| Previous changeset 0:8dfcdbeaeed8 (2020-05-05) Next changeset 2:368cb4bef9d8 (2022-06-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74" |
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modified:
drep_dereplicate.xml macros.xml |
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added:
test-data/001 test-data/002 test-data/003 |
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| diff -r 8dfcdbeaeed8 -r ef7cd2e7bc05 drep_dereplicate.xml --- a/drep_dereplicate.xml Tue May 05 06:12:47 2020 -0400 +++ b/drep_dereplicate.xml Sat Feb 12 17:40:42 2022 +0000 |
| [ |
| @@ -1,33 +1,34 @@ -<tool id="drep_dereplicate" name="dRep dereplicate" version="@VERSION@.0" python_template_version="3.5"> +<tool id="drep_dereplicate" name="dRep dereplicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5"> <description>De-replicate a list of genomes</description> + <expand macro="biotools" /> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="1.1.3">checkm-genome</requirement> + </expand> <command detect_errors="exit_code"><![CDATA[ - @PREPARE_GENOMES@ - dRep dereplicate outdir - @FILTER_OPTIONS@ - @GENOME_COMPARISON_OPTIONS@ - @CLUSTERING_OPTIONS@ - @SCORING_OPTIONS@ - @TAXONOMY_OPTIONS@ - @WARNING_OPTIONS@ - @GENOMES@ - --debug - || (rc=\$?; - ls -ltr `find outdir -type f`; - cat outdir/data/checkM/checkM_outdir/checkm.log; - cat outdir/log/logger.log; - exit \$rc) +@PREPARE_GENOMES@ +dRep dereplicate outdir +@GENOMES@ +@FILTER_OPTIONS@ +@QUALITY_ASSESSMENT_OPTIONS@ +@COMPARISON_CLUSTERING_OPTIONS@ +@SCORING_OPTIONS@ +@WARNING_OPTIONS@ +--debug +|| (rc=\$?; + ls -ltr `find outdir -type f`; + cat outdir/data/checkM/checkM_outdir/checkm.log; + cat outdir/log/logger.log; + exit \$rc) ]]></command> <inputs> <expand macro="genomes"/> <expand macro="filtering_options"/> - <expand macro="genome_comparison_options"/> - <expand macro="clustering_options"/> + <expand macro="quality_assessment_options"/> + <expand macro="comparison_clustering_options"/> <expand macro="scoring_options"/> - <expand macro="taxonomy_options"/> <expand macro="warning_options"/> <expand macro="select_drep_outputs"/> </inputs> @@ -38,23 +39,29 @@ <expand macro="drep_outputs" /> </outputs> <tests> - <expand macro="test_defaults_log"> - <has_text text="dRep dereplicate finished" /> - </expand> - <test> - <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/> - <conditional name="filter"> - <param name="set_options" value="yes"/> - <conditional name="quality"> - <param name="source" value="checkm"/> - <param name="checkM_method" value="taxonomy_wf"/> - </conditional> - </conditional> - <output name="log"> - <assert_contents> - <has_text text="dRep dereplicate finished" /> - </assert_contents> - </output> + <test expect_num_outputs="8"> + <expand macro="test_string_inputs"/> + <expand macro="test_default_filtering_options"/> + <expand macro="test_default_quality_assessment_options"/> + <expand macro="test_default_comparison_clustering_options"/> + <expand macro="test_default_scoring_options"/> + <expand macro="test_default_warning_options"/> + <expand macro="test_default_select_drep_outputs"/> + <expand macro="test_log_output"> + <has_text text="dRep dereplicate finished" /> + </expand> + </test> + <test expect_num_outputs="8"> + <expand macro="test_integer_inputs"/> + <expand macro="test_default_filtering_options"/> + <expand macro="test_default_quality_assessment_options"/> + <expand macro="test_default_comparison_clustering_options"/> + <expand macro="test_default_scoring_options"/> + <expand macro="test_default_warning_options"/> + <expand macro="test_default_select_drep_outputs"/> + <expand macro="test_log_output"> + <has_text text="dRep dereplicate finished" /> + </expand> </test> </tests> <help><![CDATA[ @@ -62,10 +69,6 @@ `dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets. - - - - `De-replication <https://drep.readthedocs.io/en/latest/overview.html#genome-de-replication>`_ is the process of identifying sets of genomes that are the “same” in a list of genomes, and removing all but the “best” genome from each redundant set. How similar genomes need to be to be considered “same”, how to determine which genome is “best”, and other important decisions are discussed in `Choosing parameters. <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ Detailed options for each module are described at: https://drep.readthedocs.io/en/latest/module_descriptions.html A common use for genome de-replication is the case of individual assembly of metagenomic data. If metagenomic samples are collected in a series, a common way to assemble the short reads is with a “co-assembly”. That is, combining the reads from all samples and assembling them together. The problem with this is assembling similar strains together can severely fragment assemblies, precluding recovery of a good genome bin. An alternative option is to assemble each sample separately, and then “de-replicate” the bins from each assembly to make a final genome set. @@ -87,12 +90,12 @@ **OUTPUTS** - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs. - - `Warnings <https://drep.readthedocs.io/en/latest/example_output.html#warnings>`_ report two things: de-replicated genome similarity and secondary clusters that were almost different. + - `Warnings <https://drep.readthedocs.io/en/latest/example_output.html#warnings>`_ report two things: de-replicated genome similarity and secondary clusters that were almost different. - A Dataset collection of the “best” genome of each secondary cluster. - - `Tables from intermediate steps <https://drep.readthedocs.io/en/latest/advanced_use.html>`_ + - `Tables from intermediate steps <https://drep.readthedocs.io/en/latest/advanced_use.html>`_ * Chdb.csv # CheckM results for Bdb - * Widb.csv # Winning genomes' checkM information + * Widb.csv # Winning genomes' checkM information ]]></help> |
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| diff -r 8dfcdbeaeed8 -r ef7cd2e7bc05 macros.xml --- a/macros.xml Tue May 05 06:12:47 2020 -0400 +++ b/macros.xml Sat Feb 12 17:40:42 2022 +0000 |
| [ |
| b'@@ -1,8 +1,16 @@\n+<?xml version="1.0"?>\n <macros>\n- <token name="@VERSION@">2.5.4</token>\n+ <token name="@TOOL_VERSION@">3.2.2</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">20.01</token>\n+ <xml name="biotools">\n+ <xrefs>\n+ <xref type="bio.tools">drep</xref>\n+ </xrefs>\n+ </xml>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="@VERSION@">drep</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">drep</requirement>\n <yield/>\n </requirements>\n </xml>\n@@ -13,250 +21,295 @@\n </citations>\n </xml>\n \n+ <xml name="genomes">\n+ <param argument="--genomes" type="data" format="fasta" multiple="true" label="Genomes to filer"/>\n+ </xml>\n \n- <xml name="genomes">\n- <param argument="--genomes" type="data" format="fasta" label="genomes fasta files" multiple="true"/>\n- </xml>\n+<!-- Addition of ".fasta" after names to avoid string to be read as integer\n+Bug in dRep: probably fixed in next version -->\n <token name="@PREPARE_GENOMES@"><![CDATA[\n- #import re \n- #set $genomefiles = [] \n- #for $genome in $genomes\n- #set $input_name = $re.sub(\'[^\\w\\-_.]\', \'_\',str($genome.element_identifier.split(\'/\')[-1]))\n- ln -s \'${genome}\' \'${input_name}\' &&\n- $genomefiles.append($input_name)\n- #end for\n-]]></token>\n+#import re\n+#set $genomefiles = []\n+#for $genome in $genomes\n+ #set $input_name = $re.sub(\'[^\\w\\-_.]\', \'_\',str($genome.element_identifier.split(\'/\')[-1]))\n+ln -s \'${genome}\' \'${input_name}.fasta\' &&\n+$genomefiles.append($input_name)\n+#end for\n+ ]]></token>\n <token name="@GENOMES@"><![CDATA[\n- -g \n- #for $genomefile in $genomefiles\n- \'${genomefile}\' \n- #end for\n-]]></token>\n-\n-\n- <xml name="checkm_method">\n- <param argument="--checkM_method" type="select" label="checkm method" optional="true">\n- <option value="taxonomy_wf">taxonomy_wf (faster)</option>\n- <option value="lineage_wf">lineage_wf (more accurate)</option>\n- </param>\n- </xml>\n- <token name="@CHECKM_METHOD@"><![CDATA[\n- #if $checkM_method:\n- --checkM_method $checkM_method \n- #end if\n-]]></token>\n+ -g\n+#for $genomefile in $genomefiles\n+ \'${genomefile}.fasta\'\n+#end for\n+ ]]></token>\n \n <xml name="filtering_options">\n- <conditional name="filter">\n- <param name="set_options" type="select" label="set filtering options">\n- <option value="yes">Yes</option>\n- <option value="no" selected="true">No (use --checkM_method taxonomy_wf)</option>\n- </param>\n- <when value="yes">\n- <param argument="--length" type="integer" value="50000" label="Minimum genome length"/>\n- <param argument="--completeness" type="integer" value="75" min="0" max="100" label="Minimum genome completeness percent"/>\n- <param argument="--contamination" type="integer" value="25" min="0" max="100" label="Maximum genome contamination percent"/>\n- \n- <conditional name="quality">\n- <param argument="source" type="select" label="genome quality">\n- <help>\n- --ignoreGenomeQuality is useful with\n- bacteriophages or eukaryotes or things where checkM\n- scoring does not work. Will only choose genomes based\n- on length and N50. \n- </help>\n- <option value="checkm" selected="true">Run checkM</option>\n- <option value="genomeInfo">User supplied genomeInfo csv file</option>\n- <option value="ignoreGenomeQuality">--ignoreGenomeQuality (NOT RECOMMENDED!)</option>\n- </param>\n- <when value="checkm">\n- '..b'ng.set_options == \'yes\':\n- --warn_dist $warning.warn_dist\n- --warn_sim $warning.warn_sim\n- --warn_aln $warning.warn_aln\n- #end if\n+ --warn_dist $warning.warn_dist\n+ --warn_sim $warning.warn_sim\n+ --warn_aln $warning.warn_aln\n ]]></token>\n \n <xml name="select_outputs">\n@@ -278,8 +331,14 @@\n <option value="Chdb">Chdb.tsv</option>\n </expand>\n </xml>\n+ <xml name="test_default_select_drep_outputs">\n+ <param name="select_outputs" value="log,warnings,Primary_clustering_dendrogram,Clustering_scatterplots,Cluster_scoring,Winning_genomes,Widb" />\n+ </xml>\n+ <xml name="test_default_select_outputs">\n+ <param name="select_outputs" value="log,warnings,Primary_clustering_dendrogram,Clustering_scatterplots" />\n+ </xml>\n \n- <xml name="common_outputs">\n+ <xml name="common_outputs">\n <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log">\n <filter>\'log\' in select_outputs or not select_outputs</filter>\n </data>\n@@ -299,8 +358,6 @@\n <filter>\'Clustering_scatterplots\' in select_outputs</filter>\n </data>\n </xml>\n-\n-\n <xml name="drep_outputs">\n <expand macro="common_outputs"/>\n <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">\n@@ -316,19 +373,19 @@\n <filter>\'Chdb\' in select_outputs</filter>\n </data>\n </xml>\n-\n- \n- <xml name="test_defaults_log">\n- <test>\n- <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>\n- <output name="log">\n- <assert_contents>\n- <yield/>\n- </assert_contents>\n- </output>\n- </test>\n+ <xml name="test_string_inputs">\n+ <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>\n+ </xml>\n+ <xml name="test_integer_inputs">\n+ <param name="genomes" ftype="fasta" value="001,002,003"/>\n </xml>\n-\n+ <xml name="test_log_output">\n+ <output name="log">\n+ <assert_contents>\n+ <yield/>\n+ </assert_contents>\n+ </output>\n+ </xml>\n <token name="@GENOMES_HELP@"><![CDATA[\n I/O PARAMETERS:\n -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]]\n@@ -337,7 +394,6 @@\n \n \n ]]></token>\n-\n <token name="@FILTERING_HELP@"><![CDATA[\n FILTERING OPTIONS:\n -l LENGTH, --length LENGTH\n@@ -364,7 +420,6 @@\n \n \n ]]></token>\n-\n <token name="@GENOME_COMPARISON_HELP@"><![CDATA[\n GENOME COMPARISON PARAMETERS:\n -ms MASH_SKETCH, --MASH_sketch MASH_SKETCH\n@@ -383,7 +438,6 @@\n normal = default ANIn parameters (default: normal)\n \n ]]></token>\n-\n <token name="@CLUSTERING_HELP@"><![CDATA[\n CLUSTERING PARAMETERS:\n -pa P_ANI, --P_ani P_ANI\n@@ -413,10 +467,9 @@\n scipy.cluster.hierarchy.linkage (default: average)\n \n ]]></token>\n-\n <token name="@SCORING_HELP@"><![CDATA[\n SCORING CRITERIA\n-Based off of the formula: \n+Based off of the formula:\n A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)\n \n A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight:\n@@ -433,7 +486,6 @@\n \n \n ]]></token>\n-\n <token name="@TAXONOMY_HELP@"><![CDATA[\n TAXONOMY:\n --run_tax generate taxonomy information (Tdb)\n@@ -457,7 +509,6 @@\n (default: None)\n \n ]]></token>\n-\n <token name="@WARNINGS_HELP@"><![CDATA[\n WARNINGS:\n --warn_dist WARN_DIST\n@@ -469,6 +520,4 @@\n dereplicated genomes (ANIn) (default: 0.25)\n \n ]]></token>\n-\n-\n </macros>\n' |
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| diff -r 8dfcdbeaeed8 -r ef7cd2e7bc05 test-data/001 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/001 Sat Feb 12 17:40:42 2022 +0000 |
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| b'@@ -0,0 +1,48964 @@\n+>gi|478483683|ref|NC_020995.1| Enterococcus casseliflavus EC20, complete genome\n+AAAGTATTTTTTTCTAACCTTTTTTATCGTAATCTGTGGAAAACTTTTTCAATCCGTGCTATTTTAGTTA\n+TATCTATTCTTAGTTATAGGAGGACAATTTATGCCATCTGCTGATTCTATTTGGCAAGATCTTCAACGTT\n+CCTTTAAAGAAGAGCTGAATCCGGCCAGTTATAGTGCTTGGATCGAGACTGCCAATGTCTTGTCGTTTGA\n+AAAAAATCAGCTGCTGATCGAAGTACCCAGCGATCTTCATAAATCTTATTGGGAAAAAAATCTAGCTGCC\n+AAAATTGTTGAAATGGGATTTATGAAAACTGGTGAAGAATTGATTCCTAGTTTTGTGACTGTCGAAGAAG\n+CAGAAGCTTTAAAAACAGCCCCTTCTACTATTCAAACAGCTGCAGAAGAAAACGAGCGGCCGCCGAAATC\n+GATCTTAAATGAAAAATACACATTTGATACCTTTGTCATCGGGAAAGGCAATCAGATGGCCCACGCTGCT\n+GCTTTAGTTGTTGCAGAAGATCCTGGGTCTATTTATAATCCGCTGTTCTTCTATGGTGGCGTTGGTTTAG\n+GGAAAACCCACTTGATGCACGCGATCGGTCATCAAATGTTGCTGAAACGTCCCAATGCCAAAATCAAGTA\n+TGTTAGTAGTGAAAATTTCACCAATGATTTCATTACTTCTATTCAAAAGAACAAAATGGAAGATTTTCGA\n+AACGAATACCGCAATGTTGATCTTTTGCTGGTGGATGATATTCAATTCTTAGTCAATAAAGAAGGAACCC\n+AAGAAGAATTCTTTAATACCTTCGAAGAACTGTATCGCAATAATAAACAGATCGTTCTGACAAGTGATCG\n+TTTGCCAAATGAGATCCCGACTTTGCCGGAACGTTTGGTTTCCCGTTTTGCTTGGGGCTTGTCCGTTGAT\n+ATCACCCCGCCGGATCTAGAGACGCGGACTGCGATTTTGCGGAAAAAAGCCGAAGCCGAACGCTTGGAGA\n+TCCCCGACGATACCTTAAGTTATATCGCTGGGCAGATCGATTCGAATATCCGAGAACTTGAAGGAGCACT\n+CGTGCGGGTGCAAGCTTTTGCTACGATGCAAAACTCAGACATTACAACGAGCTTGGCAGCTGAAGCCATC\n+AAAGCCTTAAAATCAAGCCATGGCTCGACCCAAGTTTCGATTTTGCAAATCCAAGAAGAAGTCGCAAAAT\n+ACTATCACATTCATGTCAATGATCTAAAAGGGAAAAAACGGGTCAAAGGCATCGTGGTTCCACGGCAGAT\n+CGCGATGTATCTCTCTCGAGAATTGACCGATAGTTCTTTACCAAAAATCGGCGGCGAATTTGGCGGCAAA\n+GACCATACAACGGTCATTCATGCCCATGAAAAAATTCAGCATTTAGTCGAAACAGATCCCACGATCAAAA\n+ATGAGATCGCTGAAATCAAACAAATCCTCTTCAGCTGATCTGTGGATAAGAAAAGAAGAACCAAAAAAGT\n+TGTCCACAAGTTATTCACAGGCATTTTCGTTAGTCTAATCACTCTTTTCTCGAGTTATCCACATTACTAA\n+CAAGCCTATTACTACTATTACTTTTATTTAATAACTATAAATTAAAGGAGTATCGCTATGAAGCTAACTT\n+TAAACCGAACAGAGTTCATGCAAGAATTACAAACTGTCCAACGGGCGATTTCAACCAAAACCACCATCCC\n+GATCTTAACTGGAGTAAAATTATCCCTTTCAGAAAAAGGATTGACCATGACTGGGAGCAACGCCGATATT\n+TCCATTGAAACTTTTTTAAGTGTGGAAAACGAAAAAGCGCAAATGCAAATCGAAAAAACAGGAGCGATCG\n+TTTTACAAGCACGTTTCTTCAGTGAAATCGTTCGTCGTTTGCCTGAAAGTACCTTAACCTTAGAAGTATT\n+AGACAATAATCAAGTAGCGATCACTTCTGGAAAAGCCAACTTTACCGTCAACGGCTTGGATGCCGATAGT\n+TATCCACATTTACCAGTTGTCGAAAGTCAAGATTCGATCGAGATTCCAGCGCACGTGTTGAATAAGGTCG\n+TTAGTGAAACAGTCTTTGCGGTTTCGCAACACGAAAGCCGTCCGATCTTGACTGGGGTCCACTTTGTCTT\n+AGAAAATCAAAAATTATTAGCTGTTGCGACGGACTCACACCGTCTGAGCCAACGGGTGATTCCATTGGAA\n+AGTGGAGAAACAGCCTTCAACATCGTAATTCCTGGCAAAAGCTTAACGGAACTTTCTCGTTCCTTAACAG\n+ATGAAGAAGAAGCGATCCAAATCAGCATTATGGATAACCAAGTGTTGTTCCAAACGAAAACCATGAAATT\n+CTATTCTCGTTTATTGGAAGGAACTTACCCAGATACCAACCGTCTGATTCCTTCAAGCTTCAATACTGAG\n+ATTGAATTTTCTGTCCCAGAATTGTTACAAGCCATCGAACGGGCGTCATTGCTTTCTCATGAAGGCCGTA\n+ATAACATCGTTCGTTTGGCGATCTCCGAAGAAGCCGTTGTCTTATATGGAAACTCACCAGAAATCGGGAA\n+AGTCGAAGAAGATCTTTCTTTTGAAAAAGTGACCGGCGACCCATTAGAGATCTCTTTCAATCCTGACTAT\n+ATGAAAGCAGCACTACGAGCATTTGGTGACACCAGCATTGTGATCCGCTTTATCTCAGCGATCCGTCCCT\n+TTACATTGGAGCCGACAGAGAGCAAAGGCAGCTTTATCCAGCTGATCACACCGGTGCGAACCAACTAGTT\n+TTTCATGTCTTTTGAAAAAAGTTGAAACAATCATCTGAAAATGAATAAATGAGTTAAAAGGGCTTAAAAT\n+CGTTTTTAAGCCCTTTTTTCTATTTTGGCTTCTTTTTTGTCTAAAAGCAGTAAGTCTTCTGAGAATGAAA\n+AATATGCCGATGAATTTGTTTTCTTGGCAAAAAAAGAGTATAATAGAGCTAAACGCTCTTTGATAGAATT\n+GAGGGGAATTATGAAAATGCAAATACCGTTAGAAACGGAATACATGACACTTGGACAAATGCTCAAAGAA\n+GTCAGTGTGATCAGCAGCGGCGGCCAAGCGAAATGGTACCTTGCAGAGCACACCGTTTTTGTCGACGGCG\n+AGCCAGAAAATCGACGAGGGCGCAAATTGTATGCGGGAATGCGTGTTGAGCTACCTGATGAAGGTACTTT\n+TTTTATGGTGAAGAAGGAAGACGCCGATGCGCCTGAATGAGTTGCATTTAAGCAATTATCGGAACTATGA\n+TTCGCTGACACTGACTTTTGAGAAAGGTCTGGTCATTTTTTTAGGCGAAAACGCGCAAGGAAAAACCAAT\n+ATTTTAGAAAGTATCTATGTATTGGCGATGACCAAAAGCCACCGCACCTCCAGCGAGCAAGAGCTTATCC\n+GCTGGGACACAGAAGGTGCGCGGATCTCTGGCAGTGTCAGTCGGGGACGCTCAACGATCCCGTTAGAACT\n+GTTTTTGTCAAAAAAAGGACGAAAAACGAAAGTAAACCACATTGAGCAAAAAAAGCTCAGTAGTTACATA\n+GGGCAGTTGAATGTCATTTTATTTGCTCCAGAAGACCTCTCCCTTGTAAAAGGAAGTCCCCAAGTCCGCC\n+GTAAATTTCTCGATATGGAAATTGGGCAGATCGATCCAATCTATCTCTATGATCTCGTTCAATACCAATC\n+CGTTTTGAAACAGCGCAATCAATACTTAAAACAGCTGAATGAAAAAAAACAGACCGATGAGATCTATTTA\n+GATGTTTTGACGGAACAGCTGGTGGCTTTCGGCAGTAAAATCATTTTAGCCAGACAACGATTTGTTCAGC\n+GCTTGGCGT'..b'ACTGCGAGATTCATCGCCTTATCGGTCT\n+TGGCACGAATCAGGTCCATCACCGCCTCGGCTTGAGAAAGGTCAACCCGTCCGTTTAAAAAGGCCCGCTT\n+CGTGAATTCTCCCGGCTCAGCCAACCGTGCGCCTTGTCGCAAAACCAGCTGCAAGAGTTGATTGACGACA\n+ACGATCCCGCCGTGGCAGTTGATCTCAACGACATCTTCTCGGGTAAAGGTCCGCGGCTTTTTCATCACTG\n+ATAGCATCACTTCATCCATCAAACGGTTTTCTTCTGGGTCTACGATATGACCATAATGGATCGTATGACT\n+AGGGACTTGGGCGAGGGTTTTAGTGCCTGCTTGAAAAATCCGATCCGCAATTGCGATCGCTTTTTCCCCG\n+CTTAATCGCACAATACTGATGGCCCCTTCGCCTGGCGGGGTGGAAATCGCGGCAATCGTATCAAATTCTT\n+GCGTTATATTCGCCATGTTGCTTGCTCCTCCTATTTTTTCACATAAAAAAAGTGCCCACTCCACCCGTCA\n+AATTGATTGAAAATCAATAAAAACGAGTAGACTTAGCACTTTGACTGCTTGTCAATTAAATTCTGGAAAT\n+AGATTAGCACATTTTTGCGTGAGTCGCAAGCTTCCTTCAAAAACTTTTAAATTTTGCATCTGTCCGCAAA\n+AACCTTTAAAATAAAAGCAAAGAATAAGAAAAGAGGGATCTATTATGGAAACCATCAAATCATCAAACAG\n+CGCTGCTCGCATTAAAGAAATCATTTTATCGACAGGAAACGTGAATCGGCCTTACGTCGTGCGGGATATC\n+GTCTTTGCGGCAGACAAAATCGAAGTAGATCTATTTGATACATCTGTGAATTTGAACGATCTGTTGGCAG\n+ATGTGACCTATCGCTTAAAAGAAACCGCCCACAGCTACGGAGCGAATGCAGTGATCAACTGTCATTTCGA\n+ACATGACCGCATCGTCGAAGGCGACAAAACCTACCTTGAGATCTTTGCCTATGGTACAGTGGTTCAATTT\n+ACTCAATCAACCATCGGCGGCTAATTGCCTCTATCATCAAAGAAAAATACAAAAAAGAGTCCGCGGCATA\n+CGGACTCTTTTTTGATACCAAAGGCTGACCTACGTAACGTATGTTGACTTTGATAAGAATGATTTCTAGT\n+CAAGGATACTTGGTTTTAAATTTGTTGTCAATCGCTTTTTCCCATCAAAAAAGGGAAAGGCTTGTCAGAC\n+CGCCTTTCCCTTTTTTCATTAAATTCGTTTGTCCGCAGGTTCCACTACTAAGTAGCGATACGGTTCATCC\n+CCTTCAGAATGAGTTTGAACATACGCATCTTTACTCAAAACTGAATGGATCTGCTTTCTTTCAAACGCCG\n+GCATCGGTTCTAAAAAGACTGGGCGGCCTGTTCGTTTGACTTTTTCAGCAGTACGGCTAGCCAAACGTTC\n+TAAGATCGCTTGACGTTTTTCACGGTAATCTCCGACATTCACTACAATCGACAATTTGTTTTTCGCGATG\n+CGGTGAATATACACTTGCGCCAAATATTGCAGTGCATTCAAGGTTTTGCCGTGCTTCCCAATCAAAATGC\n+CTTGTTTTTGCGTTTCTAAATGAAAGACGACCACGCCGTCTTGACGAGCGGTTTTTACTAAGGCGGGTGC\n+ATTCAATGCTTTTGAAATATTTGTCAGATAGAGTCCCAGCTGAGCCAGCGCTTCCTCATCTGAAAGATCC\n+GTCAGCAAAACAGGTTCGCTCGCTGCTGCTTCCATCACACTGCTTGCATCCTCTGTCGTCACAGGATCTG\n+GTTCTACCAGCGGTTTTGCTGGTACTTCTTCAACGGGTGCCGGTTCTTCAACGATTCGTTTTTCAATGGA\n+GACCCTTGCTTGTTTTTTTCCTAGACCCAAGAAGCCTTTTTTTCCTTCATCCAGGACTTCGATTACTGCT\n+TGATCTTTGGTGATACCAAGGACTTGCAATCCCTCTTGAATTGCTTCATCTACTGTCAGATTTTCATAAA\n+TCGGCATTGCAGTGCAACCTCCTCTTATTTTTTCCGTTTCTTTTTAGGACTCATTGCTTTTTTCAGCGCA\n+CGTTCACGCTCGCGTTCTTTGCGGGCAGCTTCTTCTCTTTCTTGGCGAATCTTGAATGGGTTATTTAAGA\n+TCATTGTTTGCACAACTTGGAATGCATTGGAAACGACCCAGTACAAGGAAAGACCGCTGGCAATGTTGAT\n+CCCCATCAGTAAGATCATCATCGGCATAGCGAAATTCATGATTTTCAGACTCGCATTTGATTCCACTTGG\n+CTCATACTTGATAAGTAAGTACTTGCAAAAGTAAAGAGCGCCGCTAAAATCGGCAAGATGAAGTATGGGT\n+CACGATCACCCAGCTGCAGCCATAAGAATTTTCCTTCTTGCAGAGCAGGAACCCGTGAGATCGATTGCCA\n+CAAGGCCATCAAAATCGGCATTTGTACCAATAATGGCAGACAGCCGGCATAAGGATTGACATTGTTTTCC\n+GCATACAAACGTTGTGTTTCTTCTTTTAACTTGCTTTGTGTTTCTGTATCTTTTGACGCATATTGCTGTT\n+GCAGCGCTTTTAGCTTCGGTTGTAATTCTTGCGTTTTGCGCATGCTTTTGGTTTGGAAGTGCATCAACGG\n+CATCAAAATGACCCGAATGATCAATGTAAAGAGGATGATCCCGATCCCGGCATTGCCAAAGGAGAGGGCT\n+TTGATCGCCTCTGCAAAATAATAAACGATGTAACGGTCCCATAGACCAGTACTTTGTGCATTTACTTCAC\n+CTGTTGCACCGCAGGCAGATAAGACAACTACTAATGAGAGGACTCCCAAAAATAGTAAGACGCGTTTCCC\n+TTTTTTCACGTAACTAATTCCTTTCCATTAATGAATAATTTTGGCAAGTTTTAAGACATGCTCTAAATTC\n+GAGTAGATTTCCTTTGAGGAACAAGTGGCGATACTTGGACGGGCGATCACGATGAAATCGACCGCTGGTT\n+CGATTCGCGGCTTCATTTCCGTTAAACTTGCACGGATCTTGCGCTTGATCTCATTTCGCTTCACTGCATT\n+ACCGACTTTTTTCCCTACAGATAAACCAACTCGAAAATGTGATTGCTCTTTAGGTAAGACATACACCACG\n+AACTTCCGATTTGCAAAAGAATTTCCTGCCTGAAAAACTTTTTGAAAATCTTGCTCTGTTTTTACTCGAT\n+AGGATTTTCTCATCTTCGGTTCCTTCACTTCTTTCAATTAAGCTTCGCGAAACGGATTGAATCCGTAACC\n+ACTCACCTGTCAATAATACCATATTTGCCAAAAGTCAGACACTATATTCCGCAAAAACGGCATAAAAAAA\n+AACCACTGGCATTCAGTGGCTTACGCAGAAATAACCTTTCTGCCTTTACGACGACGGCTAGCTAAAACAC\n+GACGTCCATTTTTTGTACTCATACGTTTACGGAATCCGTGAACTTTTTGACGTTTACGTTTATTTGGTTG\n+ATACGTTCTTTTCATTTATTTCCACCTCCATCAGGATAATGCTTATGCGCACAGACATACTTTGATAGTA\n+TAACGAGTCAAGTACTAGTTTGTCAATAAGAAGTTTGCTCAAAATCAGGCATTCTTTATCCACAATCCCT\n+TTGATTTGTGTGGGTTTACTGTTTATAGCCAATTTTTGTGGATAACTTTTTCCCCAGAGTTATTTTGGCT\n+TTTTCCACAAACAAGCAGCCTGTAGAAAAGTTTTCCACAATCACTTTTTTAACTGTTGATAACTACCCCG\n+AAACCTAGTGTTATCAAGGTGTGATCTTCACATCGATCTGTGGATAAAGGAGATTGTTTTACAGTTATGC\n+ACATTCTTTTTCTACCTGTGGATAGTCGGATTTCGAACATGTGCATTTCCATTTTTCTTTTATCCCGTTT\n+TGTGGA\n+\n' |
| b |
| diff -r 8dfcdbeaeed8 -r ef7cd2e7bc05 test-data/002 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/002 Sat Feb 12 17:40:42 2022 +0000 |
| b |
| b'@@ -0,0 +1,40833 @@\n+>NZ_GG692854.1 Enterococcus faecalis T2 plasmid scaffold supercont1.22, whole genome shotgun sequence\n+TAAAATTAATGTGCCAGTCTTTTTTATCAAAACACCTATTAATAGAGGGGTATTTGAAGAGATCTTCGGCGAAACATTAA\n+AAGGATAGGGTGAAAAAAATGAGTAATAAAAATGAACACGGGTTTTGGGAATGGCTACAAATAGACTACTTTTCAAGGTT\n+TCCAGATGCAACGAATGATGATGTGACTAAATTCTTGTTACGCTTTACAGAAGCTAGTAAAAATTCAACCAAAGAAGGAT\n+CAAAAATCATTGAAGAATTGTTTGAGGAAGAACGAAAACGCAGAAAAGGACGGTGATTTTTCGATGAACGAACGTGAAAA\n+AGATATAAAAAAGTGGCTTTGCCAGTTATTAGATCAGACCTACCTAAATGCGGAAGCGTATAAAAATTTTTTTGTAAGAG\n+TTCTTCCAAAACAGCGTAAACGGACACTTGGTAACTATTTAGAAGTAGAACGTGTATTAGAAGTGAGCAATTTGTTACGA\n+GAGCCTGTGGAAGTCATGCTGACACTGATACGCTTATTAGCTGCTCATATTGTTGTTGTTAATCGTGAGCAATTTCAAGA\n+GGAAGAAGCAAAAGAGAAAATAGTGAAGGAATTATTAGGGGAATTGCTTAAGCAAGGGAAAATTAGTCAAAAAGAACAAA\n+CAATTATGTTAGGCACTGGTTTTTTAGAAGAAGAAACTGCTCTTTATGGCGAGTTAGAAAGTTGGGCGACTGATGCGAAA\n+GAAACCATTTATTGTACGGTAGTTGAGAATGGCTTCCCTATTAAAATGGAGTTACACAAACTTGGGTATCAATGGCTAAA\n+AAGTCGCCAAGCTTGGGTGAAAAGTTACGAGACACAAGAAGCTGCTGAAGTCGCCAAAGGTCAGCTTTGGGCATTAAGTA\n+GTGAAATAGAAGTTAGTGTAGAGACACCGATTACTTGTTTGTTTCATTTTGATTATTATTTATCCGTTAAGCCAGCGGAA\n+CGTTACAATGAAACGATTGTTGCTTTTGGGTATATCTATGAAAATTACGGCTTTAAAAAGAAATTTGTCAAACAAGTACC\n+AGTAAAAGATTTTTCAGGAGAACGTGAGCGTTTAGCACGATTAGAAATTCCTTTTGAACTAGTAGTACCAAAAGAAAGAC\n+AAGTGATTTATTGACTATTTAAGAATAAATTAGGAGGAATAACAATGGCAGTGAAAATTGATGGAACGATAAAAAAACGT\n+GTTCAATCTTTAATGGCTTTAAATGGACAGTCTTATGAAGAATGGCTTAATAATCAGCACCAAAAGTATTTAAATGAACA\n+ATCAGAAGTCATTGACCGACTATTGAAAAAAGAATTGGAACGGAAAAAAGGAACAAATGAATAGTTAAAGTAAGTAGAAT\n+AATTTAGGAGGAAATCAACGTGAAAAACAAAATTAAGAAAAAAGTGAAGTATTTTACAGCTGTAATTCAAACGATTATTG\n+GTCTTGGATGGATTGAAGTGAGTACGATGATGCCGGCATTTGCCGATGTTGAACGAACAATTCAAGGCGTTGAAACTGGT\n+TTAGGATCGGAATTTAAAAAGTTTGCTAATCCGGCATTAGGTATAGCAGTCCTCATTTATGGAGGAGCTAGATTTATGGG\n+ACATGATATTGCACAATGGGCAAAAAAATGGGTTTTCGGAGCATTTGTTGGTGCAGCAATTATTGTGAACTTTACTTGGA\n+TTAAAGATACTGTTTGGGGTTGGTTAGGAGGTTGATTCTTAAATGACTGTAGAAGTGGAGATTTTATCGTCTAACGTTGA\n+AGTCTTAGAAAAACAACCACCGTTGGAGTTACTTCCCTTCGCAGATTTTATTGAAATCACAAGATGCATGTATGTTAAGG\n+AGGCAGTAACTTTCCAACTATTGGAAGTTGGTGGAGATCCTTTTTATCGGGGAAGTTTTGAAAAATTAAATGATGAATGG\n+ACACTAGAAAAAGATATACAAAAGAAGTTAAATCAACTAGTCAAAAAAAAGAAAATGACGGCAGAGCAGGCGGAGGGCTT\n+ACTCTACAAAATTCCTTTTAAGAATCTACAGGAGGCTAGTTTTTCGAACGAAAAGAAAACGAGATTCTTCAAAAAAGAGA\n+AGAAGCCCAAAAATACCCAAAAAGTCGGGAGGCTTAAAAGGAAAATACACGTTATTTCTCCAATAAAACTTTCCCAGAAA\n+CAATTGAGAATTTTAGGAGTGTTTGTGATAGGAATACTCTTAATTGTGATTGGTTGGAAATTTATGGCGGGAAGTCAATC\n+GACGGCCAAAACTAGTTTAGAACCTACGTATCAGCAGTTAGTCAATAAAGAAAAGTACGCTGAAATAGTAAAAAAATATC\n+CTGAGAAAGAACCAGAGCTAATTGAGGAGTTATTTCAAAAAGAAGATAAAGCTGGTTTGAAAAAAATAGCTGAACACTCT\n+AATACACAGTTAGCTCAGCTATATCTTGCTTTTTTAGACAAAGATTGGCAGAAAGTAACAGAACTTTCCAAGTTACCACA\n+GGATAGTGATGTTCAAGCAATGGTAGGCTATGCTTTTTTAGAACAAGGTAAGATAGAAGAAGCAAAGCTTATTAATAAAG\n+AAATTCAAAACGATACGCTAACAAAACAAATCAAAAGTAAGGAAATCGAACAGGCGTATAAACTTCTTAGAGAGCGAAAA\n+ATATCTGAAGCGGAGAGAATAAACGAAAGATTGAAGGATAATGGATTATCCGAAGCAATTAAAGTAGCCAAAAGTATTCA\n+TAACTTGTTAGAAAAATACGCCAAAGATAAGGAAAATAAAGAATTATCAGAAAACGAGCGAAAAGAAGCTGCTGATAATT\n+ATCAGCTATGGCTGAAAAATTTGGAACAAATTGGTAAGTCTGTTCATTAATTCGGAGGATAAAATTATGAATGAATTTAC\n+GAATTTCAACTCTTTGTTCCACTGATTACTTTTACGGATTAGATAAAAAAAGAGCGAAAAATGTGATATAATCACCAAGA\n+GTAAATGGAAGTTGAAGACGGTAGCATAAATCCACCGCAAAGGAGCTGGTGCCTATGAGAGTACTCATAGTAAATCAGAA\n+AAACTGGCAAAGGAGTTGTGCAGTTGTGTCTGTATTAGAAGTGTTGGCCTTGCTTACACTATTAATACAAGTCTATAAAT\n+TAGGCAAAAAAGACGACAACAAAAAAGACCGTCGGTAAACTTTAGCAGGTTTCGACGGTCTTTTTTTGATTGTTGAAATA\n+TATGCTGCCGATCTTCTATCGGTCATTTACTCTAAGGGGACATGTTTCGAGCATGTCCTCTTTTCATAATCTATTATACG\n+TATAACGAACGAGAAAGTAAATAAAAAAGCAAAAAAAGGGCTGTTCTAAAAAGAATAGCTCTTTTTTTGTACACAACAAT\n+TGAGAGGGATGAAAGAAATGAACGGAAATCAAAAAGAAACCGCTAAAAAGCAGCATAAATATCTAATTATTGGATTATGT\n+TCAGTTGCGTTACTAGGAAGTGGCTTGACGTATGCCGCACTCAACCAGGGGGAAAAGAAGGAAGCACAGACAGAGCAACA\n+AGGTACAAAACCTAAAGAAGAGCGTCAAACACCAAAAAGTAAACAGTCCCCTTGGGAACGGAAAGTGACGGAGAATGAAG\n+AAAAAAACAAGGATAAAGACAAAAAAATTAAAAGTAAGCAGCCACATAAAACAAAAGATTCGTTAGCAGAAATAGTTAGC\n+GGTTTTGAACGTACAAAAGAAGAAAAACCAAAACTTTTTGGTGTGGAGATACCTGAAATAAAAAGCGATTTATTAGGACA\n+ACTAGCGAATGCTCTTGTTCA'..b'TGAGA\n+ACTACATTTATTATTACAATCATCACCGAATCAAGGAAAAACTTAACTGGAAAAGCCCAGTAGAATTTCGACAATTCAAT\n+CAAAAAACTGCATAAAAATAGAGTGGAAAAATCCACTCTA\n+>NZ_GG692836.1 Enterococcus faecalis T2 genomic scaffold supercont1.4, whole genome shotgun sequence\n+GAAAAGAGTTCTAAATGATAAATACAAACATGCACTAGAGCTAATGGAAACAAACAGCATGCGAGAAGTGGAACGAAAAA\n+CAGGTATTTCTTTGTCTACTCTCAAAAGAATCAAGAAACAAGCAAAGGAAGAACAGTTACTTAATGAGAAATAATTCAGG\n+AGTAGTTATTATGGAAAATAGAGAGAAAATTATTCAGTTGTTGAAGAATCCTTTAGTAACAGGTTATGGGATTGAGATGA\n+TGTCAAATGGGCGACTCTATTCAGCGAACTTTCAAAGATATAGGAATCGGATGAAGAAAGAAGAAAATCCAATGATTATC\n+TTTGATACTATGACTGAAAAAGTTGAAAAGGTATTTTTAGAATTAGCTGAAGAAGTCATACGAACGAACCCTAAAACAAA\n+ACAAGAATTCAAAGATATGATTAAAGAATATAGTTATAAGGAGGATAACAAATGGTAGTTCGAAAAACATATGATCATTG\n+GGGGATCGAAATCAGCACATGGAACAAAAGTAATATAGTTACTTTTATTGATTGTGACTGCGGTCAATTAGCTAAAAGAG\n+AACTAGGAAAGTATAATCAGTATAAATGTGATAGCTGCAATAAAGAATACAAATTGTATCAAGGCAATTATATCGCAATT\n+GATGAAAAAATAAATGAAGTAGCTCAAAACGATTGAAAAAGTAAAAAAGATTTTTGATAGTGTGATAGTGTGCTTTCAAT\n+AATT\n+>NZ_GG692835.1 Enterococcus faecalis T2 genomic scaffold supercont1.3, whole genome shotgun sequence\n+TCAGAATGGTGCATCCCTCAAAACGAGGGAAAATCCCCTAAAACGAGGGATAAAACATCCCTCAAATTGGGGGATTGCTA\n+TCCCTCAAAACAGGGGGACACAAAAGACACTATTACAAAAGAAAAAAGAAAAGATTATTCGTCAGAGAATTCTCATGTTT\n+GACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGGCACCGTGTATGAAA\n+TCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCC\n+GGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGC\n+AATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGA\n+GCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCAC\n+CGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCA\n+TGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGG\n+>NZ_GG692834.1 Enterococcus faecalis T2 genomic scaffold supercont1.2, whole genome shotgun sequence\n+AGCCCTTCAATCGCCAGAGAAATCTACGAGATGTATGAAGCGGTTAGTATGCAGCCGTCACTTAGAAGTGAGTATGAGTA\n+CCCTGTTTTTTCTCATGTTCAGGCAGGGATGTTCTCACCTAAGCTTAGAACCTTTACCAAAGGTGATGCGGAGAGATGGG\n+TAAGCACAACCAAAAAAGCCAGTGATTCTGCATTCTGGCTTGAGGTTGAAGGTAATTCCATGACCGCACCAACAGGCTCC\n+AAGCCAAGCTTTCCTGACGGAATGTTAATTCTCGTTGACCCTGAGCAGGCTGTTGAGCCAGGTGATTTCTGCANTAGCCA\n+GACTTGGGGGTGATGAGTTTACCTTCAAGAAACTGATCAGGGATAGCGGTCAGGTGTTTTTACAACCACTAAACCCACAG\n+TACCCAATGATCCCATGCAATGAGAGTTGTTCCGTTGTGGGGAAAGTTATCGCTAGTCAGTGGCCTGAAGAGACGTTTGG\n+CTGATCGGCAAGGTGTTCTGGTCGGCGCATAGCTGATAACAATTGAGCAAGAATCTTCATCGAATTAGGGGAATTTTCAC\n+TCCCCTCAGAACATAACATAGTAAATGGATTGAATTATGAAGAATGGTTTTTATGCGACTTACCGCAGC\n+>NZ_GG692833.1 Enterococcus faecalis T2 genomic scaffold supercont1.1, whole genome shotgun sequence\n+GGGAGCGTCAATAATTTTGTGTAAATAAATTGTCCTCCTGCAAAATAATTAGTTACTCAGTAAACATTGAAACTAATGTA\n+TCGGTTACCTGTTGAAAACCTTTATGGCTTCTGTTTAGAAATTTTTGATTGTATGTATCAAAAATGCTGACTAGAAAGCG\n+TTCTAGTGATTCTTCATTTTGAAACTGCTCTTTTCTACGGCTGTATCTTTTAATTTGCTTATTGAAAGACTCGATTAGAT\n+TGGTTGAGTAAATGGTTCTACGAATGCTAGGTGGAAAATCATAAAAAGTTAATAAGTCTTGGTTTTCTATGAGTGACTGC\n+GTCACTTTAGGATAGTTTTTCTTCCATTTCTCAATCATGCCGGATAAGAAGGTATTCGCTTCTTCTTTTGAGTTAGCTTG\n+ATAAACAGCCTTAAAGTCATCACAGATTTCTTTTCGGTCTTTGACACGTACTTTATGAGCGATATTACGAGATACATGGA\n+TACAACAATGCTGATATTTTGCTTTAGGATAAATTTGATGGATAGTATCTTTCATGCCTTTTAAGCCGTCCGTAATAAAA\n+AGCAAGACTTCTTGAACTCCTCTGGAGTTAATATCCTGTAGCAGCTCATTCCAAACGTATGTTGATTCAGTTGGAGCAAT\n+CGCATAACTCAGTACTTCTTTAGTGCCGTCTTCTCGTATACCAATGGCAATATAAATCGCTTCTTTGGATACGGTTTGAC\n+GTTTTAGTGGAATGTAAGTAGCGTCCATAAAAATAGCGACATACTTATCATTTAAGGCTCTGGATTTAAAGGCATTTACT\n+TCTTCAGTCAGAACTTTAGTCATGTTGGACATGGTTTGTGGAGTATAGTGATGACCGTACATTTTTTCGATCAAATCAGC\n+AATTTCAGACATCGTAACACCTTTTTCGAATAAATGGATAATAGTGGTTTCCAATGTATCGTTTGTTCTTTTGTAGGCTG\n+GTAAAGTTTGTTGTTTAAACTCACCATTACGATCTCTAGGTATTTCCAATGTTAATTCACCATATTCGGTTTTGATTGAT\n+CGAAAGTAAGAACCGTTTCTCGAATTACCTGAATTAAAACCAGTGCGATCATATTTTTCGTAATCTAAAAAAGCCGTTAA\n+TTCAGTCCGTAGGAGTGTGTTTATCGCTTTTTCTAAGTGCGAACGGAATAATTCATTTAAATCGCCTTTAGTGACTAGAG\n+TTTGCACAATTTCTGTAGTAAAATCATTCATAGGGAAGTCCTCTTTTCTGTGAATTGGTTGTCGTTAACTTTATTCTACA\n+GAAGCGACTTCCTTTTTTGTATGGATTTTTTCATTTACACAAAATATTTTACACTCTC\n' |
| b |
| diff -r 8dfcdbeaeed8 -r ef7cd2e7bc05 test-data/003 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/003 Sat Feb 12 17:40:42 2022 +0000 |
| b |
| b'@@ -0,0 +1,39594 @@\n+>NZ_GG669016.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD95, whole genome shotgun sequence\n+TTCAAGATAAGTTTTAAGTCTGTGTCCTTACACGAGATTTTTTACGCAAAAATAATTCTTTGTAGTTCATCAGCACAAGC\n+ACATTTTTATATAACTGATTAATTTTGTTGAATTATAGTTATATCTATATTGATTAATAGCTGATCTTGCTAAGCATGGA\n+TTTAATAAGAATATTTTTGTTAAAAAATCATATAACCTTACGT\n+>NZ_GG669015.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD94, whole genome shotgun sequence\n+ACAAAGAAAGAGAATAAATAAATGAGATAGGAAGTGTTTCAATTTTTTTGTTACGAGTAATCCAAGAAGAAACAGTTCCT\n+TGAGAGAAAGCATGTAATTCACAAAATTCTTCTACAGTAATCCCTAGATGCTTGATAATGTATGCGTTGATAGGGTGTGG\n+ATATACAAAGGTTTTTCTAGGCATGGTGGGTAAGTTTCCTTTCTT\n+>NZ_GG669014.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD93, whole genome shotgun sequence\n+AATTTTTCTTGGATGGCGCGGGACAGAATCGAACTGCCGACACATGGAGCTTCAATCCATTGCTCTACCAACTGAGCTAC\n+CGAGCCAAAAACGGTCTGGACGGGACTCGAACCCGCGACCTCCTGCGTGACAGGCAGGCATTCTAACCAGCTGAACTACC\n+AAACCAATTCGTTTTTGCTTTATGCAAATGTATGCTTTAAAAAAT\n+>NZ_GG669013.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD92, whole genome shotgun sequence\n+GGAGGATTACCCAAGTCCGGCTGAAGGGAACGGTCTTGAAAACCGTCAGGCGGGTAAAACCGTGCAAGGGTTCGAATCCC\n+TTATCCTCCTTTCTTAGGAATCAATTTTCCNTGGTCTAATTATCGCGGGGTGGAGCAGTCAGGTAGCTCGTCGGGCTCAT\n+AACCCGAAGGTCGTAGGTTCAAATCCTGCCCCCGCAATTGCTTTT\n+>NZ_GG669012.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD91, whole genome shotgun sequence\n+GGAGTCTGACGAAGCTTATAAGCAGTTTATTGATGAGTATTTTCCATCTTACGACTATGCAAAAGTCAATCGTCTATTGC\n+AATTACGAGCAGACATTTTTTCTACTCTTGCAGGTGAAGCAATCGCAAGCGACGTTAACGGTAAATTTAATAACGACTTA\n+GAAAACATTACAAAACGAATCTACAATTCTAATTCTAATGCGTTGATG\n+>NZ_GG669011.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD90, whole genome shotgun sequence\n+GGAATCAGATGAAGTTTATAAACAATTCATTGATGAATATTTTCCATCCTTTGACTATGCGAAAGTTAATCGCTTGTTAC\n+AATTACGAGCAGACATTTTTTCTACCATTGCAGGTGAAGCAATAGCTAGTGATGTTAACGGTAAATTTAATAACGACTTA\n+GAGAATATCACAAAACGAATCTACAATTCTAATTCTAATGCGTTGATA\n+>NZ_GG669010.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD89, whole genome shotgun sequence\n+GTCGTATTTTTCACGAATAAAGATATCTGCATTTTCGTATTTTTCAGCTTTCCATGGTTCGATATTGCTCGCCCATAATT\n+GCCAACCTTCCTTGGTTTCAACAGGTTCTAACAAACGAAAAGCAACACCGCAAGCACCTTGAAACCGAGCTGTGTCAGAA\n+TCAAGCATGGCAAACCGCATATCATTCACTAACTCTGTCAGCCGTTCGAACTCTTT\n+>NZ_GG669009.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD88, whole genome shotgun sequence\n+CGCCAATGAAACATTAACCGCCGTAGCGAAAAACGCCAGCGGTACAGAAAGTACGCCAACAACGTTCCAAACGCCAGCGG\n+ATGAGACAACCGTAACCGCACCAACAATCACAGGAGTGACAGGTAATTCAACGGCAGGTTACGAGGTTAAAGGAACTACT\n+GATGCCAATGCCACGGTTGAGATCCGAAATGCAGGAGGTGCCGTGATAGGCACAGGGAGCGCC\n+>NZ_GG669008.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD87, whole genome shotgun sequence\n+CAGGATAGTATTTTCAGATGTATTCCCTGGTGTAGAAATAAAATCAGGTGATGGCGCTATGAATTTGTGGAGTTTGAACG\n+GTGGGTACAATAATTATTTAGCGACATCCCCAACAGGAACAGCTACAGGTTTTGGTGCAGACATTATTATCATTGATGAT\n+TTAATTAAAAATGCCGAAGAAGCAAATAATGCTATGGTTTTAGAGAAGCACTGGGATTGGTTTACC\n+>NZ_GG669007.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD86, whole genome shotgun sequence\n+GTATTTTTCATTTGCAACTATCCTTTTATTTTTTATTTGTATCAGTATCAATTTTACAGTAAACATGCATTTATGCCGAG\n+AAAATTTATTGATGTTGAGAAGAACCCTTAACTAAACTTGGAGACGAATGTCGGCATAGCGTGAGCTATTAAGCCGACCA\n+TTCGACAAGTTTTGGGATTGTTAAGGGTTCCGAGGCTCAACGTCAATAAAGCAATTGGAATAAAGCAAT\n+>NZ_GG669006.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD85, whole genome shotgun sequence\n+ATCAACTTTTCATAGTTCTTCTCAATATACTTACGGTACTTCTCTTGGTCTCGTTTGCTAAAATCTTCTAGCATCTCACT\n+TTGAGTAATACCGTGTAAATCAGCTTGTGCCAATAACTGTCTTTGAATTTTAACTAAAGCACGTTCGAAAACAGATTCTA\n+GTTCACTAAGAGTTTTCTTTTCCAGTTTCAAGCGTGCTTTGTCTTCTAATTCACGACGTTTTTCCCAGTA\n+>NZ_GG669005.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD84, whole genome shotgun sequence\n+TGGCAAAAGGTGCCGATTTTATTGGTGGCGTGGATCCTTATTCACTAGATGGTGATTACAAAAAATCATTGGCTGAAACA\n+TTCCGCTTAGCAGATAAACATGGTGTCGGTGTGGATATTCATTTACATGACCGTCATGAAGCTGGGACAACAACGATTAA\n+AGAAATTATTCGTTTAACGAAAGAATATGGTCTACAAGACAAAGTATTTATCAGTCATGCCTTCGGGTTAAA\n+>NZ_GG669004.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOL'..b'GTGGTATTACCCAAGTTACATTTTGTGTTACTGGAGAAACCCAACTTAAAATCTGTTACTAAATA\n+AGCCACACTAGACATTACAGCAGGACATAACAAAAATGGAATAAATAAAATAGGATTTAATACAGTAGGTAATCCATACA\n+TTACTGGTTCACCAATATTAAACAAAACAGGCATAATTCCAAGTTTTGCAACTTCTTTATAATGACTATTTTTTGATACC\n+CAAAAAATCGCAATTAATAAACCTAAAGTTGCATACCAGACAAACGATCCGTATGATACACTTGTCCAAACATAAGGAAT\n+AGTTTCATTGTTTTGATAAGCTTCTAAATTAACTAAAAGCGCTACTCCAAATACACCTTCCATAATAGGTGCCATAACAT\n+TTCCACCATGAATACCGAAAAACCAGAAAAATTGAACTAAGAAAGCAACTAATATAACAACAAAAAAACTTTGGGAAAGT\n+CCTAACATAGGGCGTTGTAATATTTCGTAAATTACATCTGTTAAAATTTTTCCTGTAATTCTATTTAACAAAAATGTCAA\n+AATAGCAATTATATAAAGAGAAACTAAAGCCGGAATAATTGATAAAAATGGTTTAGCGATAGCTGGAGGAACTGTATCAG\n+GTAATTTAATTGTCCAATTTTTATTCATGAGTTTACAAAAAATAATTGAAGATAAAAAACCTATGATTATTGCGGTAAAA\n+TAACCATTTGAATTAATTTGTGTACCAGGCAACAATCCTGATATAGTCACATTTAAACTGTTACCTGTAACTGTTATTCC\n+CTCAACATCAGTAAATAGTGTTGTTAAGTCAATATTATTATTATTCGATAAATTATAAGTTGAAGTCATAGAATTACTTA\n+TAGAAATAATAAATGAAGACAGGGCGACTAGTCCTGAAGACAAAGTATCTGTTTTATATATTTTAGCAATATTTACTCCT\n+AAACAATAAATAAACAGTAAGGAAACAATAGAAATGCTTCCTTTTGATATCAAATTATTTATATCTACTAACCATTGAAA\n+ATAATCAGTAATCTTCTCATAGCCAAATTGCATAGGAAAATCTACTAAAAAAGCATTTAATAATATTGCAACCGAACCTG\n+TCATTATTACAGGCATCGTACCCATAAATGAATCTCTTAACGCTACTAAAAATCGTTGATTCCCAATCTTAGTAGCTATA\n+GGTAAAACTTTATTCTGGATTGTATTCATTATTTTCTCACTCATTATGATTGACTCCTTCAAAAAATAGTTAGAAAGCGC\n+TATCTAATTATAGTATAGATTTTTTTGACCATTTGAACATGATAATCTATACTTAAAACATGGTATTTTCTTCATAGTTA\n+GTTCTATAAAGGAGGATAATAATGGAGGATTTTTGGTATCATAATAAGTCAGTTTCTGCTCCAATTTCCCTTTCCCAATG\n+CGGATATGAATCTTATCATCCCAATTCTTCTATTCGTAATTATATAGTTCAACAAAAATGGATATTTCATTATGTTTTAT\n+CTGGTAAGGGATTCTTAGAAGTAGAAGCTCAACATTTTGAACTTATAGAACACGATATTTTCTTTTTTTTCAAGGTCAAA\n+AAGTGAAGTATTATACAGATAAAAAGGAACCTTGGACACTGATTTGGTTAGGTATACAAGGTGATAAGACTTCTGAATTT\n+TTGAAAGAAACAACTTTACTAAATACTCATACAGTTAGCTTGACTAAGAATATAAATAAAAAACACACTATTGAAAATAG\n+TATGTGAAAATAGAGAACTAATTGGGGTTTGTCAACTAAACTGTGGAAGTTAAATAGTTAAGAGTTTTTAACCACCATAA\n+TTCTCTCGGCTATTTTGAAATCAGATAAATTTTGATCGGACACATAGTTGAATAAACCTACCGTTGTTACGGAAGGTAAA\n+TCGCATACTTTTCATTCTAGAGGAGAAGGTCTCGTTGATCATTAACTGCTTAAGCACCATAGCCCAGTTTTGAATTCGAC\n+CACCTGACCACTTCGCGTGTAATTCTTTCGTGCGTAAATAAAGTAGTTTTAGGAGTGCATTCTCATTAGAGAACGCTCCT\n+TTTTTTGTGACTTTTCTGAAGCTGGAGTGGACACTTTCAACCGCATTGGTAGTGTACATAATTTTTCGAATGGCACTACC\n+ATAATCAAATAGTTGTTCAACATGTGCAAAGTTCCGTTTCCAGACATCTACAGCACCAGAATAATGAGACCACCGATTTT\n+GAAAACTGCCAAAAGCAGCATGTGCAGCGTTTAGAGAAGAAGCACCGTAGAACTTTTTCATATCTCGGCAGACTTCCTTA\n+TAGTCCTTACTTGGAATATAGCGCAATGCATTTCGAACAAGATGAACAATACAGCGCTGAACAATTACCGATGGAAAGAT\n+CGCTTTTGCGCCTTCTTCGAGGCCAGAAACACCGTCCATCGAAATGAAAAAGACATCTTCGACACCACGTGCTTTCAGTT\n+CATCAAATACTTGCATCCAGCGATTTTTAGATTCTGTTTGATTTAACCATAATCCTAAAATCTCCTTATTTCCTTTGAGA\n+TCATAGCCAAGAATGGTGTATACAGCATATTCTTTGGCTTCATAATTTTCTCGTAAAGTAACATACATACAATCAACGAA\n+TAGAAAGGCATAACACTTTGCTAGGGGGCGGGCTTGCCATTCTTCCAATTCAGGAAGGACAGCGTCAGTGATATCTGAAA\n+TCATTTCATGGGAAATATCAAAGCCATAGATAGCTTCGACGGTTGCGGCAATATCTCGTTGACTCATTCCTCGTGCATAC\n+ATGGAAAGAACCTTCCCTTCGATGTCGGAGACATCTCGTTTTCTCTTAGGAATTAACTCTGGTTCAAAGGAAGCTTCCCG\n+GTCTCTAGGAACATCAATAGCTACTTCACCAAAACTGGTTTTAAGCGTTTTAGTTCCATAGCCATTTCGACGGTTATCGT\n+GTTCCTTAGGCTCTTTAGAATGGGCATCATAACCTAAATGATTATTCAATTCTCCTTGAAGCATTTTTTCAAAAAGGGGC\n+CCAAACACATCTTTCAAAGCATCTTGCATGTCATCGACAGATTCAGGTTGATAGGCATTCAGAATGGATTCAGCTAACTT\n+TTCGGCATCAGGATTTCTTTTCTTTCTAGCCATCGTGTAATCACCTCTTGATCTTATTGTAGAAAAAGAAAAACCGCGAA\n+GCAACCACCTGCCTAGGATTAATGGTTACTTACACGGTTTACATTACACTCTCATCATTAAAAAATATCTTTCGATATTA\n+CTAAAAAATGAAATTATCTATTTGAAATTTAAATCTGATAATATATTGAGTGTTCCAATGAGGGCTTTGATCCTATTATC\n+CATATCTTTTTCAGTTTTAATATTGATACACATTATAAGAAAAAGAAACTTTTGGTTAATTTATTTCATCCCAGTGCAAA\n+ATATAAAAAAGTAAAATAGACCATAGGCAATAGATTAACAATTAATATAATACAAGCAAATATTCTATTCATTGTATTTC\n+TGCTTTCAAAAAGTTCTAATATTGAAAGTATAATTCCACAAATGCCTATAATAAGTATGGGAATAAGATTAGAAAATAAC\n+ACCCCGAGCCAATCTGTGAAAATTACTATATTTACTAATATCCCTATTAACATACCTATCATATTTATTAAATCAATTTT\n+TTTCATTAGATATTTCTCCTTTATTAAATCTGAAGTACTTATATTAAAATAATTCTAAACTATTTACCTCAAAAAGTGCA\n+ATAAATTATTTCTGAACAATAAAATGATAGTCAAAACAAAAAAATATTGTTAATCGTTCAGAGCCATCCACCATTTTTAC\n+AATTAATGTATTCATATAAACTATTTACGATACTATAATAAAAGCATTATAGTTATTTATAAATAATTAAAGCAACT\n' 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