| Previous changeset 1:82f2b6f20fa2 (2019-01-26) Next changeset 3:feb7e635c6af (2019-04-02) |
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Commit message:
planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 |
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modified:
macros.xml snippy-core.xml snippy.xml test-data/S1.tgz test-data/S2.tgz test-data/fna_ref/snps.gff test-data/fna_ref/snps.txt test-data/wildtype.gbk |
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added:
test-data/GCF_000293905.1_ASM29390v1_genomic.fna test-data/S3.tgz test-data/a.tgz test-data/a_1.fastq test-data/a_2.fastq test-data/a_b_c.core.txt test-data/a_fna_ref_mincov_2_minqual_60.snps.gff test-data/a_fna_ref_mincov_2_minqual_60.snps.txt test-data/b.tgz test-data/b_1.fastq test-data/b_2.fastq test-data/b_fna_ref_mincov_2_minqual_60.snps.gff test-data/b_fna_ref_mincov_2_minqual_60.snps.txt test-data/c.tgz test-data/c_1.fastq test-data/c_2.fastq test-data/ref.fna test-data/reference.fasta test-data/snippy-core-samples |
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removed:
snippy_core_wrapper.pl test-data/core/core.txt |
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| diff -r 82f2b6f20fa2 -r 776ebd1239da macros.xml --- a/macros.xml Sat Jan 26 14:36:48 2019 -0500 +++ b/macros.xml Mon Mar 18 10:59:29 2019 -0400 |
| [ |
| @@ -10,7 +10,7 @@ <version_command><![CDATA[snippy --version]]></version_command> </xml> - <token name="@VERSION@">3.2</token> + <token name="@VERSION@">4.3.6</token> <xml name="citations"> <citations> |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da snippy-core.xml --- a/snippy-core.xml Sat Jan 26 14:36:48 2019 -0500 +++ b/snippy-core.xml Mon Mar 18 10:59:29 2019 -0400 |
| [ |
| @@ -1,3 +1,4 @@ +<?xml version="1.0" encoding="utf-8"?> <tool id="snippy_core" name="snippy-core" version="@VERSION@"> <description> Combine multiple Snippy outputs into a core SNP alignment @@ -7,16 +8,19 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - - perl '$__tool_directory__/snippy_core_wrapper.pl' - '$is_reference' - --indirs '${" ".join(map(str, $indirs))}' - + #for $indir in $indirs + #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0] + mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 && + #end for + #set snippy_dirs = ' '.join([os.path.splitext(os.path.basename(str($indir.name)))[0] for $indir in $indirs]) + snippy-core + --ref '$ref' + ${snippy_dirs} ]]></command> <inputs> <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" /> - <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." /> + <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" /> <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection"> <option value="outaln" selected="True">A core SNP alignment in the fasta format</option> <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option> @@ -42,11 +46,11 @@ </outputs> <tests> - <test><!-- Test #1 - test with 2 zipped directories --> - <param name="indirs" value="S1.tgz,S2.tgz" /> - <param name="is_reference" value="false" /> + <test><!-- Test #1 - test with 3 zipped directories --> + <param name="indirs" value="a.tgz,b.tgz,c.tgz" /> + <param name="ref" value="reference.fasta" /> <param name="outputs" value="outtxt" /> - <output name="alignment_summary" ftype="txt" file="core/core.txt" /> + <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" /> </test> </tests> @@ -71,6 +75,5 @@ snippy **must** have been run with --cleanup False ]]></help> - <expand macro="citations" /> </tool> |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da snippy.xml --- a/snippy.xml Sat Jan 26 14:36:48 2019 -0500 +++ b/snippy.xml Mon Mar 18 10:59:29 2019 -0400 |
| [ |
| b'@@ -11,37 +11,39 @@\n <command detect_errors="exit_code"><![CDATA[\n \n #if $ref.is_of_type("fasta")\n- cp \'$ref\' \'foo.fna\' &&\n+ cp \'$ref\' \'ref.fna\' &&\n #end if\n #if $ref.is_of_type("genbank")\n- cp \'$ref\' \'foo.gbk\' &&\n+ cp \'$ref\' \'ref.gbk\' &&\n #end if\n snippy\n --outdir \'out\'\n- --cpus "\\${GALAXY_SLOTS:-1}"\n+ --cpus \\${GALAXY_SLOTS:-1}\n+ --ram \\$((\\${GALAXY_MEMORY_MB:-4096}/1024))\n #if $ref.is_of_type("fasta")\n- --ref \'foo.fna\'\n+ --ref \'ref.fna\'\n #end if\n #if $ref.is_of_type("genbank")\n- --ref \'foo.gbk\'\n+ --ref \'ref.gbk\'\n #end if\n --mapqual $adv.mapqual\n --mincov $adv.mincov\n --minfrac $adv.minfrac\n+ --minqual $adv.minqual\n #if $adv.rgid\n- --rgid \'$advanced.rgid\'\n+ --rgid \'$adv.rgid\'\n #end if\n #if $adv.bwaopt\n- --bwaopt \'$advanced.bwaopt\'\n+ --bwaopt \'$adv.bwaopt\'\n #end if\n \n #if str( $fastq_input.fastq_input_selector ) == "paired"\n- --pe1 \'$fastq_input.fastq_input1\'\n- --pe2 \'$fastq_input.fastq_input2\'\n+ --R1 \'$fastq_input.fastq_input1\'\n+ --R2 \'$fastq_input.fastq_input2\'\n #end if\n #if str( $fastq_input.fastq_input_selector ) == "paired_collection"\n- --pe1 \'$fastq_input.fastq_input.forward\'\n- --pe2 \'$fastq_input.fastq_input.reverse\'\n+ --R1 \'$fastq_input.fastq_input.forward\'\n+ --R2 \'$fastq_input.fastq_input.reverse\'\n #end if\n #if str( $fastq_input.fastq_input_selector ) == "single"\n --se \'$fastq_input.fastq_input\'\n@@ -52,19 +54,20 @@\n \n &&\n \n- gunzip out/snps.depth.gz\n-\n- &&\n-\n #import re\n #if str( $fastq_input.fastq_input_selector ) == "paired"\n #set $dir_name = re.sub(\'[^\\w_]\', \'_\', $fastq_input.fastq_input1.element_identifier)\n+ #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"\n+ #set $dir_name = re.sub(\'[^\\w_]\', \'_\', $fastq_input.fastq_input.name)\n #else\n #set $dir_name = re.sub(\'[^\\w_]\', \'_\', $fastq_input.fastq_input.element_identifier)\n #end if\n \n- mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ &&\n+ mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&\n tar -czf out.tgz ${dir_name}\n+ #if "outcon" in str($outputs) and $adv.rename_cons\n+ && sed -i \'s/>.*/>${dir_name}/\' out/snps.consensus.fa\n+ #end if\n \n \n ]]></command>\n@@ -99,8 +102,10 @@\n <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />\n <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />\n <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />\n+ <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />\n <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />\n <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />\n+ <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" />\n </section>\n \n'..b'ram name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />\n- <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />\n+ <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />\n+ <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />\n+ <param name="mincov" value="2" />\n+ <param name="minqual" value="60" />\n <param name="outputs" value="outgff,outsum" />\n- <param name="mapqual" value="40" />\n- <output name="snpsum" ftype="tabular" file="map_qual/snps.txt" lines_diff="6" />\n- <output name="snpgff" ftype="gff3" file="map_qual/snps.gff" />\n+ <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />\n+ <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />\n </test>\n \n- <test> <!-- test 4 - gbk mincov=15 -->\n- <param name="ref" value="wildtype.gbk" ftype="genbank" />\n- <param name="fastq_input_selector" value="paired" />\n- <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />\n- <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />\n- <param name="mincov" value="15" />\n- <param name="outputs" value="outgff,outsum" />\n- <output name="snpsum" ftype="tabular" file="min_cov/snps.txt" lines_diff="6" />\n- <output name="snpgff" ftype="gff3" file="min_cov/snps.gff" />\n- </test>\n-\n- <test> <!-- test 5 - gbk minfrac=0.7 -->\n- <param name="ref" value="wildtype.gbk" ftype="genbank" />\n- <param name="fastq_input_selector" value="paired" />\n- <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />\n- <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />\n- <param name="minfrac" value="0.7" />\n- <param name="outputs" value="outgff,outsum" />\n- <output name="snpsum" ftype="tabular" file="min_frac/snps.txt" lines_diff="6" />\n- <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />\n- </test>\n-\n- <test> <!-- test 6 - fasta ref default paired_collection -->\n-\t <param name="ref" value="wildtype.fna" ftype="fasta" />\n+ <test> <!-- test 2 - fasta ref one snp paired_collection -->\n+ <param name="ref" value="reference.fasta" ftype="fasta" />\n <param name="fastq_input_selector" value="paired_collection" />\n <param name="fastq_input">\n <collection type="paired">\n- <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />\n- <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />\n+ <element name="forward" ftype="fastqsanger" value="b_1.fastq" />\n+ <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />\n </collection>\n </param>\n+ <param name="mincov" value="2" />\n+ <param name="minqual" value="60" />\n <param name="outputs" value="outgff,outsum" />\n- <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />\n- <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />\n+ <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />\n+ <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />\n </test>\n \n </tests>\n@@ -250,6 +228,8 @@\n \n - minimum fraction - Float - Minumum proportion for variant evidence (default \'0.9\')\n \n+ - minimum quality - Float - Minumum QUALITY in VCF column 6 (default \'100.0\')\n+\n - rgid - String - Use this @RG ID: in the BAM header (default \'\')\n \n - bwaopt - Extra BWA MEM options, eg. -x pacbio (default \'\')\n' |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da snippy_core_wrapper.pl --- a/snippy_core_wrapper.pl Sat Jan 26 14:36:48 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,82 +0,0 @@ -#!/usr/bin/env perl - -#-------------------------------------- -# -# snippy_core_wrapper.pl -# -# This is an intermediary script between snippy-core.xml and snippy-core -# It: -# - Copys the supplied zipped snippy output files to the working dir -# - Untars them to their datafile name -# - Builds the snippy-core command -# - Runs the snippy-core command -# -#-------------------------------------- - -use warnings; -use strict; -use File::Copy; -use File::Basename; - -my(@Options, $indirs, $noref); -setOptions(); - -my @list_of_dirs = split /\s+/, $indirs; - -#The list of final directories to be passed to snippy-core will be stored here. -my @snippy_outs; - -foreach my $d (@list_of_dirs){ - print STDERR "$d\n"; - my $bn = basename($d); - my ($name, $dir, $ext) = fileparse($d, '\..*'); - copy($d, $bn); - print STDERR "$d, $bn, $name, $dir, $ext\n"; - `tar -xf $bn`; -} - -my $test_list = `ls -d */`; -$test_list =~ s/\///g; -print STDERR "$test_list\n"; - -@snippy_outs = split /\s+/, $test_list; - - -my $commandline = "snippy-core "; - -$commandline .= "--noref " if $noref; -$commandline .= join(" ", @snippy_outs); -print STDERR "snippy-core commandline: $commandline\n"; - -my $ok = system($commandline); - -#---------------------------------------------------------------------- -# Option setting routines - -sub setOptions { - use Getopt::Long; - - @Options = ( - {OPT=>"help", VAR=>\&usage, DESC=>"This help"}, - {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."}, - {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."}, - ); - - &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage(); - - # Now setup default values. - foreach (@Options) { - if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) { - ${$_->{VAR}} = $_->{DEFAULT}; - } - } -} - -sub usage { - print "Usage: $0 [options] -i inputfile > ... \n"; - foreach (@Options) { - printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC}, - defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : ""; - } - exit(1); -} |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/GCF_000293905.1_ASM29390v1_genomic.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GCF_000293905.1_ASM29390v1_genomic.fna Mon Mar 18 10:59:29 2019 -0400 |
| b |
| b'@@ -0,0 +1,59475 @@\n+>NZ_AMBU01000001.1 Salmonella enterica subsp. enterica serovar Heidelberg str. CFSAN00322 CFSAN00322_22, whole genome shotgun sequence\n+GAGCAGTGCCGCTTCGTTTTTTCTCAGCGGCGCGGGGTGTGCATATTACGCTTTCCCGCTTCAGAGTCAAGCGTTTATTT\n+TCGCTTTTCTCCGTGAGGTTCTGGTCCGAACCCCGCTGACCCGGCGGCCTGTGTGCCGTTGTTCCGTGTCAGTGGTGGCG\n+CATTATAGGGAGTTATTTTTGCCTGACAAGAGGAAATTTAAAATAATTTTCTGAGTGCGCACTTTTTATTCTTTGCGTTT\n+ATTTTGCCGACGATTTGTTGGTTAAATGGGCTATTTCACGGGCAAAGTGCGCAACCTGCTCCCAGTCGGTGTACACCACT\n+TCTTTACTGGTATCCGTTTCGCCGCCCGACATCTTCATAATAAGCTTGATCATCAGACGGTCATACCAGCGATAGCGGGG\n+ATAGCGAAGCGCGCCTGCAATGACGGCACAGTAGTCAGGTCGCCACGGAGAGCTCATTAAAAACTTACGCGCGTAGCTGT\n+TAGTCTGCGGCGTCCGTTTTTCAGCTTTACGCGCCACCAGGTTAACGGAATAAAAGGCGCTCGGCATTCCGTTCAACCGC\n+GTGGCATATTTCTTAACAAACTCCTGAAAGGCGCTGTGGTAATGACCATAACGAATAGACGCGCCAATCACTACGCGATC\n+ATAGCTATCCCAGTCCGGCTCTTCTGCGCGATGCAGATTAACGACATCGGCCCAGATCCCCATCTCTTTGAGTTCAGAAG\n+CCAGATAAGAGGCAATTTCGCGCGTTTGTCCGTCCCGGGTAGAGAAAAGAATCAATGTTTTCACGTGTTACTCCATTATT\n+CACGCCAGAAAGTCGGGGTAAAAAGTACCAGCAAAGTGAATACTTCCAGACGACCAAATAGCATGTTGGCGATGAGTATC\n+CATTTCGCAACCGGATTCATACTGGCGAAGTTATCAGCAACCACCCCCAGCCCCGGTCCCAGGTTATTAAGCGTAGCCAC\n+TACCGAGGCGAAAGCCGAGAAATCATCTACGCCTGTAGCGATAATGGCCAGCATACTGACGATAAATACCAGCGCGTAGG\n+CAGAAAAGAATCCCCAGACGGCTTCCAGAATACGTTCTGGCAGCGCCCGGTTCCCCAGCTTAATACTGTAAACGGCATTC\n+GGATGCACCAGACGTTTGAGTTCGCGGTTCCCCTGTTTAAACAACAACAGAATACGGATGACCTTTAACCCCCCGCCCGT\n+TGACCCGGCGCAACCGCCAATAAACGCGGAACATAGCAGCAAGACGGGCAAAAACAGCGGCCAGCGCGCAATGCTGTCCG\n+TGGTAAACCCTGCCGTTGTCGCCATCGACACAACCTGGAAGAACGCCTGATTTAGCGTTGTCAGCGCCGAGTCGTAGATA\n+TTATGGAACCACAGTACCAGCGTGCAGATCACCACCAGTGTCAACTGTACGCCGATGAACATGCGGAATTCCGGATCGCG\n+CCAGTATACTTTCAGGCTACGTCCGCTTAATAAAGAGAAATGCAGGCCATAGTTACAACCGGAGATCAGCAGGAAAATAG\n+CGATGATGGTATTAATAGTGGGACTATCAAAATAGCCTACGCTGGCGTCATGCGTTGAGAAGCCGCCGATAGCGATAGTG\n+GAGAAGCTGTGTCCGATAGCGTCAAACGCGGGCATCCCTGCAAACCATAGCGCCAGCGCGCAGGCTACCGTTAGCAAGAC\n+ATAGATAAGCCACAGCGTTTTCGCCGTCTCGGCAATACGCGGGCGCATTTTGTTATCTTTGAGCGGCCCCGGCATTTCCG\n+CCCGATAGAGCTGCATCCCCCCGACGCCGAGGATAGGGAGAATCGCCACCGCCAGCACAATGATCCCCATACCGCCAAAC\n+CATTGCAGCATCTGACGATAAAAGAGAATGGCGTGCGGTAATGAATCCAGCCCCACCAGAGTAGTGGCGCCCGTGGTGGT\n+TAACCCGGAGAACGATTCAAAAAAAGCATCGGTAATGGTGAGGTTTGGGCTTTCCGAGAAAATAAACGGCAGCGCACCCA\n+CGCTGCCCAGCACGGTCCAGAACAGCACCACGATAAGAAATCCTTCGCGGGATTTCAGCTCGCCCTTTTCCCTACGGTTC\n+GGCCACCACAGTATGGAACCGATCGCCAGCGCGACAAAAAAGGTCTGCGTGAACGCTCTTCCTGCGCCATCACGATATAT\n+TAGCGCTACCAGTCCCGGGAGAATCATTGTCCCCGAAAATAAGATAACCAGTAGTCCAACGATTCGGGTAATGGCGCGAA\n+AATGCATCTCTGCCGCTTCCTTTATTCTTAAAAATGAGGTGGGGATTATTCTTCAATCGCTAACAATTGCAATGAACCAC\n+GGCTAAAATCCGCCAGTTTTGTGGAAAATGCATTCACATGAGCAAAAGGAAGCGCCACCCTGAGCCGAACAGACGCCTGA\n+TAATCGCTGGAAACGATCTTCCCGGCAAACTGTCCTAATAATGCTTCGATTCCGGCCAACTGACCGTACTCACACTGCAA\n+AGTATATTCGGTTAATGGCGTCTTGCGTTGTGTGGCAAGCTGACGTAATGCCTGATTCACACCGCCGCCATAGGCTTTTA\n+CCAGCCCGCCCGTACCCAGCAGAATACCACCATAGTAGCGCACGACGACGGCAGTAATTTCTCCGACGCCGCTGCCCATC\n+AATTGCGCAAGCATCGGCTTGCCTGCCGTTCCCGCCGGTTCGCCGTCGTCTGAAAAGCCCAGTTGCTGTGAGTCGTCCGG\n+CGCACCCGCCACCCACGCCACACAATGGTGGCGCGCATCAGGGTGCTCAGCTCTGACTGACTCAACAAACGCTTTCGCCG\n+CGTCTACGCCATCGGTATGCGCCAATAGCGTAATAAAGCGGCTTTTTTTGATCTCTTCAACAACGGTGACCGGCGCTGCA\n+GGGATTAACCAACTGTCCATTACGCCAGTTTTAAATCCCGCGTCATGTTTTCCACGCCGTTTTCGTGGATGACCACGTTA\n+TCTTCAATGCGAATACCGCCGAAAGGCTTGAGCGCTTCAATTTTCTGCCAGTTGAAGTGCTTGCTGAACGGGCCTTCGCG\n+CCACGGCGCTAACAGCGATTCGATGAAGTAAATCCCCGGTTCGATGGTCAACACCATTCGCGGCTGTAACACACGCGTGC\n+AGCGCAGATACGGGTATTTGGACGGTGCAGCGAGATGCGTACCGGAATCATCCTGCATAAACCCGGCCACATCGTGTACC\n+TGCAGACCCAACGGATGTCCAATACCGTGCGGCATAAACGGCCCGGTAAGATCATTTTCCACCATCGCCTCTTCACTCAT\n+GTCGGTAATGATTTGATGTTTACGCAGCAGCTTCGCGATACGTTGATGGAACTGAATATGATAATCCACATAGCTGACGC\n+CCGCCTTCATGGTAGCGATCAGCGCCAACTGTTCGTCGTTAACATCTTTCACCAGGTGGGCGTAGTCGTTATCGCTTTTC\n+GCCGACCAGGTCCGCGTCAGATCCGCCGCGTAGCCGTTGTATTCCGCGCCCGCATCCAGCAGGAAACTGCGCATTTCAGA\n+CGGTGCCTGATGATCCAGTTTCGTGTAATGCAGCACGGCGGCATGTTCGTTCAGCGCCACAATGTTGCTGTACGGAACAT\n+CGGTATCGCGATGTCCCGTGGCGGTCAGGTACGCCAGATTGATGTCAAACTCGCTCATGCCGGAACGGAAGGCCTCTTCC\n+GCCGCCCGATGACCGCTCACCGCCATTTTCTGCGCTTCGCGCATACAGGCCAGTTCATAATCCGTTTTAT'..b'CAGGCAGCGTACTGTTTGTCAGTTATG\n+AAATATGCCTGGCGCTTTCTCTCGGTTATGCCGCCACTCGCCATCAGGCTATCGAAGTCGGCATGGTTAACTATTTATGG\n+CCCAGCCTGACCATTCTGTTTGCCATTCTTTTTAATGGGCAAAAAACTAACTGGCTTATTGTTCCTGGATTGCTTATTGC\n+ACTTACTGGCGTTTGCTGGGTTCTGGGGGGCGAGAATGGTCTTAATCCAGGAGAAATTATCAGCAATGTCGCCACCAGTC\n+CGCTAAGTTATTTACTGGCATTTCTTGGGGCGTTTATATGGGCGACGTACTGCACGGTCACAAATAAATATGCGCGTGGT\n+TTTAACGGTATCACCGTCTTTGTGTTACTCACCGCCGTGGCGCTGTGGTTCCACTATTTTCTTACGCCGCAACCTGCCAT\n+GATATTTAGCCTACCGGTGATTGCTAAACTTTTTACCGCGGCATTAACGTTAGGGTTTGCCTACGCCGCATGGAATGTGG\n+GCATACTTCATGGCAATGTGACTATCATGGCCGTAGGGTCTTATTTTACCCCCGTCATGTCCTCTGCTCTGGCAGCGCTG\n+TTACTCAGCTCACCACTGTCATTCTCCTTCTGGCAAGGCGCAGTCATGGTTTGCGTAGGTTCGCTACTTTGTTGGCTGGC\n+AACGCGGCGGCGCTAATAGCGACGGGCGGGCCGATGTTGATATTAAATCGACCCGCTGTACCTTGACACTCTTCATAACA\n+CAACTACGCTTTTATCTATCGCCTGTGTGTATTTGACGATTTTTCATTTTCACGTGCTCCCCCTGCGCCATACCAGGATG\n+CGCTGGTAAAAATGGATTTTATAAAATCGTTAAATATGTTAATGCAATGATATAATCATATTAACAAATATATAATTAAC\n+GTTAGCTCGCAACTGTATTAGTGCATATAATAATCAGTCGTTACTACCAAAAATAAAACCATAAACAGCCCAATAGTCCC\n+CTCCGAAAATATATCTTATTAGACAGTCCCTATTTAAATTAATACTCTCAAATGTATTAAGGAGATCTCGATCACACAAA\n+TTAAAATAATTTGTAATCTTATGAAACTTATTATTGAACTTATGCCACTCCGTCATTTAAAAATAGTCTGCCATTGACAA\n+ACGCCTCGTTTAACAATGGTTGAGGAAACACGCTAAGAAAATTATAAGGATTATTAAAATGAAACTTAAGTTAGTGGCAG\n+TGGCAGTGACTTCCCTGTTGGCAGCAGGCGTTGTAAATGCAGCCGAGGTATATAACAAAGACGGCAATAAACTGGATCTG\n+TACGGTAAAGTTCACGCTCAGCATTATTTCTCGGATGATAACGGAAGTGATGGTGACAAAACTTACGCGCGTCTGGGCTT\n+TAAAGGCGAAACGCAGATCAACGATCAGTTAACCGGTTTTGGCCAGTGGGAATATGAATTCAAAGGCAACCGTACTGAAA\n+GCCAGGGCGCTGACAAAGACAAAACCCGTCTGGCGTTTGCTGGTCTGAAATTCGCTGACTACGGTTCTTTCGACTACGGT\n+CGTAACTACGGCGTTGCTTACGACATCGGCGCATGGACCGACGTTCTGCCAGAGTTCGGTGGCGATACCTGGACTCAGAC\n+TGACGTCTTCATGACTGGCCGTACTACTGGTGTTGCCACCTACCGTAACACTGACTTCTTTGGCCTGGTTGAAGGTCTGA\n+ACTTTGCCGCGCAGTACCAGGGCAAAAACGACCGTGACGGCGCGTACGAGTCTAACGGCGACGGTTTCGGTCTGTCCGCA\n+ACGTATGAGTACGAAGGTTTTGGCGTAGGTGCGGCCTATGCGAAGTCTGACCGTACTAACAACCAGGTGAAAGCAGCGAG\n+CAACCTGAATGCTGCGGGTAAAAACGCTGAGGTCTGGGCTGCTGGTCTGAAATATGATGCGAACAACATCTACCTGGCGA\n+CCACTTACTCCGAAACGCTGAACATGACCACCTTCGGTGAAGATGCAGCGGGTGATGCGTTTATCGCGAATAAAACCCAG\n+AACTTCGAAGCGGTTGCTCAGTATCAGTTCGACTTCGGTCTGCGTCCGTCCATCGCTTACCTGAAATCCAAAGGTAAAAA\n+CCTGGGTACTTACGGCGACCAGGATCTGGTTGAGTACATCGATGTTGGCGCAACCTACTACTTCAACAAAAACATGTCCA\n+CCTTCGTTGATTACAAAATCAACCTGCTGGACGACAGCGACTTCACCAAAGCGGCTAAAGTGTCTACCGACAACATCGTT\n+GCTGTTGGTCTGAACTACCAGTTCTAATTTTGTTGTAGTCTGAATACAAAGCCAGTCCTTTCAGGGCTGGCTTTTTCTCT\n+TGATGTAGACTCGGTCATAAGGAGTATGCCGTGCAGACGTTCACTGGTCGTTGTCTTTGCGGACAGAGCCATTTTACCGT\n+TGACGTCGAAATGCTGGATGTCTATGCCTGCCATTGTACGCTGTGTCAAAAATGGTCGGGTGGAATAGCCATGTATCTGG\n+AAGCCTGCGGGCAACCACAGCTAGCCCCCCTTTCCCCGGAACCGCCATACTTTTCATCCTCTTCGCGCGGCGAACGCTAC\n+TTCTGTTCCGGCTGCGGGTGTCCGCTGTGGTTCCGGCTTACCGATACCGATCGCTATTTTATTCCCTGGACCTTACTGGA\n+GCTGAACGAAGTTGATCGCCGTCGGCTGATTCTGGCTGCGGAAATTTATACCGAAACCCAGCCTGCCTTCTGGCGACTGA\n+CGGGGCAATACGCACGCCTCAGCGGTAAAGAGGTTGAGGAAATGGACTCCCCCTGCCAGCTAGCGCATTAAGCGCTTATC\n+TCATCAGGCGTTATGTTATCGGCGTTGGGCTTTTGCCAGGCTGAACCACATCCCTACCGCCAGCAAAAGAAGCATACTCC\n+CGGCGCTGCTTAATGCCACGCTATGCGACCAGATAAAGGCATGTCTGGCGGCGTCCAGTATTGCCTGCCCCTGCGTGGGC\n+GGCAGGCAATTCGCCAATTGCACGGCTTCTCCCATTGAAGATGACGCTCTGGCAATCTCTTGCGCCTCAAGCCCGGCAGG\n+CAGACGGATAGACGCGGAGAAGCTACGGCTTAACAACAGACCGAAAATGGCGATGCCCAGTCCCGCGCCCAGTTCATAAG\n+CCATCGTTTCTATCGCGCCGGCCGCCGCCGCTTTTTCTGCCGGCGCAGCGGCCATAATTGCCGACGTGGAAGCCAGCAAT\n+GCGCTGGCGGCGCTAAATCCCAGCAGCGCCATCAGCCCCCAGGCCTGCCATTGTTGGGTGCTGAAATCCGTCATCGCCAG\n+GCCATAAAAACTCAGCGCGCTTAACGCCATGCCGCCCGTCGCGACCAGCCGTAGTCCCAGACGCGAGACCAGCACGCCCG\n+CAATCGGCCCGCTGAATCCACTGGCGACCATCACCGGCAGCATAAATACCCCGGCCTCATAAGGCGATAGTCCGTGAACA\n+AACTGCAGCTCTTGCGCCATCAGCAGCTCAAAACCCACCAGCGTGATCATCGCGGTCATTGCCATCACGACGCCGCTCAG\n+GATAATGCGATGGGTAAATAGTCGCATATCAATCATCGGACGCGATGTCGCAAGCTGTGTGCGGATAAAGAGTCCCAGTA\n+GCAACGCGCCGGTAAGCAGGGTAAGCGAGATGACCCACAGCGACAGATGCCCTTTCAGCGCGGTTTTAGCGCTATAGACC\n+AACAGCAAAATGGCAATAATCAGCATCACCGCATGGCCAAGATTGAGCGGTTGATCGCGACGGCCCGCCTGGCGAGGAAC\n+ATAACGGGCGGTTAAGCCCATGACGACCAGCACAATCGGCACGTTGATCAGGAAAACCGATCCCCAGTAAAAATGCTCTA\n+ATAATATGCCGCCGATGAGCGGCCCAAACGCCG\n' |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/S1.tgz |
| b |
| Binary file test-data/S1.tgz has changed |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/S2.tgz |
| b |
| Binary file test-data/S2.tgz has changed |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/S3.tgz |
| b |
| Binary file test-data/S3.tgz has changed |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/a.tgz |
| b |
| Binary file test-data/a.tgz has changed |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/a_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a_1.fastq Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@1 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttaaact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttaaact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttaaact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@4 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttaaact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@5 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttaaact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/a_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a_2.fastq Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@1 +agtttaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2 +agtttaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3 +agtttaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@4 +agtttaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@5 +agtttaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/a_b_c.core.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a_b_c.core.txt Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +ID LENGTH ALIGNED UNALIGNED VARIANT HET MASKED LOWCOV +a 700 51 649 0 0 0 0 +b 700 51 649 1 0 0 0 +c 700 51 649 1 0 0 0 +Reference 700 700 0 0 0 0 0 |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/a_fna_ref_mincov_2_minqual_60.snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a_fna_ref_mincov_2_minqual_60.snps.gff Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +##gff-version 3 |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/a_fna_ref_mincov_2_minqual_60.snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a_fna_ref_mincov_2_minqual_60.snps.txt Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +DateTime 1970-01-01T00:00:00 +ReadFiles a_1.fastq a_2.fastq +Reference reference.fasta +ReferenceSize 700 +Software snippy 4.3.6 +VariantTotal 0 |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/b.tgz |
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| Binary file test-data/b.tgz has changed |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/b_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_1.fastq Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@1 +tcctcaagccattgtgtgtaattaaccactaattgtgtataagtttaaact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2 +tcctcaagccattgtgtgtaattaaccactaattgtgtataagtttaaac ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3 +tcctcaagccattgtgtgtaattaaccactaattgtgtataagtttaaa ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@4 +tcctcaagccattgtgtgtaattaaccactaattgtgtataagtttaa ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@5 +tcctcaagccattgtgtgtaattaaccactaattgtgtataagttta ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/b_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_2.fastq Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@1 +agtttaaacttatacacaattagtggttaattacacacaatggcttgagga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2 +gtttaaacttatacacaattagtggttaattacacacaatggcttgagga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3 +tttaaacttatacacaattagtggttaattacacacaatggcttgagga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@4 +ttaaacttatacacaattagtggttaattacacacaatggcttgagga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@5 +taaacttatacacaattagtggttaattacacacaatggcttgagga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/b_fna_ref_mincov_2_minqual_60.snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_fna_ref_mincov_2_minqual_60.snps.gff Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +##gff-version 3 +reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:10 A:0 |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/b_fna_ref_mincov_2_minqual_60.snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_fna_ref_mincov_2_minqual_60.snps.txt Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +DateTime 1970-01-01T00:00:00 +ReadFiles b_1.fastq b_2.fastq +Reference reference.fasta +ReferenceSize 700 +Software snippy 4.3.6 +Variant-SNP 1 +VariantTotal 1 |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/c.tgz |
| b |
| Binary file test-data/c.tgz has changed |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/c_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/c_1.fastq Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@1 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttacact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttacact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttacact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@4 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttacact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@5 +tccacaagccattgtgtgtaattaaccactaattgtgtataagtttaaact ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/c_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/c_2.fastq Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +@1 +agtgtaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@2 +agtgtaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@3 +agtgtaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@4 +agtgtaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@5 +agtttaaacttatacacaattagtggttaattacacacaatggcttgtgga ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/core/core.txt --- a/test-data/core/core.txt Sat Jan 26 14:36:48 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -ID Aligned Bases Reference bases % Aligned Bases -S1 2732313 3000464 91.06 -S2 2731269 3000464 91.03 |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/fna_ref/snps.gff --- a/test-data/fna_ref/snps.gff Sat Jan 26 14:36:48 2019 -0500 +++ b/test-data/fna_ref/snps.gff Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -1,17 +1,16 @@ ##gff-version 3 -Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 -Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 -Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:25 T:0 -Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 -Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:21 T:0 -Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0 -Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:22 T:0 -Wildtype snippy:3.2-dev variation 106722 106722 . . 0 note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 -Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:17 T:0 -Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 -Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:19 GT:0 -Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 -Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 -Wildtype snippy:3.2-dev variation 138954 138954 . . 0 note=snp A=>G G:10 A:0 -Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 -Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 +Wildtype snippy:4.3.6 variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 +Wildtype snippy:4.3.6 variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 +Wildtype snippy:4.3.6 variation 47299 47299 . . 0 note=snp T=>A A:25 T:0 +Wildtype snippy:4.3.6 variation 102969 102969 . . 0 note=snp G=>C C:18 G:0 +Wildtype snippy:4.3.6 variation 103048 103048 . . 0 note=snp T=>A A:23 T:0 +Wildtype snippy:4.3.6 variation 103379 103379 . . 0 note=del GA=>G G:9 GA:0 +Wildtype snippy:4.3.6 variation 106602 106602 . . 0 note=snp T=>G G:22 T:0 +Wildtype snippy:4.3.6 variation 106722 106722 . . 0 note=ins G=>GT GT:11 G:0 +Wildtype snippy:4.3.6 variation 109833 109833 . . 0 note=snp T=>A A:17 T:0 +Wildtype snippy:4.3.6 variation 114540 114540 . . 0 note=del AT=>A A:26 AT:0 +Wildtype snippy:4.3.6 variation 129881 129881 . . 0 note=mnp GT=>AA AA:19 GT:0 +Wildtype snippy:4.3.6 variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 +Wildtype snippy:4.3.6 variation 138954 138954 . . 0 note=snp A=>G G:10 A:0 +Wildtype snippy:4.3.6 variation 160547 160547 . . 0 note=del GT=>G G:19 GT:0 +Wildtype snippy:4.3.6 variation 190866 190866 . . 0 note=del GT=>G G:17 GT:0 \ No newline at end of file |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/fna_ref/snps.txt --- a/test-data/fna_ref/snps.txt Sat Jan 26 14:36:48 2019 -0500 +++ b/test-data/fna_ref/snps.txt Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -1,8 +1,8 @@ -DateTime 2019-01-24T13:08:34 -ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq -Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.fna -ReferenceSize 200694 -Software snippy 3.2-dev +DateTime 1970-01-01T00:00:00 +ReadFiles mutant_R1.fastq mutant_R2.fastq +Reference wildtype.fna +ReferenceSize 197394 +Software snippy 4.3.6 Variant-DEL 4 Variant-INS 1 Variant-MNP 1 |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/ref.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fna Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>reference +TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAAGGTTATCCAC +AATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATGTGTTAAA +CTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAA +AACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTA +ATTCACGATAAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAG +AAGCTTTTTCAGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAA +ACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGA +AAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAAATTACTATTCCAGACACAACGAG +AGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fasta Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>reference +TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAAGGTTATCCAC +AATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATGTGTTAAA +CTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAA +AACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTA +ATTCACGATAAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAG +AAGCTTTTTCAGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAA +ACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGA +AAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAAATTACTATTCCAGACACAACGAG +AGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/snippy-core-samples --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snippy-core-samples Mon Mar 18 10:59:29 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +S1 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR302/001/SRR3028781/SRR3028781_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR302/001/SRR3028781/SRR3028781_2.fastq.gz +S2 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR302/009/SRR3028789/SRR3028789_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR302/009/SRR3028789/SRR3028789_2.fastq.gz +S3 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR302/002/SRR3028792/SRR3028792_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR302/002/SRR3028792/SRR3028792_2.fastq.gz |
| b |
| diff -r 82f2b6f20fa2 -r 776ebd1239da test-data/wildtype.gbk --- a/test-data/wildtype.gbk Sat Jan 26 14:36:48 2019 -0500 +++ b/test-data/wildtype.gbk Mon Mar 18 10:59:29 2019 -0400 |
| b |
| b'@@ -1,4 +1,4 @@\n-LOCUS Wildtype 197394 bp DNA linear 13-JUN-2016\n+LOCUS Wildtype 197394 bp DNA linear 18-JAN-2019\n DEFINITION Staphylococcus aureus strain WT.\n ACCESSION \n VERSION\n@@ -6,7 +6,7 @@\n SOURCE Staphylococcus aureus\n ORGANISM Staphylococcus aureus\n Unclassified.\n-COMMENT Annotated using prokka 1.12-beta from\n+COMMENT Annotated using prokka 1.13.3 from\n https://github.com/tseemann/prokka.\n FEATURES Location/Qualifiers\n source 1..197394\n@@ -33,12 +33,11 @@\n CDS 1640..2773\n /gene="dnaN"\n /locus_tag="WILD_00002"\n- /EC_number="2.7.7.7"\n /inference="ab initio prediction:Prodigal:2.6"\n /inference="similar to AA sequence:UniProtKB:P99103"\n /codon_start=1\n /transl_table=11\n- /product="DNA polymerase III subunit beta"\n+ /product="Beta sliding clamp"\n /translation="MMEFTIKRDYFITQLNDTLKAISPRTTLPILTGIKIDAKEHEVI\n LTGSDSEISIEITIPKTVDGEDIVNISETGSVVLPGRFFVDIIKKLPGKDVKLSTNEQ\n FQTLITSGHSEFNLSGLDPDQYPLLPQVSRDDAIQLSVKVLKNVIAQTNFAVSTSETR\n@@ -62,6 +61,7 @@\n /codon_start=1\n /transl_table=11\n /product="DNA replication and repair protein RecF"\n+ /db_xref="COG:COG1195"\n /translation="MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIY\n TLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGTMPLTMFITKKGKQVKVNHLEQS\n RLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQK\n@@ -124,6 +124,7 @@\n /codon_start=1\n /transl_table=11\n /product="ADP-dependent (S)-NAD(P)H-hydrate dehydratase"\n+ /db_xref="COG:COG0063"\n /translation="METLNSINIPKRKEDSHKGDYGKILLIGGSANLGGAIMLAARAC\n VFSGSGLITVATHPTNHSALHSRCPEAMVIDINDTKMLTKMIEMTDSILIGPGLGVDF\n KGNNAITFLLQNIQPHQNLIVDGDAITIFSKLKPQLPTCRVIFTPHLKEWERLSGIPI\n@@ -147,13 +148,9 @@\n AFALDHLKLGVSELANVSERRLERLVNPQLNGDLPAFLSPEPGLQSGAMIMQYAAASL\n VSENKTLAHPASVDSITSSANQEDHVSMGTTAARHGYQIIENARRVLAIECVIALQAA\n ELKGVEGLSPKTRRKYDEFRSIVPSITYDRQFHKDIEAVAQYLKQSIYQTTACH"\n- misc_RNA 11968..12177\n- /locus_tag="WILD_00009"\n- /product="T-box"\n- /inference="COORDINATES:profile:Infernal:1.1"\n CDS 12267..13553\n /gene="serS"\n- /locus_tag="WILD_00010"\n+ /locus_tag="WILD_00009"\n /EC_number="6.1.1.11"\n /inference="ab initio prediction:Prodigal:2.6"\n /inference="similar to AA sequence:UniProtKB:P99178"\n@@ -169,42 +166,35 @@\n YDLEVWLPSYNDYKEISSCSNCTDFQARRANIRFKRDKAAKPELAHTLNGSGLAVGRT\n FAAIVENYQNEDGTVTIPEALVPFMGGKTQISKPVK"\n CDS 14197..14892\n- /gene="ygaZ"\n- /locus_tag="WILD_00011"\n+ /locus_tag="WILD_00010"\n /inference="ab initio prediction:Prodigal:2.6"\n- /inference="similar to AA sequence:UniProtKB:P76630"\n /codon_start=1\n /transl_table=11\n- /product="Inner membrane protein YgaZ"\n+ /product="hypothetical protein"\n /translation="MTTHLSFRQGVQECIPTLLGYAGVGISFGIVASSQNFSILEIIL\n LCLVIYAGAAQFIMCALFIAGTPISAIVLTVFIVNSRMFLLSMSLAPNFKTYGFWNRV\n GLGSLVTDETFGVAITPYLKGEAINDRWMHGLNITAYLFWVIPCVAGALFGEYISNPQ\n ALGLDFAITAMFIFLAIA'..b'rence="ab initio prediction:Prodigal:2.6"\n /inference="similar to AA sequence:UniProtKB:P60298"\n@@ -2367,13 +2348,14 @@\n KN"\n CDS complement(189540..190895)\n /gene="brnQ"\n- /locus_tag="WILD_00166"\n+ /locus_tag="WILD_00164"\n /inference="ab initio prediction:Prodigal:2.6"\n /inference="similar to AA sequence:UniProtKB:P0AD99"\n /codon_start=1\n /transl_table=11\n /product="Branched-chain amino acid transport system 2\n carrier protein"\n+ /db_xref="COG:COG1114"\n /translation="MKKKLTFKENMFIGSMLFGLFFGAGNLIFPIHLGQAAGSNVFIA\n NLGFLITAIGLPFLGIIAIGISKTSGLFEIASRVNKTYAYIFTIALYLVIGPFFALPR\n LATTSFEIAFSPFLSPKQITLYLFIFSFVFFVIAWFFARKPSRILEYIGKFLNPVFLV\n@@ -2385,26 +2367,28 @@\n A"\n CDS complement(191173..191730)\n /gene="yecD"\n- /locus_tag="WILD_00167"\n+ /locus_tag="WILD_00165"\n /EC_number="3.-.-.-"\n /inference="ab initio prediction:Prodigal:2.6"\n /inference="similar to AA sequence:UniProtKB:P0ADI7"\n /codon_start=1\n /transl_table=11\n /product="Isochorismatase family protein YecD"\n+ /db_xref="COG:COG1335"\n /translation="MINFDKTALVLIDLQQGILKMDYAPHTAENVVQNANKLIEAFRK\n NNGFIAFVRVNFYDGKDALQPNAMISLPPKEGDDYSHFHYLLDKRDDDFVIDKRQFSA\n FVGTDLDLQLRRRGIDTIVLGGVATHVGVDTTARDAYQLNYDQYFVTDMMSAQNETLH\n QFPIDNVFPLMGQTITTNDLLNILN"\n CDS complement(191797..193437)\n /gene="ipdC"\n- /locus_tag="WILD_00168"\n+ /locus_tag="WILD_00166"\n /EC_number="4.1.1.74"\n /inference="ab initio prediction:Prodigal:2.6"\n /inference="similar to AA sequence:UniProtKB:P23234"\n /codon_start=1\n /transl_table=11\n /product="Indole-3-pyruvate decarboxylase"\n+ /db_xref="COG:COG3961"\n /translation="MKQRIGAYLIDAIHRAGVDKIFGVPGDFNLAFLDDIISNPNVDW\n VGNTNELNASYAADGYARLNGLAALVTTFGVGELSAVNGIAGSYAERIPVIAITGAPT\n RAVEQAGKYVHHSLGEGTFDDYRKMFAHITVAQGYITPENAATEIPRLINTAIAERRP\n@@ -2416,7 +2400,7 @@\n VLFVINNDGYTVERLIHGMYEPYNEIHMWDYKALPAVFGGKNVEIHDVESSKDLQEVF\n NTINGHPDVMYFVEVKMSVEDAPKKLIDIAKAFSQQNK"\n CDS 193568..193702\n- /locus_tag="WILD_00169"\n+ /locus_tag="WILD_00167"\n /inference="ab initio prediction:Prodigal:2.6"\n /codon_start=1\n /transl_table=11\n@@ -2425,7 +2409,8 @@\n "\n CDS complement(193709..195754)\n /gene="ptsG"\n- /locus_tag="WILD_00170"\n+ /locus_tag="WILD_00168"\n+ /EC_number="2.7.1.199"\n /inference="ab initio prediction:Prodigal:2.6"\n /inference="similar to AA sequence:UniProtKB:Q7A807"\n /codon_start=1\n@@ -2444,7 +2429,7 @@\n PSQGEVRAPFNGKVQMIFPTKHAIGLVSDSGLELLIHIGLDTVKLNGEGFTLHVEEGQ\n EVKQGDLLINFDLDYIRNHAKSDITPIIVTQGNITNLDFKQGEHGNISFGDQLFEAK"\n CDS 196339..197394\n- /locus_tag="WILD_00171"\n+ /locus_tag="WILD_00169"\n /inference="ab initio prediction:Prodigal:2.6"\n /codon_start=1\n /transl_table=11\n' |