACAAAGGGCAAATTTGCTTGATTTACAAAGGAACTCTT +CTGTACAAGCCAGAAGAGTGTTCCCATTGTCTTTGTGTCGTCCCCTCTAGGATCATTCGT +TGGGGGACGACAACCGTTCGGTTGTTACTGAATGATGTGTCTGAGTATCGCACTTATCTG +GAGCTGAAGAAACAACGATTTAAATGTAAGTCTTGCCAAAGAACATTCGTAGCGGATACC +TCTGTTGCTGAAAAACACTGTTTCATTAGTCAAAAAGTTCGTTGGTCTGTCATTGCTCGC +TTAAAAGAGAATACTTCCATGACGGAAATCGCTCGTCAGAAAAATATTTCCACTTCTTCG +GTCTATCTTGTCATGAAGCGATTCTACCGCCCATTGAATCCTTTCAAACAGACTTTGCCA +AAGGTCTTATGCTTTGATGAATTCAAATCGGTTCGAAGTGTTGCCAGTGCAATGAGTTTT +ATCATGATGGACGGACAAAGCCATGCATTATTGGATATTGTCGAAAATCGACGCTTGCCT +TATTTAGAACGCTATTTTTCTCGGTTTTCATTAGCGACTCGTGAAGCCGTTCAATTGATT +GTTATTGATATGTATGCGCCTTATGTTTCGTTGGTGAAAAAGCTTTTCCCGAATGCTCAG +TTGATCATCGATCGTTTCCACATCGTCCAACATATTGGCAGAACTTTCTTGAATCATCGA +GTGAAAGAAACCACGGTACGACTTAAAGGAAATTCCCACTCTCAACGAGGGTTAGGGAAA +AAATTGAAGCGCTATTGGAAACTCCTACAAAAAGAAGAAGCAAAGTTAAACTATGAAAAA +CGGGTTTGGCGTGCCAGTTTTAAAGATTATTTGACTGAAAGTGAGATTGCCGATCGACTG +TTAGCTGCTTGTCCCAACTTACGCCAAGGCTATCAGTTATACCAAGACATTCTTTATGCG +GTAAAGAAAAGAGATCAGTCACTATTTGAGGATTGTTTAACTAGAGACATTAGCGGTCTG +CCAGAAACCTATACAACCACTTTACGAACGTTTAAAAAGTTTCTGCCACAGATCCAAAAT +GCGCTTCACTACAGCTATTCAAACGGACCATTGGAATGCTTAAACAACCACATCAAAGTA +TTAAAACGCAATGCGTACGGCTTTCGCAACTTTTACAATTTCAAACTACGAATTATGATT +CGTCATGGCAAAACATTTTTAACCAAATAAACAGAACAGAAAGAGGTTTTCTTCTTTCTG +TTCTGTCCAAATTATTCTAAGATTTCTCTTTACCAACATCATTTGACAAAGAGCCCGTTT +TTCATACATGTTTATCTGTCTCAACCATACATATATGGAGACGGCGGGAGTCGAACCCGC +GTCCAAACACATCGCCACTTAAAAATCTACGTTCATAG +>contig00011 len=1047 cov=2.1 corr=0 origname=NODE_82_length_1047_cov_2.069565_pilon sw=shovill-spades/1.1.0 date=20220302 +ACTTATGATACACTTTTGAAACTCGCATTACGGCATCGTCCAGACTTGCTAATCATTGGC +GAGATAAGAGATGAATCAACTGCACATGCTGCGGTAAGAGCAGCACTAACAGGGCACCGG +GTTTTTGCAACCGTACATGCACGCAATCTTGAAGGTACATTGGTCAGAATCCATGAACTG +ACAAAGAAAAAAGAAGAGCTATCTGAATGTTTAGCTGGTGTCATTTATCAAGAACTTTTG +GAAGATGCCAATCACCATCCTTCTGTTTTATGGAGTTATCAATTTATGGAGGAAGAATCA +GTAAAAAAATCATGGGAGGAAAGTTATGAAGAAGCTCAGGAAAATATTTGGCAGTCAGAA +CTATTCTAAAGGATTAACAAGAAGCCAGCAAAACCAGTTTGCACAAACCATGGGAGAACT +GCTTTTATCTGGTTTTAGTCTGCAAGAATCCCTTTATTTATTACTCACGATCCGTTCGTT +TCCACCTGTTATTTTGGCAAATATCCAACATCAGCTAAAGGAAGGGCAAGCGTTTAGTGA +GGTACTTTCGCAAATAGGATATGGAGCAGAGCAACTGGTACAGATCGAGTTAGCTGAACG +TCATGGGAATCTGCCGACAACTTTGTTGGAAATTGCCAAACAGTTTCGGCTTGTTGAAGG +ATTTCGCAATGATTTGAAAAAGCTGCTTGCATATCCGATGCTATTGCTCACCTTTTTGCT +AGGTATCTTGTTTAGTATGCGGTTGTTCGTTTTGCCTCAGCTTATTGGTTCAGGAATGGT +CATGCAAGAGCATTGGGGTATTCAGCTGATACAAGTCTTTCATTGGTATGTTCTACTATT +CATCCTAGCGGTTACTCTATTGGCTTTACTAGTAAGGTATCGTCTGATGAAGTTGTCTCC +TGTTGATCAGAGTGAATGGATAAGCAGACAATTATTGATTGGACCGATATATTCCTTGTA +TCAATCGGCTTATTTGTCACTAGAGATTGGAAAGCTTTTTCATGAAGGTTTCGAATTAAG +GCAAATCATAGTCTGCTTAAAGGAAAC +>contig00012 len=887 cov=2.0 corr=0 origname=NODE_144_length_887_cov_2.006579_pilon sw=shovill-spades/1.1.0 date=20220302 +AATCGATATCGATGCGTCAAAATTTGGACGACGCCATGAAACATCTTTGTCGATCCTCGG +TGATGCAAACACAGCTTTGCAAAGACTTGTCGAGTTAGGGGATGCTCGCCCTGCTGATAG +CTGGTACCTAGCAAATCAAGAAAATAAAGAAAAATGGGTAAATTGGTTGAAATCTTTTGA +AGATCGAGAGGAAGAACCGATTCGTCCAGAGGCTGTCTATAAAGAAATCAATCGTATTGC +TGAAGACGATGCGATTTTCGTCACAGATGTCGGTAACACGACTATCCATTCTATTCGTTT +ATTGAATATGAACGGTAAACAAAAACATACGACATCTGGATGGTTCGCAACTATGGGTAA +TGGTGTGCCAGGAGGAATTGCCGCACAACTAAGCTACCCAGAAAAACAAGTATTTACCTT +AAGTGGTGATGGCGGGTTTGCTATGGTCATGCAAGATATCATTACACAAGTCAAATATCA +GCTTCCAATTATTAATGTTGTCTTTTCGAATGATTCTTTTGGTTTCATCGAAGCAGAACA +AGAAGATACGGAACAAAAGAAATTTGGTGTATTTTTAGAAGATGCAGATTTCGGTAAAGT +TGGAGAAGCGCTCGGGGCAAATAGCTTTACAGTCACAGAATACTCGCAACTTCGATTTGC +CTTTGATGCAGCTGCAAAATCAGATCGTCCTGTAGTAATCGATGTGAAGATCAATAACAA +GCGCCCATTGCCAGTAGAAGATCTGCATTTAGATCCAAGAAAATATTCTGAAGAAGAAAT +CCAAGCATTCAAAGAAAAATATGAAGTCCATGATTTGCCAGTATTGAATGAATTATATGA +AAAGAGGTTGTGACAACTGCGCTATGCTTCGAGTATTAAGATAAAAT +>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 +ATCGACAATGTAGGTATTCGCCGTAAAATAGGTGTGGCAGCCACGACAGTGGTAGCGTTG +TTTCGCTAAAGCAAGATAAGTCAGTTGGTTCGCACATTTATTAAGTTGAATGAGCGATTT +TTTCTTTCCGTTCTTAACGATCATGCCTTCATGATTCATCTGTTTACACAAAGGACAGCG +ACGAATTTCTTTACTTAACGTCGCAGAAACAACAAGACTCTTGATATTCTTAATGCTCTT +CGATTCCACATTTGTGATGAAAATGTTTTTATCTTTGATTCCAAGTAGTAGTTTGATATG +ATGAAGATCAGGCATACAGAACGCTCCTTTGATTGTGTTGTGGTGATTCAATTCTAACGG +AGCTTCTGTATGTTTTGTTTTTTCATGCTCAAAAGGGACCGATAGAATGATTTTCTATCA +GTCCTAGAAATTATAGAGCCTTTTTTATTTGGTCTTGAAGAAGAAAAGTAAGCGCCCCAT +AGAACAGTACCTGTACGTCAAATAACCCGACCTATAGAATAGAATCGGGAATGTTTGGCG +TTTTTAGTTACGAGAAAAATGTTGTTGTACATCCTTGTTCCAAGGCAACAGTTGATCTAA +AGTTTCTGCTGAAAGTACGGGAAGATTTGGTATCTTATCAAATAGAAACTCTAGATACTT +TACAGGATTCAATCCGTTAAGTTCTGCTGTTTTATATACACTCAGAATGATTCCTGAAGT +TCGTGCTCCTTCAAGACTTGTGGAATGCAACCAATTTTTCCGTCCTATCACCAGCTCTTT +GATATTTCGCTCCGCACGATTATTTGTGAGTTCTAAACGACCATCTTCAAAAATAGGTTC +AAAACCACTTCGTAGTTTACACGCATATTGAACGGCTGCATCCAAC +>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 +GGGGCTACATGCCAACGCTAATTTTAGAATCAGATCATGGTTATCAAGTTTATTTTGTAC +TAAAGACACCAGGCTATGTCACAAAGAAAAGCAATTTCAAGGTGATCGATGTAGCAAAAA +AAATTTCAAAAACAATTCGTCTACAGTTGGCTGAAAAATTGTCCGGAGTGGATCTAGGAT +GTAACCACTTCGGAATTGCTCGATTCCCACAAGAAAATAATATTGTTTTTAAAGAAATGA +ACTATCAGTATTCTTTTGCTGACTGGATTCAATGGTCGATGAAGCTTGAATCAGATCAAA +AAACAAAAGAAGATCGAGAACGAAAACTAATTGTCTTTCCTGAGAAAAAAGAAATTCGTC +AAGTAGATGAACCGTGGTTCGATATGTTACTTCATAAAGCAAACATCGTCGGCGGAGAAG +GACGTCTTGGTCGAAATAATGTGATTTTCACGCTTTCTTTAGCTTATTACTCTTCAGGTT +ATGCATTGGATACTTGCGAATACAATATGTTCACATTCAACGAACGGTTACAGGAACCGC +TATCTGAAGCAGAATTAGTAAAGATTGTACGTAGTGCTTATTCTGGTAATTATCAAGCAG +CAAGCAGAGAATTCATTATTGAATTGTGCCAGCAATGGGTTTCACCAACCTTAAAAAATA +ATGATCTGTTCATTCAACGACGTGGCTGGTGGAAATTTAAAAAGCCACGAGATCAAAGAA +AATATAGTCATAAAAATGAATGGAAAGAAGATCTATTGGCTTATCTAAGCGAAAAAAGTC +TTGCTAGTGAGCCTTATTTGAACCTGTCAAAAAAAGAATTGGCTTCACAACTAACG +>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 +TAGAAAATGACAATGGTTTAGTGTCTATTAAAGGTACGGGGAAAAGAACTATAGTTGAGG +TTTCATCTACGTATCCAACTACGATGATTCTATCTTTATTAATTAGTTCAATAACTTTTA +TATTCTTATTTACACGTTATTTAATAAGATGCTGCGGTGAAATGAAAATAGATTAGATAG +ATATTATAAATATGTTGATTCTATTTTCATAGCAATGGAGAAAATACATTAGCAATATAT +AAAAGAAGGTATCAAGAGTCACAGTGAATTTATTCCGAAAAGTGAAAAGAGCAAATATAA +AATTTAATGAAAATATAGAACTAAATAGGAAAACGTAGACGTAATTTTCTACGTTTTCCT +TTTCATATATATTAAATATTACGGAAAATTATATAAACTAATTTAGTGTTTTGTTTGTAA +TTCCTAATTTTGCTCCACTTTTAGATAATTTTTAGGTCTATTTAACTCATCAGACATTCT +ATGCTCATTTTTCTCCAAATTTGTTTCAACTCTTTCGTACTTAATTTTGCGTATTTGAAA +ATTCTTCTTTTAGAGTACTTTTATTACGATACTAGTATGATATATATCTATAGCAAACAG +TTAAAATCTTCCTAAAATAAGCGAATAGCATTCCTAAAACCTATAAAATTTTTAGATGAA +GCGACAAGTGGACAATTAATAAACTACTTGAACATGAAATTATGGATCACCTTTCAAATT +TAGAAAATGGAATTCTTATACTTATTGCGCAACATTTATTGATTGCAAAATTATGTGACA +AAAAAAACTAGTAGAAGAAAGAATAATGGCTTGATAATAAAGTACTACCTATTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder_db.loc Mon Sep 19 08:47:42 2022 +0000 @@ -0,0 +1,1 @@ +test-plasmindfinder-db Test Database ${__HERE__}/test-db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/.gitignore Mon Sep 19 08:47:42 2022 +0000 @@ -0,0 +1,2 @@ +*.b +*.name
--- /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 @@ -0,0 +1,2 @@ +>rep2_2_repR(pEF1)_DQ198088 +atgttgagcgaaatttattcagctattcttaaaaacggcttacgtacatacaaatatcgaaacagcaccatgaaacctgcaggtcatattgattccagtaggagtggtgctatctttgcgtaccttagcaagcaattaatgaatgttgggcgtggtatggtcattacttcggaagaagctattttagagaacgaaaagaaactaacgcattggacacctaatacctatcgctttggtacttatgcggatgattatcgaacagtggttaaaggtcattctgagaaaaacttaagtcaaatcaacacatttgtagttgatatcgattcaaaagagaaccatcaaggcgaaattattttagcctgtttagatcaagtgggctacatgccaacgctaattttagaatcagatcatggttatcaagtttattttgtactaaagacaccaggctatgtcacaaagaaaagcaatttcaaggtgatcgatgtagcaaaaaaaatttcaaaaacaattcgtctacagttggctgaaaaattgtccggagtggatctaggatgtaaccacttcggaattgctcgattcccacaagaaaataatattgtttttaaagaaatgaactatcagtattcttttgctgactggattcaatggtcgatgaagcttgaatcagatcaaaaaacaaaagaagatcgagaacgaaaactaattgtctttcctgagaaaaaagaaattcgtcaagtagatgaaccgtggttcgatatgttacttcataaagcaaacatcgtcggcggagaaggacgtcttggtcgaaataatgtgattttcacgctttctttagcttattactcttcaggttatgcattggatacttgcgaatacaatatgttcacattcaacgaacggttacaggaaccgctatctgaagcagaattagtaaagattgtacgtagtgcttattctggtaattatcaagcagcaagcagagaattcattattgaattgtgccagcaatgggtttcaccaaccttaaaaaataatgatctgttcattcaacgacgtggctggtggaaatttaaaaagccacgagatcaaagaaaatatagtcataaaaatgaatggaaagaagatctattggcttatctaagcgaaaaaagtcttgctagtgagccttatttgaacctgtcaaaaaaagaattggcttcacaactaacgatgcccaagcgaacacttgataagatcttaaatgagttacgagaggagaataaagtcttctacaaggtaacacgaggaagaaatggcggaatgatcattgcttcagtcaaaacgttgttcgcgagagttattcaactaagtaaagaaaagagactagattattcaacaaggatcacagaggtatttggactcaacgagagcttagtagaagagacatttagacaattatcaacccccttgaaccctcttaaagaagtgaatctttttgaagtagatacaggttga
--- /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 @@ -0,0 +1,3 @@ +rep2_2_repR(pEF1)_DQ198088 +rep11a_1_repA(pB82)_AB178871 +rep14a_2_ORF1(pKQ10)_EFU01917
--- /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 @@ -0,0 +1,2 @@ +>rep11a_1_repA(pB82)_AB178871 +atggctaatgagattgtaaaataccaccatgaattaaatacaattcctttaagaaaatttacaccggttgaaatgaatttgtttttttccatcgtgtctagaatgcgtgaaaaaggggataagacagttcgttttacgtttgaccaactaaaagatttaagtaactacaaagcaactgcaaatgtacgatttgtagaagatttaaaagcaacttatgaaaaaatcttatctttacgctttggtcgtagaagtgagtctgggctttcttacgatatgtttgtaatgtttacagaatttaaaatcaacggggacgtagaaaatccttacgtagatatacgaatttacgaaaaagcactgcctttgttaaataatttagacgagtgggtacgctattctttacaacaattcaacgagctacaaagtggctatgcaaagactatgtttcgtctgttaaagcaatacagaaccaaaggtttcgcatatttctccaaagaagactttcttgaattattagatattcctaaaagttataagcaacctgatatagataaacgagttataaaacctatacgtcaagaactaactgcaatcttcaaaggactaacaatcaaaaagaaatacggaaaaggacggggaaaacctgttattggctatcaatttacgttcaaacctgagatcaaaaaagcagacgactttaacaaacatgcaccaaccaaagaagaccaaaataaagcattggctttagctgataaacaaaaagaatacgaagaacccgctacaacaattaacgaaaaaatcaaacagaagaaacgagaacttgaactcctccaacaaatcaaacaactagaaaaagagaaaaaagctcttgaaaaacaaacagagtccgcactttcggaaaaagagaaaaaaagtttattatctgatttagataatttattccagtag
--- /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 @@ -0,0 +1,1 @@ +rep11a_1_repA(pB82)_AB178871
--- /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 @@ -0,0 +1,2 @@ +>rep14a_2_ORF1(pKQ10)_EFU01917 +gtgcgactgtacaacaaaaagctagagcaggaacgaaaaaaagtaatcgtgccaaaagaaatcgatacgtggtggcggttagaaatgcagctaagacgtggcaaagcaacggattggcatgcgatggttcaggaaagcttagatagttttgcaagcccgcattttttgccgattgatataaaacctattgataaaatagttattgaaggtttgatagctgagccttctaattggtcgataattgctagacatacaaaatataaatatcggaatttgctgaagcaagaaagtcaaaatgatgagttaacgaaccatttacgagagacttttaaggaatctgcagacgaattaaaaaaagaattggatacgtggcttttggggttggatgtgacagagaagtga
--- /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 @@ -0,0 +1,1 @@ +rep14a_2_ORF1(pKQ10)_EFU01917
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/config Mon Sep 19 08:47:42 2022 +0000 @@ -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
--- /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 @@ -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
--- /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 @@ -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
--- /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
--- /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 @@ -0,0 +1,57 @@ +Found: rep2_2_repR(pEF1)_DQ198088 +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 +Found: rep11a_1_repA(pB82)_AB178871 +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 +Found: rep14a_2_ORF1(pKQ10)_EFU01917 +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 +{'plasmidfinder': {'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': {'HSP_length': 945, + 'accession': 'AB178871', + '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', + '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', + 'identity': 99.89, + 'note': 'repA(pB82)', + 'plasmid': 'rep11a', + 'position_in_ref': '1..945', + 'positions_in_contig': '308..1252', + 'template_length': 945}}, + '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': {'HSP_length': 402, + 'accession': 'EFU01917', + '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', + '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', + 'identity': 99.5, + 'note': 'ORF1(pKQ10)', + 'plasmid': 'rep14a', + 'position_in_ref': '1..402', + 'positions_in_contig': '1703..2104', + 'template_length': 402}}}}, + 'run_info': {'date': '09.09.2022', 'time': '08:52:55'}, + 'user_input': {'file_format': 'fasta', + 'filename(s)': ['/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat'], + 'method': 'blast'}}}
--- /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 @@ -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
--- /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 @@ -0,0 +1,127 @@ +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 +******************************************************************************************************************************************************************************************************************************** +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 +********************************************************************************************************************************************************************************************************************************** +Plasmid Identity Query / Template length Contig Position in contig Note Accession number +********************************************************************************************************************************************************************************************************************************** +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 +================================================================================================================================================================================================================================== + + + + +Extended Output: + +# rep11a_AB178871 +template: ATGGCTAATGAGATTGTAAAATACCACCATGAATTAAATACAATTCCTTTAAGAAAATTT + |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| +query: ATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTT + +template: ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT + +template: AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA + +template: AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT + +template: GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA + +template: ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT + +template: TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA + +template: AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA + +template: TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT + +template: GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA + +template: CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT + +template: ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA + +template: GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA + +template: ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA + +template: CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA + +template: GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG + ||||||||||||||||||||||||||||||||||||||||||||| +query: GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG + +# rep14a_EFU01917 +template: GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA + +template: ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT + +template: GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA + +template: AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA + |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| +query: AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA + +template: ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +query: ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT + +template: GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA + ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| +query: GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA + +template: TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA + |||||||||||||||||||||||||||||||||||||||||| +query: TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA +
--- /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
--- /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'}}}
--- /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 @@ -0,0 +1,1 @@ +Database Plasmid Identity Query / Template length Contig Position in contig Note Accession number
--- /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 @@ -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: +
--- /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 @@ -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
--- /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 @@ -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
--- /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 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder.loc.sample Mon Sep 19 08:47:42 2022 +0000 @@ -0,0 +1,2 @@ +#value name path +test-db-2022 "Test Database" ${__HERE__}/test-db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Sep 19 08:47:42 2022 +0000 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of plasmid database to plasmidfinder --> + <table name="plasmidfinder_db" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/plasmidfinder_db.loc" /> + </table> +</tables>
--- /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 @@ -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>