| Previous changeset 0:ef1c257adcbd (2020-05-05) Next changeset 2:54aa421c2911 (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_compare.xml macros.xml |
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added:
test-data/001 test-data/002 test-data/003 |
| b |
| diff -r ef1c257adcbd -r 7157accd23d0 drep_compare.xml --- a/drep_compare.xml Tue May 05 06:20:45 2020 -0400 +++ b/drep_compare.xml Sat Feb 12 17:40:04 2022 +0000 |
| [ |
| @@ -1,23 +1,20 @@ -<tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5"> +<tool id="drep_compare" name="dRep compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5"> <description>compare a list of genomes</description> + <expand macro="biotools" /> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - @PREPARE_GENOMES@ - dRep compare outdir - @GENOME_COMPARISON_OPTIONS@ - @CLUSTERING_OPTIONS@ - @TAXONOMY_OPTIONS@ - @WARNING_OPTIONS@ - @GENOMES@ +@PREPARE_GENOMES@ +dRep compare outdir +@GENOMES@ +@COMPARISON_CLUSTERING_OPTIONS@ +@WARNING_OPTIONS@ ]]></command> <inputs> <expand macro="genomes"/> - <expand macro="genome_comparison_options"/> - <expand macro="clustering_options"/> - <expand macro="taxonomy_options"/> + <expand macro="comparison_clustering_options"/> <expand macro="warning_options"/> <expand macro="select_outputs"/> </inputs> @@ -25,9 +22,24 @@ <expand macro="common_outputs" /> </outputs> <tests> - <expand macro="test_defaults_log"> - <has_text text="dRep compare finished" /> - </expand> + <test expect_num_outputs="4"> + <expand macro="test_string_inputs"/> + <expand macro="test_default_comparison_clustering_options"/> + <expand macro="test_default_warning_options"/> + <expand macro="test_default_select_outputs"/> + <expand macro="test_log_output"> + <has_text text="dRep compare finished" /> + </expand> + </test> + <test expect_num_outputs="4"> + <expand macro="test_integer_inputs"/> + <expand macro="test_default_comparison_clustering_options"/> + <expand macro="test_default_warning_options"/> + <expand macro="test_default_select_outputs"/> + <expand macro="test_log_output"> + <has_text text="dRep compare finished" /> + </expand> + </test> </tests> <help><![CDATA[ **dRep compare** @@ -39,9 +51,9 @@ dRep performs this in two steps: - first with a rapid primary algorithm (Mash) - - second with a more sensitive algorithm (ANIm). + - second with a more sensitive algorithm (ANIm). -We can’t just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ and `Module Descriptions <https://drep.readthedocs.io/en/latest/module_descriptions.html>`_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists. +We can't just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ and `Module Descriptions <https://drep.readthedocs.io/en/latest/module_descriptions.html>`_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists. dRep first compares all genomes using Mash, and then only runs the secondary algorithm (ANIm or gANI) on sets of genomes that have at least 90% Mash ANI. This results in a great decrease in the number of (slow) secondary comparisons that need to be run while maintaining the sensitivity of ANIm. |
| b |
| diff -r ef1c257adcbd -r 7157accd23d0 macros.xml --- a/macros.xml Tue May 05 06:20:45 2020 -0400 +++ b/macros.xml Sat Feb 12 17:40:04 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' |
| b |
| diff -r ef1c257adcbd -r 7157accd23d0 test-data/001 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/001 Sat Feb 12 17:40:04 2022 +0000 |
| b |
| 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 ef1c257adcbd -r 7157accd23d0 test-data/002 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/002 Sat Feb 12 17:40:04 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 ef1c257adcbd -r 7157accd23d0 test-data/003 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/003 Sat Feb 12 17:40:04 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' |