| Previous changeset 2:ac7c9e40d601 (2015-07-10) Next changeset 4:b762ecbe2314 (2015-12-11) |
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Commit message:
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modified:
VCFToolFilter/VCFToolsFilter.pl VCFToolFilter/vcfToolsFilter.sh VCFToolFilter/vcfToolsFilter.xml VCFToolsSlidingWindow/VCFToolsSlidingWindow.pl VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml VCFToolsStats/VCFToolsStats.pl VCFToolsStats/vcfToolsStats.sh VCFToolsStats/vcfToolsStats.xml tool_dependencies.xml |
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added:
VCFToolFilter/.svn/entries VCFToolFilter/.svn/text-base/VCFToolsFilter.pl.svn-base VCFToolFilter/.svn/text-base/vcfToolsFilter.sh.svn-base VCFToolFilter/.svn/text-base/vcfToolsFilter.xml.svn-base VCFToolFilter/test-data/result.frq VCFToolFilter/test-data/result.map VCFToolFilter/test-data/result.ped VCFToolsSlidingWindow/test-data/groups.txt VCFToolsSlidingWindow/test-data/result.Tajima.D VCFToolsSlidingWindow/test-data/result.TsTv VCFToolsSlidingWindow/test-data/result.snpden VCFToolsSlidingWindow/test-data/result.windowed.pi VCFToolsSlidingWindow/test-data/result2.Tajima.D VCFToolsSlidingWindow/test-data/result2.TsTv VCFToolsSlidingWindow/test-data/result2.combined.dtajima.txt VCFToolsSlidingWindow/test-data/result2.combined.pi.txt VCFToolsSlidingWindow/test-data/result2.fst.by_marker.genes.txt VCFToolsSlidingWindow/test-data/result2.fst.txt VCFToolsSlidingWindow/test-data/result2.snpden VCFToolsSlidingWindow/test-data/result2.windowed.pi VCFToolsSlidingWindow/test-data/sample.vcf VCFToolsSlidingWindow/test-data/sample_group.vcf VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh |
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VCFToolFilter/test-data/result.log VCFToolsStats/test-data/result.log |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/.svn/entries --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolFilter/.svn/entries Mon Nov 09 05:18:45 2015 -0500 |
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| @@ -0,0 +1,133 @@ +10 + +dir +37 +svn+ssh://svn.sb-roscoff.fr/svn/logiciel/galaxy/galaxy4sniplay/VCFToolFilter +svn+ssh://svn.sb-roscoff.fr/svn/logiciel/galaxy + + + +2014-11-24T14:55:35.793365Z +37 +gandres + + + + + + + + + + + + + + +0f93037e-e277-4375-988d-e0ab8f9fda44 + +VCFToolsFilter.pl +file + + + + +2014-11-17T10:18:36.000000Z +713d0c1b4b872bf4341b4c46b72b0d88 +2014-11-24T14:55:35.793365Z +37 +gandres + + + + + + + + + + + + + + + + + + + + + +3264 + +vcfToolsFilter.xml +file +52 + + + +2015-02-27T08:42:37.846989Z +ca55985559a2840519ab7043604076a7 +2015-02-27T08:46:21.315931Z +52 +gandres + + + + + + + + + + + + + + + + + + + + + +8340 + +test-data +dir + +vcfToolsFilter.sh +file + + + + +2014-11-24T12:47:45.000000Z +b4221436582c30d0e2e4a4d076ea0740 +2014-11-24T14:55:35.793365Z +37 +gandres + + + + + + + + + + + + + + + + + + + + + +1378 + |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/.svn/text-base/VCFToolsFilter.pl.svn-base --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolFilter/.svn/text-base/VCFToolsFilter.pl.svn-base Mon Nov 09 05:18:45 2015 -0500 |
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| @@ -0,0 +1,158 @@ + +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use Bio::SeqIO; + +my $usage = qq~Usage:$0 <args> [<opts>] + +where <args> are: + + -i, --input <VCF input> + -o, --out <Output basename> + + <opts> are: + + -s, --samples <Samples to be analyzed. Comma separated list> + -c, --chromosomes <Chromosomes to be analyzed. Comma separated list> + -e, --export <Output format (VCF/freq/plink. Default: VCF> + -f, --frequency <Minimum MAF. Default: 0.001> + -m, --max_freq <Maximum MAF. Default: 0.5> + -a, --allow_missing <Allowed missing data proportion per site. Must be comprised between 0 and 1. Default: 1> + -n, --nb_alleles <Accepted number of alleles (min,max). Default: 2,4> + -t, --type <Type of polymorphisms to keep (ALL/SNP/INDEL). Default: ALL> + -b, --bounds <Lower bound and upper bound for a range of sites to be processed (start,end). Default: 1, 100000000> +~; +$usage .= "\n"; + +my ($input,$out); + + +#my $indel_size_max = 500; +#my $indel_size_min = 1; +my $frequency_max = 0.5; +my $frequency_min = 0.001; +my $pos_max = 100000000000; +my $pos_min = 0; +my $filter_snp_type = "all"; + +my $missing_data = 1; +my $export = "VCF"; +my $type = "ALL"; +my $nb_alleles; +my $bounds; +my $samples; +my $chromosomes; + +GetOptions( + "input=s" => \$input, + "out=s" => \$out, + "samples=s" => \$samples, + "chromosomes=s" => \$chromosomes, + "frequency=s" => \$frequency_min, + "max_freq=s" => \$frequency_max, + "allow_missing=s"=> \$missing_data, + "export=s" => \$export, + "type=s" => \$type, + "nb_alleles=s" => \$nb_alleles, + "bounds=s" => \$bounds, +); + + +die $usage + if ( !$input || !$out); + + +my @dnasamples; +if ($samples) +{ + @dnasamples = split(",",$samples); +} +my @nalleles; +if ($nb_alleles) +{ + @nalleles = split(",",$nb_alleles); +} +my @boundaries; +if ($bounds) +{ + @boundaries = split(",",$bounds); +} +my @chromosomes_list; +if ($chromosomes) +{ + @chromosomes_list = split(",",$chromosomes); +} + + +my $experiment = "chromosomes"; +my $table = ""; +my %genes; +my @snp_ids; +my @snp_ids_and_positions; +my @snp_ids_and_positions_all; +my $gene; +my $snp_num = 0; +my %ref_sequences; +my %snps_of_gene; + + + + +my $indiv_cmd = ""; +if (@dnasamples) +{ + $indiv_cmd = "--indv " . join(" --indv ",@dnasamples); +} + +my $chrom_cmd = ""; +if (@chromosomes_list) +{ + $chrom_cmd = "--chr " . join(" --chr ",@chromosomes_list); +} + +my $export_cmd = "--recode"; +if ($export eq "freq") +{ + $export_cmd = "--freq"; +} +if ($export eq "plink") +{ + $export_cmd = "--plink"; +} + + + +my $nb_alleles_cmd = "--min-alleles 1 --max-alleles 4"; +if (@nalleles) +{ + $nb_alleles_cmd = "--min-alleles $nalleles[0] --max-alleles $nalleles[1]"; +} +my $bounds_cmd = "--from-bp 1 --to-bp 100000000"; +if (@boundaries) +{ + $bounds_cmd = "--from-bp $boundaries[0] --to-bp $boundaries[1]"; +} + + +my $type_cmd = ""; +if ($type eq "INDEL") +{ + $type_cmd = "--keep-only-indels"; +} +if ($type eq "SNP") +{ + $type_cmd = "--remove-indels"; +} + + +system("vcftools --vcf $input --out $out --keep-INFO-all --remove-filtered-all $type_cmd $export_cmd $chrom_cmd $indiv_cmd $nb_alleles_cmd --maf $frequency_min --max-maf $frequency_max --max-missing $missing_data >>vcftools.log 2>&1"); + + + + + + + |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/.svn/text-base/vcfToolsFilter.sh.svn-base --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolFilter/.svn/text-base/vcfToolsFilter.sh.svn-base Mon Nov 09 05:18:45 2015 -0500 |
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| @@ -0,0 +1,46 @@ +#!/bin/bash + +tool_path=$(dirname $0) + +filein=$1 +fileout_label=$2 +fileout=$3 +filelog=$4 +export=$5 +frequency=$6 +max_freq=$7 +allow_missing=$8 +nb_alleles_min=$9 +nb_alleles_max=${10} +type=${11} +bound_start=${12} +bound_end=${13} + + +if [ "${14}" != "None" ] +then samples="--samples ${14}" +fi + +if [ "${15}" != "None" ] +then chromosomes="--chromosomes ${15}" +fi + +if [ "$bound_start" -gt "$bound_end" ] +then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2 +fi + +if [ "$nb_alleles_min" -gt "$nb_alleles_max" ] +then tmp=$nb_alleles_min ; nb_alleles_min=$nb_alleles_max ; nb_alleles_max=$tmp ; echo "Warning : Minimum number of alleles must be lower than maximum number of allele!" >&2 +fi + +perl $tool_path/VCFToolsFilter.pl --input $filein --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --nb_alleles $nb_alleles_min','$nb_alleles_max --type $type --bounds $bound_start','$bound_end $samples $chromosomes + +if [ "$export" = "VCF" ] +then cp $fileout_label.recode.vcf $fileout ; rm $fileout_label.recode.vcf +elif [ "$export" = "freq" ] +then cp $fileout_label.frq $fileout ; rm $fileout_label.frq +else cp $fileout_label.ped $fileout; cp $fileout_label.map ${16} ; rm $fileout_label.ped $fileout_label.map +fi + +cp vcftools.log $filelog +rm vcftools.log |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/.svn/text-base/vcfToolsFilter.xml.svn-base --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolFilter/.svn/text-base/vcfToolsFilter.xml.svn-base Mon Nov 09 05:18:45 2015 -0500 |
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| b'@@ -0,0 +1,268 @@\n+<tool id="sniplay_vcftoolsfilter" name="VCF tools filter" version="1.1.1">\n+ \n+ <!-- [REQUIRED] Tool description displayed after the tool name -->\n+ <description> </description>\n+ \n+ <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->\n+ <requirements>\n+ <requirement type="binary">perl</requirement>\n+\t<requirement type="package" version="0.1.12b">vcftools</requirement>\n+ </requirements>\n+ \n+ <!-- [OPTIONAL] Command to be executed to get the tool\'s version string -->\n+ <version_command>\n+<!--\n+ tool_binary -v\n+-->\n+ </version_command>\n+ \n+ <!-- [REQUIRED] The command to execute -->\n+ <command interpreter="perl">\n+\tvcfToolsFilter.sh $filein $fileout_label $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end\n+\t#if str( $samples ) == "":\n+\t\'None\'\n+\t#else\n+\t$samples\n+\t#end if\n+\t#if str( $chromosomes ) == "":\n+\t\'None\'\n+\t#else\n+\t$chromosomes\n+\t#end if\n+\t#if str( $export ) == "plink":\n+\t$fileout_map\n+\t#else\n+\t\'\'\n+\t#end if\n+ </command>\n+ \n+ <!-- [REQUIRED] Input files and tool parameters -->\n+ <inputs>\n+\t<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />\n+\t<param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/>\n+\t<param name="samples" type="text" optional="true" label="Samples" help="Samples to be analyzed. Comma separated list">\n+\t\t<validator type="regex" message="Please enter a comma separated list.">^\\w+(,\\w+)*$</validator>\n+\t</param>\n+\t<param name="chromosomes" type="text" optional="true" label="Chromosomes" help="Chromosomes to be analyzed. Comma separated list">\n+\t <validator type="regex" message="Please enter a comma separated list.">^\\w+(,\\w+)*$</validator>\n+ </param>\n+\t<param name="export" type="select" label="Output format" >\n+\t <option value="VCF" selected="true">VCF</option>\n+\t <option value="freq">freq</option>\n+ <option value="plink">plink</option>\n+ </param>\n+\t<param name="frequency" type="float" value="0.001" label="Minimum MAF." help="Minimum frequency." />\n+\t<param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." />\n+\t<param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." />\n+\t<param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" />\n+\t<param name="nb_alleles_max" type="integer" value="2" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" />\n+ <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >\n+ <option value="ALL" selected="true">All</option>\n+ <option value="SNP">SNP</option>\n+ <option value="INDEL">Indel</option>\n+ </param>\n+\t<param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." />\n+\t<param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." />\n+ </inputs>\n+ \n+ <!-- [REQUIRED] Output files -->\n+ <outputs>\n+\t<data name="fileout" format="vcf" label="${fileout_label}.#if str($export)==\'plink\' then \'ped\' else \'\' # #if str($export)==\'freq\' then \'frq\' else \'\' # #if str($export)==\'VCF\' then \'vcf\' else \'\' #" >\n+\t\t<change_format>\n+ \t<when input="export" value="freq" format="tabular" />\n+\t\t\t<when input="export" value="plink" format="txt" />\n+\t\t</change_format>\t\n+\t</data>\n+\t<data name="fileout_map" format="txt" label="${fileout_label}.map">\n+\t\t<filter>(export == \'plink\')</filter>\n+\t</data>\n+\t<data name="filelog" format="txt" label="${fileout_label}.log" />'..b'alue="0.001" />\n+ <param name="max_freq" value="0.5" />\n+ <param name="allow_missing" value="1" />\n+ <param name="nb_alleles_min" value="2" />\n+\t<param name="nb_alleles_max" value="4" />\n+ <param name="type_p" value="ALL" />\n+ <param name="bound_start" value="1" />\n+ <param name="bound_end" value="100000000" />\n+ <output name="fileout" file="result.vcf" />\n+ <output name="filelog" file="result.log" />\n+ </test>\n+ </tests>\n+ \n+ <!-- [OPTIONAL] Help displayed in Galaxy -->\n+ <help>\n+\n+.. class:: infomark\n+\n+**Authors** \n+\n+---------------------------------------------------\n+\n+.. class:: infomark\n+\n+**Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep.\n+\n+---------------------------------------------------\n+\n+================\n+VCF tools filter\n+================\n+\n+-----------\n+Description\n+-----------\n+\n+ Filter VCF file \n+\n+-----------------\n+Workflow position\n+-----------------\n+\n+**Upstream tools**\n+\n+=========== ========================== =======\n+Name output file(s) format \n+=========== ========================== =======\n+=========== ========================== =======\n+\n+\n+**Downstream tools**\n+\n+=========== ========================== =======\n+Name output file(s) format\n+=========== ========================== =======\n+=========== ========================== =======\n+\n+\n+----------\n+Input file\n+----------\n+\n+VCF file\n+\tVCF file with all SNPs\n+\n+----------\n+Parameters\n+----------\n+\n+Output file basename\n+\tPrefix for the output VCF file\n+\n+Samples\n+ Samples to be analyzed. Comma separated list\n+\n+Chromosomes\n+\tChromosomes to be analyzed. Comma separated list\n+\n+Output format\n+\tVCF/freq/plink\n+\n+Minimum MAF\n+\tMinimum frequency\n+\n+Maximum MAF\n+\tMaximum frequency\n+\n+Missing data proportion\n+\tAllowed missing data proportion per site. Must be comprised between 0 and 1.\n+\n+Number of alleles\n+\tAccepted number of alleles min and max.\n+\n+Polymorphisms\n+\tType of polymorphisms to keep (ALL/SNP/INDEL).\n+Bounds\n+\tLower bound and upper bound for a range of sites to be processed.\n+\n+------------\n+Output files\n+------------\n+\n+VCF file\n+\tVCF file filtered \n+\n+Log file\n+\n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+Input files\n+===========\n+\n+VCF file\n+---------\n+\n+::\n+\n+\t#fileformat=VCFv4.1\n+\t#FILTER=<ID=LowQual,Description="Low quality">\n+\t#FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+\t[...]\n+\tCHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tCATB1\n+\tchr1\t2209\t.\tG\tT\t213.84\t.\tAC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|)\tGT:AD:DP:GQ:PL\t1/1:0,7:7:18:242,18,0\n+\n+\n+Parameters\n+==========\n+\n+Output name -> filtered_chr1\n+\n+Chromosomes -> chr1\n+\n+Output format -> VCF\n+\n+Minimum MAF -> 0.001\n+\n+Maximum MAF -> 0.5\n+\n+Missing data proportion -> 1\n+\n+Number of alleles min -> 2\n+\n+Number of alleles max -> 4\n+\n+Polymorphisms -> All\n+\n+Lower bound -> 1\n+\n+Upper bound -> 100000000\n+\n+\n+Output files\n+============\n+\n+filtered_genelist_intron.vcf\n+---------\n+\n+::\n+\n+ #fileformat=VCFv4.1\n+ #FILTER=<ID=LowQual,Description="Low quality">\n+ #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+ [...]\n+ CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1\n+\tchr1\t5059\t.\tC\tG\t146.84\t.\tAC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|)\tGT:AD:DP:GQ:PL\t1/1:0,8:8:18:175,18,0\n+\n+\n+ </help>\n+ \n+</tool>\n' |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/VCFToolsFilter.pl --- a/VCFToolFilter/VCFToolsFilter.pl Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolFilter/VCFToolsFilter.pl Mon Nov 09 05:18:45 2015 -0500 |
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| @@ -2,7 +2,6 @@ #!/usr/bin/perl use strict; -use Switch; use Getopt::Long; use Bio::SeqIO; |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/test-data/result.frq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolFilter/test-data/result.frq Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,3617 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|
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/test-data/result.log --- a/VCFToolFilter/test-data/result.log Fri Jul 10 04:16:17 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --chr chr1 - --recode-INFO-all - --maf 0.001 - --max-alleles 4 - --max-maf 0.5 - --min-alleles 2 - --max-missing 1 - --out filtered - --recode - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting VCF file... -After filtering, kept 3616 out of a possible 4955 Sites -Run Time = 0.00 seconds |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/test-data/result.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolFilter/test-data/result.map Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,3616 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|
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/test-data/result.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolFilter/test-data/result.ped Mon Nov 09 05:18:45 2015 -0500 |
| b |
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|
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/vcfToolsFilter.sh --- a/VCFToolFilter/vcfToolsFilter.sh Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolFilter/vcfToolsFilter.sh Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| @@ -3,18 +3,18 @@ tool_path=$(dirname $0) filein=$1 -fileout_label=$2 -fileout=$3 -filelog=$4 -export=$5 -frequency=$6 -max_freq=$7 -allow_missing=$8 -nb_alleles_min=$9 -nb_alleles_max=${10} -type=${11} -bound_start=${12} -bound_end=${13} +fileout_label=$(date "+%Y%m%d%H%M%S") +fileout=$2 +filelog=$3 +export=$4 +frequency=$5 +max_freq=$6 +allow_missing=$7 +nb_alleles_min=$8 +nb_alleles_max=9 +type=${10} +bound_start=${11} +bound_end=${12} if [ "${14}" != "None" ] |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolFilter/vcfToolsFilter.xml --- a/VCFToolFilter/vcfToolsFilter.xml Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolFilter/vcfToolsFilter.xml Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.1"> +<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.2"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> </description> @@ -9,16 +9,16 @@ <requirement type="package" version="0.1.12b">vcftools</requirement> </requirements> - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + <!-- [REQUIRED] The command to execute --> <command interpreter="perl"> - vcfToolsFilter.sh $filein $fileout_label $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end + vcfToolsFilter.sh $filein $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end #if str( $samples ) == "": 'None' #else @@ -55,7 +55,7 @@ <param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." /> <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." /> <param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" /> - <param name="nb_alleles_max" type="integer" value="2" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" /> + <param name="nb_alleles_max" type="integer" value="4" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" /> <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." > <option value="ALL" selected="true">All</option> <option value="SNP">SNP</option> @@ -73,17 +73,12 @@ <when input="export" value="plink" format="txt" /> </change_format> </data> - <data name="fileout_map" format="txt" label="${fileout_label}.map"> + <data name="fileout_map" format="tabular" label="${fileout_label}.map"> <filter>(export == 'plink')</filter> </data> <data name="filelog" format="txt" label="${fileout_label}.log" /> </outputs> - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> @@ -101,7 +96,19 @@ <param name="bound_start" value="1" /> <param name="bound_end" value="100000000" /> <output name="fileout" file="result.vcf" /> - <output name="filelog" file="result.log" /> + </test> + <test> + <param name="filein" value="sample.vcf" /> + <param name="export" value="plink" /> + <param name="type_p" value="SNP" /> + <output name="fileout" file="result.ped" /> + <output name="fileout_map" file="result.map" /> + </test> + <test> + <param name="filein" value="sample.vcf" /> + <param name="export" value="freq" /> + <param name="type_p" value="ALL" /> + <output name="fileout" file="result.frq" /> </test> </tests> |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/VCFToolsSlidingWindow.pl --- a/VCFToolsSlidingWindow/VCFToolsSlidingWindow.pl Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolsSlidingWindow/VCFToolsSlidingWindow.pl Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| @@ -3,6 +3,7 @@ use strict; use Getopt::Long; +use Bio::SeqIO; my $usage = qq~Usage:$0 <args> [<opts>] @@ -72,47 +73,155 @@ } -my $VCFTOOLS_EXE = "vcftools"; +my $input_format = "--vcf $input.sorted"; +if ($input =~/\.vcf/){ + system("vcf-sort $input >$input.sorted"); + $input_format = "--vcf $input.sorted"; +} +elsif ($input =~/\.bcf/){ + $input_format = "--bcf $input"; +} +system("vcftools $input_format --out $out --window-pi $window --window-pi-step $step >>$out.vcftools.log 2>&1"); +system("vcftools $input_format --out $out --TajimaD $window >>$out.vcftools.log 2>&1"); +system("vcftools $input_format --out $out --TsTv $window >>$out.vcftools.log 2>&1"); +system("vcftools $input_format --out $out --SNPdensity $window >>$out.vcftools.log 2>&1"); -system("vcf-sort $input >$input.sorted"); - -system("$VCFTOOLS_EXE --vcf $input.sorted --out $out --window-pi $window --window-pi-step $step >>$out.vcftools.log 2>&1"); -system("$VCFTOOLS_EXE --vcf $input.sorted --out $out --TajimaD $window >>$out.vcftools.log 2>&1"); -system("$VCFTOOLS_EXE --vcf $input.sorted --out $out --TsTv $window >>$out.vcftools.log 2>&1"); -system("$VCFTOOLS_EXE --vcf $input.sorted --out $out --SNPdensity $window >>$out.vcftools.log 2>&1"); +################################################## +# Tajima distribution +################################################## +my %counts3; +my @values; +open(my $TAJIMA,"$out.Tajima.D"); +<$TAJIMA>; +my $max = 0; +while(<$TAJIMA>){ + my $line = $_; + $line =~s/\n//g; + $line =~s/\r//g; + my @inf = split(/\t/,$line); + my $val = $inf[3]; + my $arrondi = sprintf("%.1f",$val); + $counts3{$arrondi}++; +} +close($TAJIMA); + + + +open(my $M3,">$out.tajima_distrib"); +print $M3 "Values nb of values\n"; +for (my $i = -2.5; $i <= 2.5; $i=$i+0.1) +{ + my $arrondi = sprintf("%.1f",$i); + my $nb = 0; + if ($counts3{$arrondi}) + { + $nb = $counts3{$arrondi}; + } + print $M3 "Tajima $arrondi $nb\n"; +} +close($M3); + if (keys(%hash) > 0) { my $files_pi = ""; my $files_dtajima = ""; + my $cmd_fst = "--fst-window-size $window"; + my $cmd_fst_by_marker = ""; foreach my $pop(sort(keys(%hash))) { + my $cmd_part = $hash{$pop}; + + + open(my $POP,">$input.$pop.txt"); + my @ind_of_pop = split(" --indv ",$cmd_part); + print $POP join("\n",@ind_of_pop); + close($POP); + $cmd_fst .= " --weir-fst-pop $input.$pop.txt"; + $cmd_fst_by_marker .= " --weir-fst-pop $input.$pop.txt"; + my $cmd_part = $hash{$pop}; - system("$VCFTOOLS_EXE --vcf $input.sorted --remove-filtered-all --out $out.$pop --window-pi $window --window-pi-step $step $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); + system("vcftools $input_format --remove-filtered-all --out $out.$pop --window-pi $window --window-pi-step $step $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); my $sed_cmd = "sed -i \"s\/PI\/$pop\/g\" $out.$pop.windowed.pi"; system($sed_cmd); $files_pi .= "$out.$pop.windowed.pi "; - system("$VCFTOOLS_EXE --vcf $input.sorted --remove-filtered-all --out $out.$pop --SNPdensity $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); + system("vcftools $input_format --remove-filtered-all --out $out.$pop --SNPdensity $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); - system("$VCFTOOLS_EXE --vcf $input.sorted --remove-filtered-all --out $out.$pop --TajimaD $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); + system("vcftools $input_format --remove-filtered-all --out $out.$pop --TajimaD $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); my $sed_cmd = "sed -i \"s\/TajimaD\/$pop\/g\" $out.$pop.Tajima.D"; system($sed_cmd); $sed_cmd = "sed -i \"s/nan/0/g\" $out.Tajima.D"; system($sed_cmd); $files_dtajima .= "$out.$pop.Tajima.D "; - system("$VCFTOOLS_EXE --vcf $input.sorted --remove-filtered-all --out $out.$pop --TsTv $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); + system("vcftools $input_format --remove-filtered-all --out $out.$pop --TsTv $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); } system("paste $files_pi >>$out.combined.pi"); my $awk_cmd = "awk {'print \$1\"\t\"\$2\"\t\"\$5\"\t\"\$10'} $out.combined.pi >$out.combined.pi.txt"; system($awk_cmd); system("paste $files_dtajima >>$out.combined.dtajima"); - my $awk_cmd = "awk {'print \$1\"\t\"\$2\"\t\"\$4\"\t\"\$8'} $out.combined.dtajima >$out.combined.dtajima.txt"; + $awk_cmd = "awk {'print \$1\"\t\"\$2\"\t\"\$4\"\t\"\$8'} $out.combined.dtajima >$out.combined.dtajima.txt"; + system($awk_cmd); + + system("vcftools $input_format --remove-filtered-all --out $out.fst $cmd_fst --maf 0.001 >>$out.vcftools.log 2>&1"); + $awk_cmd = "awk {'print \$1\"\t\"\$2\"\t\"\$5'} $out.fst.windowed.weir.fst >$out.fst.txt"; system($awk_cmd); + + system("vcftools $input_format --remove-filtered-all --out $out.fst $cmd_fst_by_marker --maf 0.001 >>$out.vcftools.log 2>&1"); + + my %genes; + open(my $V,$input); + my $go = 0; + while(<$V>){ + if ($go){ + my @infos = split(/\t/,$_); + my $chr = $infos[0]; + my $pos = $infos[1]; + my $annot = $infos[7]; + my $gene = "#"; + if ($annot =~/EFF=\w+\((.*)\)/){ + my @parts = split(/\|/,$1); + $gene = $parts[4]; + } + $genes{"$chr:$pos"} = $gene; + } + if (/^#CHROM/){$go = 1;} + } + + my $cumul = 0; + my $previous_pos; + my %chrs; + open(my $F,"$out.fst.weir.fst"); + open(my $O,">$out.fst.by_marker.txt"); + open(my $O2,">$out.fst.by_marker.genes.txt"); + print $O "Chromosome Marker Position Fst\n"; + print $O2 "Chromosome Marker Position Fst Gene\n"; + while(<$F>){ + my $line = $_; + chomp($line); + my ($chr,$pos,$val) = split(/\t/,$line); + if (!$chrs{$chr}){ + $cumul = $previous_pos; + $chrs{$chr} = 1; + } + if ($val > 0.6 && $val !~/-/ && $val ne 'nan'){ + my $x = $pos+$cumul; + print $O2 "$chr $chr:$pos $pos $val " . $genes{"$chr:$pos"} . "\n"; + print $O "$chr $chr:$pos $x $val\n"; + $previous_pos = $x; + } + + } + close($F); + close($O); + close($O2); + + #$awk_cmd = "awk {'if (\$3>0.6 && \$3<=1 && \$3!~\"nan\"){print \$1\"\t\"\$2\"\t\"\$2\"\t\"\$3}'} $out.fst.weir.fst >$out.fst.by_marker.txt"; + #system($awk_cmd); } |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/groups.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/groups.txt Mon Nov 09 05:18:45 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +BA55_G;Pop1 +BA58_G;Pop1 +BA59_G;Pop1 +BD54_C;Pop2 +BD65_C;Pop2 +b2_UW;Pop2 +j1_UW;Pop2 |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result.Tajima.D --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result.Tajima.D Mon Nov 09 05:18:45 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +CHROM BIN_START N_SNPS TajimaD +chr1 0 3737 -nan |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result.TsTv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result.TsTv Mon Nov 09 05:18:45 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +CHROM BinStart SNP_count Ts/Tv +chr1 0 4928 1.88356 |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result.snpden --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result.snpden Mon Nov 09 05:18:45 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +CHROM BIN_START SNP_COUNT VARIANTS/KB +chr1 0 4955 24.775 |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result.windowed.pi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result.windowed.pi Mon Nov 09 05:18:45 2015 -0500 |
| b |
| @@ -0,0 +1,5 @@ +CHROM BIN_START BIN_END N_VARIANTS PI +chr1 1 200000 3764 0.01882 +chr1 50001 250000 2551 0.012755 +chr1 100001 300000 1946 0.00973 +chr1 150001 350000 732 0.00366 |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.Tajima.D --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.Tajima.D Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,767 @@\n+CHROM\tBIN_START\tN_SNPS\tTajimaD\n+chr1\t0\t428\t0.135253\n+chr1\t200000\t330\t-0.0828802\n+chr1\t400000\t129\t0.703606\n+chr1\t600000\t299\t0.825515\n+chr1\t800000\t150\t0.84434\n+chr1\t1000000\t98\t-0.0693517\n+chr1\t1200000\t248\t0.426566\n+chr1\t1400000\t361\t0.245024\n+chr1\t1600000\t312\t-0.369711\n+chr1\t1800000\t205\t0.215698\n+chr1\t2000000\t445\t-0.166095\n+chr1\t2200000\t172\t0.235908\n+chr1\t2400000\t238\t-0.409713\n+chr1\t2600000\t135\t0.526328\n+chr1\t2800000\t142\t0.878899\n+chr1\t3000000\t410\t0.924966\n+chr1\t3200000\t205\t1.49522\n+chr1\t3400000\t41\t0.557273\n+chr1\t3600000\t249\t0.0900491\n+chr1\t3800000\t157\t-0.178143\n+chr1\t4000000\t165\t0.365432\n+chr1\t4200000\t221\t0.727926\n+chr1\t4400000\t248\t0.0986787\n+chr1\t4600000\t115\t-0.448969\n+chr1\t4800000\t125\t0.786556\n+chr1\t5000000\t79\t0.636826\n+chr1\t5200000\t67\t0.307701\n+chr1\t5400000\t295\t0.480454\n+chr1\t5600000\t55\t0.394698\n+chr1\t5800000\t17\t1.07846\n+chr1\t6000000\t338\t0.602977\n+chr1\t6200000\t1\t0\n+chr1\t6400000\t46\t0.531885\n+chr1\t6600000\t64\t1.87936\n+chr1\t6800000\t122\t-0.542563\n+chr1\t7000000\t72\t0.800752\n+chr1\t7200000\t149\t-0.131246\n+chr1\t7400000\t56\t0.421664\n+chr1\t7600000\t7\t1.77614\n+chr1\t7800000\t195\t1.33557\n+chr1\t8000000\t1\t0\n+chr1\t8200000\t109\t0.466038\n+chr1\t8400000\t25\t-0.731209\n+chr1\t8600000\t15\t0.690701\n+chr1\t8800000\t16\t1.78202\n+chr1\t9000000\t46\t1.00488\n+chr1\t9200000\t8\t-0.10688\n+chr1\t9400000\t33\t-0.987647\n+chr1\t9600000\t115\t1.23652\n+chr1\t9800000\t160\t1.23533\n+chr1\t10000000\t13\t0.658965\n+chr1\t10200000\t41\t1.43081\n+chr1\t10400000\t25\t0.516761\n+chr1\t10600000\t48\t0.000179199\n+chr1\t10800000\t18\t0.647188\n+chr1\t11000000\t52\t0.484041\n+chr1\t11200000\t14\t0.805637\n+chr1\t11400000\t183\t0.967609\n+chr1\t11600000\t0\t0\n+chr1\t11800000\t0\t0\n+chr1\t12000000\t0\t0\n+chr1\t12200000\t0\t0\n+chr1\t12400000\t16\t0.449456\n+chr1\t12600000\t14\t0.727291\n+chr1\t12800000\t0\t0\n+chr1\t13000000\t38\t-0.491698\n+chr1\t13200000\t67\t-0.150119\n+chr1\t13400000\t9\t-0.0974004\n+chr1\t13600000\t6\t1.78889\n+chr1\t13800000\t12\t0.575472\n+chr1\t14000000\t33\t0.86619\n+chr1\t14200000\t35\t-0.133153\n+chr1\t14400000\t24\t0.850952\n+chr1\t14600000\t10\t-0.0295853\n+chr1\t14800000\t0\t0\n+chr1\t15000000\t5\t0.11916\n+chr1\t15200000\t0\t0\n+chr1\t15400000\t50\t1.29659\n+chr1\t15600000\t47\t0.83657\n+chr1\t15800000\t0\t0\n+chr1\t16000000\t28\t1.15075\n+chr1\t16200000\t18\t-0.113477\n+chr1\t16400000\t15\t0.168846\n+chr1\t16600000\t26\t0.274445\n+chr1\t16800000\t39\t0.171211\n+chr1\t17000000\t15\t0.738862\n+chr1\t17200000\t0\t0\n+chr1\t17400000\t11\t0.574049\n+chr1\t17600000\t25\t1.4006\n+chr1\t17800000\t122\t-0.0273032\n+chr1\t18000000\t26\t1.85989\n+chr1\t18200000\t15\t0.653359\n+chr1\t18400000\t24\t-1.62799\n+chr1\t18600000\t45\t0.221779\n+chr1\t18800000\t5\t-0.122826\n+chr1\t19000000\t0\t0\n+chr1\t19200000\t0\t0\n+chr1\t19400000\t23\t1.08863\n+chr1\t19600000\t205\t-0.262278\n+chr1\t19800000\t301\t0.990063\n+chr1\t20000000\t146\t0.316488\n+chr1\t20200000\t48\t-0.980579\n+chr1\t20400000\t14\t0.164546\n+chr1\t20600000\t66\t0.640725\n+chr1\t20800000\t15\t-1.03769\n+chr1\t21000000\t35\t0.619882\n+chr1\t21200000\t11\t-0.16299\n+chr1\t21400000\t46\t-0.271004\n+chr1\t21600000\t127\t0.195817\n+chr1\t21800000\t76\t0.449131\n+chr1\t22000000\t101\t-0.431336\n+chr1\t22200000\t97\t0.251323\n+chr1\t22400000\t148\t-0.150622\n+chr1\t22600000\t94\t0.484869\n+chr1\t22800000\t125\t1.35612\n+chr1\t23000000\t82\t-0.0709065\n+chr1\t23200000\t77\t-0.728208\n+chr1\t23400000\t166\t-0.0470761\n+chr1\t23600000\t275\t0.227475\n+chr1\t23800000\t104\t0.371299\n+chr1\t24000000\t169\t0.368894\n+chr1\t24200000\t82\t-0.585966\n+chr1\t24400000\t6\t2.55726\n+chr1\t24600000\t72\t-0.353192\n+chr1\t24800000\t40\t-0.74328\n+chr1\t25000000\t452\t0.897675\n+chr1\t25200000\t156\t0.0279002\n+chr1\t25400000\t355\t-0.594927\n+chr1\t25600000\t106\t-0.561078\n+chr1\t25800000\t171\t-0.216584\n+chr1\t26000000\t314\t-0.0744586\n+chr1\t26200000\t1067\t0.0766529\n+chr1\t26400000\t905\t0.19222\n+chr1\t26600000\t145\t1.75537\n+chr1\t26800000\t227\t0.852628\n+chr1\t27000000\t262\t-0.672669\n+chr1\t27200000\t163\t-0.299271\n+chr1\t27400000\t213\t-0.212231\n+chr1\t27600000\t174\t0.111912\n+chr1\t27800000\t153\t-0.201154\n+chr1\t28000000\t114\t0.119638\n+chr1\t28200000\t318\t-0.146756\n+chr1\t28400000\t308\t0.170923\n+chr1\t28600000\t231\t-0.422112\n+chr1\t28800000\t261\t-0.0706848\n+chr1\t29000000\t283\t-0.44018\n+chr1\t29200000\t241\t-0.450099\n+chr1\t29400000\t316\t-0.194331\n+chr1\t29600000\t181\t-0.5'..b'93154\n+chr3\t31200000\t167\t0.57134\n+chr3\t31400000\t224\t-0.139544\n+chr3\t31600000\t405\t-0.519931\n+chr3\t31800000\t606\t-0.600369\n+chr3\t32000000\t87\t0.0509089\n+chr4\t0\t344\t-0.289895\n+chr4\t200000\t400\t-0.0271053\n+chr4\t400000\t456\t-0.176043\n+chr4\t600000\t358\t-0.24177\n+chr4\t800000\t283\t-0.209419\n+chr4\t1000000\t255\t-0.338162\n+chr4\t1200000\t515\t-0.633207\n+chr4\t1400000\t375\t-0.0031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|
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.TsTv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.TsTv Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,767 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|
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.combined.dtajima.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.combined.dtajima.txt Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,767 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t-0.612872\t-0.0776582\n+chr4\t6400000\t0.145268\t0.0960817\n+chr4\t6600000\t0.41361\t0.42632\n+chr4\t6800000\t0.383816\t0.103421\n+chr4\t7000000\t0.554346\t0.574106\n+chr4\t7200000\t-0.248114\t-0.0479279\n+chr4\t7400000\t0.376391\t0.0434791\n+chr4\t7600000\t0.529464\t0.280849\n+chr4\t7800000\t0.186446\t0.329303\n+chr4\t8000000\t0.310156\t-0.214251\n+chr4\t8200000\t0.720999\t0.0331268\n+chr4\t8400000\t0\t0\n+chr4\t8600000\t-0.959628\t0.292826\n+chr4\t8800000\t0.196677\t0.0139355\n+chr4\t9000000\t0.786646\t0.384737\n+chr4\t9200000\t0.359949\t-0.134354\n+chr4\t9400000\t0.463141\t-0.313512\n+chr4\t9600000\t0.496395\t0.0606543\n+chr4\t9800000\t-0.169574\t-0.677065\n+chr4\t10000000\t0.907771\t-0.195971\n+chr4\t10200000\t1.188\t-0.358727\n+chr4\t10400000\t-0.774757\t-0.447939\n+chr4\t10600000\t-0.500832\t-0.3003\n+chr4\t10800000\t0\t0\n+chr4\t11000000\t0.691514\t0.0204499\n+chr4\t11200000\t1.74399\t0.640481\n+chr4\t11400000\t0.159121\t0.558504\n+chr4\t11600000\t0\t0\n+chr4\t11800000\t1.04512\t1.32991\n+chr4\t12000000\t-0.217044\t0.120705\n+chr4\t12200000\t0.986438\t0.801598\n+chr4\t12400000\t0.195409\t-0.0768168\n+chr4\t12600000\t0.0730632\t-0.00842354\n+chr4\t12800000\t0.91776\t1.14854\n+chr4\t13000000\t0.403244\t0.151631\n+chr4\t13200000\t0.0699714\t0.185556\n+chr4\t13400000\t0.226163\t-0.0712152\n+chr4\t13600000\t0.270696\t0.372062\n+chr4\t13800000\t0.499074\t0.360173\n+chr4\t14000000\t0.790651\t0.842404\n+chr4\t14200000\t1.20374\t0.303875\n+chr4\t14400000\t0.943238\t0.832906\n+chr4\t14600000\t0.8288\t0.578427\n+chr4\t14800000\t-0.539002\t0.0713801\n+chr4\t15000000\t0.492188\t-0.584328\n+chr4\t15200000\t-0.477734\t0.435898\n+chr4\t15400000\t0.758299\t-0.0366507\n+chr4\t15600000\t1.33871\t-0.750864\n+chr4\t15800000\t1.92888\t0.135045\n+chr4\t16000000\t0.130308\t1.01055\n+chr4\t16200000\t0.256633\t0.143231\n+chr4\t16400000\t0\t0\n+chr4\t16600000\t0.707667\t-0.149908\n+chr4\t16800000\t0.615576\t-0.255744\n+chr4\t17000000\t0.270554\t0.56647\n+chr4\t17200000\t0.758217\t1.31971\n+chr4\t17400000\t0.204093\t0.286518\n+chr4\t17600000\t-1.11755\t0.0207727\n+chr4\t17800000\t-0.453976\t-0.8727\n+chr4\t18000000\t-0.802542\t-0.128934\n+chr4\t18200000\t-0.0572223\t1.24854\n+chr4\t18400000\t-0.314715\t0.465298\n+chr4\t18600000\t-1.23311\t-0.524737\n+chr4\t18800000\t-0.314622\t0.459005\n+chr4\t19000000\t0.353387\t0.273139\n+chr4\t19200000\t0.00605781\t0.878885\n+chr4\t19400000\t-0.265115\t0.633696\n+chr4\t19600000\t-0.0870101\t-0.125323\n+chr4\t19800000\t0.245024\t0.56555\n+chr4\t20000000\t0.30865\t0.224378\n+chr4\t20200000\t1.02341\t0.0308217\n+chr4\t20400000\t0.654944\t0.616009\n+chr4\t20600000\t0.955632\t1.47806\n+chr4\t20800000\t0.145393\t0.202008\n+chr4\t21000000\t-1.23311\t1.21488\n+chr4\t21200000\t0.0672779\t0.226386\n+chr4\t21400000\t1.15544\t0.665915\n+chr4\t21600000\t1.63929\t0.635347\n+chr4\t21800000\t0.81599\t0.841388\n+chr4\t22000000\t0.382378\t0.157247\n+chr4\t22200000\t0.331706\t1.01868\n+chr4\t22400000\t1.27898\t1.51345\n+chr4\t22600000\t0.816198\t0.845043\n+chr4\t22800000\t-1.01063\t0.642289\n+chr4\t23000000\t0.563544\t0.588833\n+chr4\t23200000\t0.520431\t-1.14142\n+chr4\t23400000\t0\t0\n+chr4\t23600000\t0.243355\t0.456201\n+chr4\t23800000\t1.68213\t-0.160784\n+chr4\t24000000\t-0.161048\t0.740795\n+chr4\t24200000\t-0.410689\t0.550304\n+chr4\t24400000\t1.06414\t0.15475\n+chr4\t24600000\t0.395748\t0.853557\n+chr4\t24800000\t0.744342\t0.985101\n+chr4\t25000000\t0.164972\t-0.158307\n+chr4\t25200000\t0.306789\t0.882569\n+chr4\t25400000\t0.749725\t0.486544\n+chr4\t25600000\t-0.144576\t-0.242063\n+chr4\t25800000\t0.849841\t0.212327\n+chr4\t26000000\t0.416433\t0.137086\n+chr4\t26200000\t-0.204327\t0.471772\n+chr4\t26400000\t0.009739\t0.251937\n+chr4\t26600000\t0.023895\t-0.136805\n+chr4\t26800000\t-0.197623\t0.088879\n+chr4\t27000000\t0.141778\t0.066108\n+chr4\t27200000\t0.544634\t-0.222495\n+chr4\t27400000\t0.143995\t-0.159349\n+chr4\t27600000\t-0.221711\t-0.513039\n+chr4\t27800000\t0\t0\n+chr4\t28000000\t0.144177\t-0.0204056\n' |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.combined.pi.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.combined.pi.txt Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,2903 @@\n+CHROM\tBIN_START\tPop1\tPop2\n+chr1\t1\t0.000548356\t0.000557213\n+chr1\t50001\t0.000507686\t0.000551101\n+chr1\t100001\t0.000547355\t0.000587175\n+chr1\t150001\t0.000519688\t0.000575386\n+chr1\t200001\t0.000333344\t0.0003995\n+chr1\t250001\t0.00028568\t0.000380054\n+chr1\t300001\t0.000194342\t0.000264681\n+chr1\t350001\t7.96702e-05\t0.000135198\n+chr1\t400001\t7.10073e-05\t8.37605e-05\n+chr1\t450001\t8.46765e-05\t6.75097e-05\n+chr1\t500001\t0.000127682\t0.000155204\n+chr1\t550001\t0.000194695\t0.000239527\n+chr1\t600001\t0.000248039\t0.000303638\n+chr1\t650001\t0.000220364\t0.000295596\n+chr1\t700001\t0.000177357\t0.000207895\n+chr1\t750001\t0.000110346\t0.000131442\n+chr1\t800001\t5.50032e-05\t0.000131265\n+chr1\t850001\t4.23351e-05\t0.000102862\n+chr1\t900001\t4.23351e-05\t0.000102862\n+chr1\t950001\t4.76687e-05\t0.000105719\n+chr1\t1000001\t0.000149334\t9.55368e-05\n+chr1\t1050001\t0.000325343\t0.000210003\n+chr1\t1100001\t0.000385013\t0.000329471\n+chr1\t1150001\t0.00046169\t0.00043787\n+chr1\t1200001\t0.000321016\t0.000357867\n+chr1\t1250001\t0.00025135\t0.000345375\n+chr1\t1300001\t0.000211018\t0.000232333\n+chr1\t1350001\t0.000374694\t0.000413427\n+chr1\t1400001\t0.000486369\t0.000510399\n+chr1\t1450001\t0.00051335\t0.000548423\n+chr1\t1500001\t0.000494006\t0.00054199\n+chr1\t1550001\t0.000248334\t0.000241786\n+chr1\t1600001\t0.000387346\t0.000417868\n+chr1\t1650001\t0.000306682\t0.000326439\n+chr1\t1700001\t0.000380686\t0.000385727\n+chr1\t1750001\t0.000595032\t0.000601805\n+chr1\t1800001\t0.000341008\t0.000323931\n+chr1\t1850001\t0.000298005\t0.000284823\n+chr1\t1900001\t0.000369044\t0.000369483\n+chr1\t1950001\t0.000284371\t0.000271274\n+chr1\t2000001\t0.000592745\t0.000537194\n+chr1\t2050001\t0.000609073\t0.000544515\n+chr1\t2100001\t0.000464007\t0.000401271\n+chr1\t2150001\t0.000455335\t0.000436276\n+chr1\t2200001\t0.000190337\t0.000228589\n+chr1\t2250001\t0.000279008\t0.00029324\n+chr1\t2300001\t0.000279008\t0.000292525\n+chr1\t2350001\t0.00025634\t0.000229117\n+chr1\t2400001\t0.000328011\t0.0002709\n+chr1\t2450001\t0.000282673\t0.000227859\n+chr1\t2500001\t0.000392364\t0.000299309\n+chr1\t2550001\t0.000294022\t0.00021252\n+chr1\t2600001\t0.00017901\t0.00011251\n+chr1\t2650001\t0.000179022\t0.000106801\n+chr1\t2700001\t6.9338e-05\t3.53596e-05\n+chr1\t2750001\t0.000100676\t4.44676e-05\n+chr1\t2800001\t0.000194021\t0.000124118\n+chr1\t2850001\t0.000124672\t9.14314e-05\n+chr1\t2900001\t0.000317378\t0.000254856\n+chr1\t2950001\t0.000428068\t0.000320232\n+chr1\t3000001\t0.000463429\t0.000357583\n+chr1\t3050001\t0.000463429\t0.000357583\n+chr1\t3100001\t0.000301039\t0.000224152\n+chr1\t3150001\t0.000382759\t0.000439366\n+chr1\t3200001\t0.000260714\t0.000337719\n+chr1\t3250001\t0.000260714\t0.000337719\n+chr1\t3300001\t0.00023037\t0.000307693\n+chr1\t3350001\t3.10001e-05\t1.78574e-05\n+chr1\t3400001\t7.10015e-05\t1.05358e-05\n+chr1\t3450001\t8.90019e-05\t1.80358e-05\n+chr1\t3500001\t0.000142007\t0.000122504\n+chr1\t3550001\t0.000194682\t0.000308426\n+chr1\t3600001\t0.000181344\t0.000338787\n+chr1\t3650001\t0.000163343\t0.000331286\n+chr1\t3700001\t0.000110337\t0.000226804\n+chr1\t3750001\t0.000213667\t0.000172144\n+chr1\t3800001\t0.000238001\t0.000186791\n+chr1\t3850001\t0.000238001\t0.000186791\n+chr1\t3900001\t0.000249001\t0.000199292\n+chr1\t3950001\t0.00010734\t0.000111974\n+chr1\t4000001\t0.000118012\t0.000171086\n+chr1\t4050001\t0.000136351\t0.00021253\n+chr1\t4100001\t0.000245038\t0.000325422\n+chr1\t4150001\t0.000206354\t0.000278969\n+chr1\t4200001\t0.000184347\t0.000240934\n+chr1\t4250001\t0.000483023\t0.000489519\n+chr1\t4300001\t0.000399008\t0.000383234\n+chr1\t4350001\t0.000415677\t0.000422527\n+chr1\t4400001\t0.000386336\t0.000367327\n+chr1\t4450001\t0.000136667\t0.000130895\n+chr1\t4500001\t0.000101\t0.000111788\n+chr1\t4550001\t9.66667e-05\t7.62504e-05\n+chr1\t4600001\t0.000173334\t0.000112501\n+chr1\t4650001\t0.000168006\t0.000105541\n+chr1\t4700001\t0.000275677\t0.000195907\n+chr1\t4750001\t0.000270683\t0.000198586\n+chr1\t4800001\t0.00017701\t0.000147689\n+chr1\t4850001\t0.000115003\t0.000101074\n+chr1\t4900001\t7.33351e-06\t1.07143e-05\n+chr1\t4950001\t0.000109667\t0.000139821\n+chr1\t5000001\t0.000109667\t0.000135536\n+chr1\t5050001\t0.000123001\t0.000144465\n+chr1\t5100001\t0.000123001\t0.000144465\n+chr1\t5150001\t2.26668e-05\t2.50002e-05\n+chr1\t5200001\t4.16678e-05\t7.89292e-05\n+chr1\t525000'..b'chr4\t22900001\t5.66668e-06\t0.000129144\n+chr4\t22950001\t2.7668e-05\t7.983e-05\n+chr4\t23000001\t4.80024e-05\t0.0001293\n+chr4\t23050001\t4.80024e-05\t0.000111253\n+chr4\t23100001\t4.23353e-05\t0.000111253\n+chr4\t23150001\t2.03334e-05\t7.12502e-05\n+chr4\t23200001\t1.43333e-05\t2.17857e-05\n+chr4\t23250001\t1.43333e-05\t8.75003e-06\n+chr4\t23300001\t1.43333e-05\t1.55359e-05\n+chr4\t23350001\t1.43333e-05\t5.26796e-05\n+chr4\t23600001\t0.000333037\t5.26796e-05\n+chr4\t23650001\t0.000339705\t4.39293e-05\n+chr4\t23700001\t0.000339705\t3.7679e-05\n+chr4\t23750001\t0.000339705\t1.01786e-05\n+chr4\t23800001\t1.53334e-05\t1.01786e-05\n+chr4\t23850001\t2.03333e-05\t1.01786e-05\n+chr4\t23900001\t2.03333e-05\t9.64286e-06\n+chr4\t23950001\t4.6e-05\t0.000347545\n+chr4\t24000001\t4.26667e-05\t0.000360582\n+chr4\t24050001\t7.06669e-05\t0.000360582\n+chr4\t24100001\t7.06669e-05\t0.000360582\n+chr4\t24150001\t4.50001e-05\t1.67857e-05\n+chr4\t24200001\t3.96668e-05\t3.57143e-05\n+chr4\t24300001\t5.2667e-05\t3.57143e-05\n+chr4\t24350001\t0.000122002\t6.75e-05\n+chr4\t24400001\t0.000266683\t7.25e-05\n+chr4\t24450001\t0.000273683\t5.53574e-05\n+chr4\t24500001\t0.000254354\t5.53574e-05\n+chr4\t24550001\t0.000261021\t2.35715e-05\n+chr4\t24600001\t0.000116338\t1.48215e-05\n+chr4\t24650001\t0.000122671\t4.82146e-05\n+chr4\t24700001\t8.93344e-05\t0.000115716\n+chr4\t24750001\t1.33333e-05\t0.00027679\n+chr4\t24800001\t5.63333e-05\t0.000318755\n+chr4\t24850001\t4.3e-05\t0.000331278\n+chr4\t24900001\t0.000111667\t0.000315028\n+chr4\t24950001\t0.000268667\t0.000153942\n+chr4\t25000001\t0.000254334\t0.000123048\n+chr4\t25050001\t0.000284001\t6.66095e-05\n+chr4\t25100001\t0.000243667\t1.53575e-05\n+chr4\t25150001\t0.000160669\t4.26797e-05\n+chr4\t25200001\t0.000144335\t3.16075e-05\n+chr4\t25250001\t0.000117003\t0.000100536\n+chr4\t25300001\t0.000109669\t0.000235358\n+chr4\t25350001\t7.33383e-05\t0.000221967\n+chr4\t25400001\t0.000105674\t0.00024036\n+chr4\t25450001\t0.000103339\t0.000178216\n+chr4\t25500001\t8.23378e-05\t0.000163038\n+chr4\t25550001\t0.000153\t0.000199824\n+chr4\t25600001\t0.000319\t0.000181431\n+chr4\t25650001\t0.000516341\t0.000195003\n+chr4\t25700001\t0.000653343\t0.000157506\n+chr4\t25750001\t0.000545008\t0.000146076\n+chr4\t25800001\t0.000517017\t0.000146076\n+chr4\t25850001\t0.000415677\t0.000121432\n+chr4\t25900001\t0.000413343\t0.000156072\n+chr4\t25950001\t0.000643349\t0.000263752\n+chr4\t26000001\t0.000537679\t0.000450719\n+chr4\t26050001\t0.000441674\t0.000614828\n+chr4\t26100001\t0.000307005\t0.000498041\n+chr4\t26150001\t8.53348e-05\t0.000524291\n+chr4\t26200001\t3.6e-05\t0.000422503\n+chr4\t26250001\t5.53333e-05\t0.000368574\n+chr4\t26300001\t7.63345e-05\t0.000593045\n+chr4\t26350001\t6.8001e-05\t0.000512683\n+chr4\t26400001\t4.03339e-05\t0.000427503\n+chr4\t26450001\t6.63343e-05\t0.000317324\n+chr4\t26500001\t4.53333e-05\t0.000108393\n+chr4\t26550001\t7.46667e-05\t4.50001e-05\n+chr4\t26600001\t0.000139\t6.92859e-05\n+chr4\t26650001\t0.000124\t9.26806e-05\n+chr4\t26700001\t0.000124\t7.71445e-05\n+chr4\t26750001\t0.000125667\t4.76795e-05\n+chr4\t26800001\t0.000142667\t3.8215e-05\n+chr4\t26850001\t0.000124001\t1.48214e-05\n+chr4\t26900001\t0.000129334\t2.48214e-05\n+chr4\t26950001\t0.000132667\t5.42863e-05\n+chr4\t27000001\t9.33339e-05\t6.1965e-05\n+chr4\t27050001\t0.000255335\t6.1965e-05\n+chr4\t27100001\t0.000278669\t9.41088e-05\n+chr4\t27150001\t0.000373671\t0.000141787\n+chr4\t27200001\t0.000331671\t0.000129287\n+chr4\t27250001\t0.000158001\t0.000134287\n+chr4\t27300001\t0.000186667\t0.000148393\n+chr4\t27350001\t0.000113667\t0.00010625\n+chr4\t27400001\t0.000239002\t0.000267681\n+chr4\t27450001\t0.000322337\t0.00030215\n+chr4\t27500001\t0.000265003\t0.000349483\n+chr4\t27550001\t0.000257003\t0.000315911\n+chr4\t27600001\t0.000157334\t0.000144471\n+chr4\t27650001\t7.4e-05\t0.000166791\n+chr4\t27700001\t7.4e-05\t0.000101965\n+chr4\t27750001\t2.56667e-05\t0.000236252\n+chr4\t27900001\t1.63333e-05\t0.000331432\n+chr4\t27950001\t0.000191667\t0.000269645\n+chr4\t28000001\t0.000353002\t0.000293217\n+chr4\t28050001\t0.000353002\t0.000189286\n+chr4\t28100001\t0.000336669\t9.41071e-05\n+chr4\t28150001\t0.000161334\t9.41071e-05\n+chr4\t27750001\t3.17857e-05\t\n+chr4\t27900001\t1.57143e-05\t\n+chr4\t27950001\t0.000185714\t\n+chr4\t28000001\t0.000317146\t\n+chr4\t28050001\t0.000317146\t\n+chr4\t28100001\t0.000301432\t\n+chr4\t28150001\t0.00013143\t\n' |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.fst.by_marker.genes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.fst.by_marker.genes.txt Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,4432 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|
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.fst.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.fst.txt Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,729 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9800001\t0.0802439\n+chr3\t30000001\t0.181393\n+chr3\t30200001\t0.0576265\n+chr3\t30400001\t0.272341\n+chr3\t30600001\t0.0367333\n+chr3\t30800001\t0.1771\n+chr3\t31000001\t0.295031\n+chr3\t31200001\t0.0885696\n+chr3\t31400001\t-0.0441044\n+chr3\t31600001\t0.0611988\n+chr3\t31800001\t0.091861\n+chr3\t32000001\t0.170791\n+chr4\t1\t0.26351\n+chr4\t200001\t0.182997\n+chr4\t400001\t0.182088\n+chr4\t600001\t0.201967\n+chr4\t800001\t0.154393\n+chr4\t1000001\t0.199255\n+chr4\t1200001\t0.166769\n+chr4\t1400001\t0.202122\n+chr4\t1600001\t0.154788\n+chr4\t1800001\t0.238744\n+chr4\t2000001\t0.168285\n+chr4\t2200001\t0.16528\n+chr4\t2400001\t0.187013\n+chr4\t2600001\t0.154811\n+chr4\t2800001\t0.0841722\n+chr4\t3000001\t0.219282\n+chr4\t3200001\t0.145288\n+chr4\t3400001\t0.165108\n+chr4\t3600001\t0.284694\n+chr4\t3800001\t0.220334\n+chr4\t4000001\t0.154413\n+chr4\t4200001\t0.257402\n+chr4\t4400001\t0.142154\n+chr4\t4600001\t0.111462\n+chr4\t4800001\t0.0998644\n+chr4\t5000001\t0.158536\n+chr4\t5200001\t0.0613765\n+chr4\t5400001\t0.26583\n+chr4\t5600001\t0.106665\n+chr4\t5800001\t0.164433\n+chr4\t6000001\t0.16116\n+chr4\t6200001\t0.271033\n+chr4\t6400001\t0.352814\n+chr4\t6600001\t0.240766\n+chr4\t6800001\t0.352263\n+chr4\t7000001\t0.183066\n+chr4\t7200001\t0.241104\n+chr4\t7400001\t0.227432\n+chr4\t7600001\t0.315656\n+chr4\t7800001\t0.3282\n+chr4\t8000001\t0.229738\n+chr4\t8200001\t0.145038\n+chr4\t8600001\t0.0983264\n+chr4\t8800001\t0.302797\n+chr4\t9000001\t0.0796279\n+chr4\t9200001\t0.322837\n+chr4\t9400001\t0.243717\n+chr4\t9600001\t0.299535\n+chr4\t9800001\t0.101557\n+chr4\t10000001\t0.258603\n+chr4\t10200001\t0.201786\n+chr4\t10400001\t-0.099655\n+chr4\t10600001\t0.263958\n+chr4\t11000001\t0.28402\n+chr4\t11200001\t0.377824\n+chr4\t11400001\t0.206276\n+chr4\t11800001\t-0.0018873\n+chr4\t12000001\t0.150879\n+chr4\t12200001\t0.0226933\n+chr4\t12400001\t0.116041\n+chr4\t12600001\t0.0767385\n+chr4\t12800001\t0.00728285\n+chr4\t13000001\t0.219254\n+chr4\t13200001\t0.170133\n+chr4\t13400001\t0.0841722\n+chr4\t13600001\t0.197767\n+chr4\t13800001\t0.103222\n+chr4\t14000001\t-0.0722425\n+chr4\t14200001\t0.0379186\n+chr4\t14400001\t0.0257446\n+chr4\t14600001\t0.109136\n+chr4\t14800001\t0.102398\n+chr4\t15000001\t0.0526779\n+chr4\t15200001\t0.173094\n+chr4\t15400001\t0.128483\n+chr4\t15600001\t0.0051823\n+chr4\t15800001\t-0.0260366\n+chr4\t16000001\t0.252996\n+chr4\t16200001\t0.0876859\n+chr4\t16600001\t0.171171\n+chr4\t16800001\t-0.0517632\n+chr4\t17000001\t0.166333\n+chr4\t17200001\t0.297571\n+chr4\t17400001\t0.0950415\n+chr4\t17600001\t0.335263\n+chr4\t17800001\t0.00496724\n+chr4\t18000001\t0.119919\n+chr4\t18200001\t0.0983344\n+chr4\t18400001\t-0.0944617\n+chr4\t18600001\t-0.0295359\n+chr4\t18800001\t0.120674\n+chr4\t19000001\t-0.0578221\n+chr4\t19200001\t0.00284494\n+chr4\t19400001\t-0.0155241\n+chr4\t19600001\t-0.0180601\n+chr4\t19800001\t0.0401891\n+chr4\t20000001\t0.191873\n+chr4\t20200001\t0.125394\n+chr4\t20400001\t0.167374\n+chr4\t20600001\t0.0564925\n+chr4\t20800001\t0.0647701\n+chr4\t21000001\t-0.556714\n+chr4\t21200001\t-0.0284392\n+chr4\t21400001\t0.16636\n+chr4\t21600001\t0.220916\n+chr4\t21800001\t-0.0971482\n+chr4\t22000001\t-0.117066\n+chr4\t22200001\t0.00282381\n+chr4\t22400001\t-0.0969166\n+chr4\t22600001\t0.336404\n+chr4\t22800001\t0.0622177\n+chr4\t23000001\t0.232383\n+chr4\t23200001\t0.191379\n+chr4\t23600001\t0.0222326\n+chr4\t23800001\t-0.0245746\n+chr4\t24000001\t0.0598236\n+chr4\t24200001\t0.0536733\n+chr4\t24400001\t-0.0421205\n+chr4\t24600001\t0.0692525\n+chr4\t24800001\t-0.0277018\n+chr4\t25000001\t0.0434389\n+chr4\t25200001\t0.0400117\n+chr4\t25400001\t-0.0272649\n+chr4\t25600001\t0.0983775\n+chr4\t25800001\t-0.0234888\n+chr4\t26000001\t0.0207477\n+chr4\t26200001\t0.0349918\n+chr4\t26400001\t0.0627024\n+chr4\t26600001\t0.139464\n+chr4\t26800001\t0.118812\n+chr4\t27000001\t0.0272443\n+chr4\t27200001\t0.0220976\n+chr4\t27400001\t0.0838591\n+chr4\t27600001\t0.0891551\n+chr4\t28000001\t0.0405308\n' |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.snpden --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.snpden Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,767 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|
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/result2.windowed.pi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/result2.windowed.pi Mon Nov 09 05:18:45 2015 -0500 |
| b |
| b'@@ -0,0 +1,2929 @@\n+CHROM\tBIN_START\tBIN_END\tN_VARIANTS\tPI\n+chr1\t1\t200000\t428\t0.000608762\n+chr1\t50001\t250000\t403\t0.000586421\n+chr1\t100001\t300000\t432\t0.00063033\n+chr1\t150001\t350000\t435\t0.000604495\n+chr1\t200001\t400000\t330\t0.00041295\n+chr1\t250001\t450000\t321\t0.000376215\n+chr1\t300001\t500000\t240\t0.000264312\n+chr1\t350001\t550000\t140\t0.000126686\n+chr1\t400001\t600000\t129\t9.49236e-05\n+chr1\t450001\t650000\t126\t8.94841e-05\n+chr1\t500001\t700000\t191\t0.000163709\n+chr1\t550001\t750000\t274\t0.000246271\n+chr1\t600001\t800000\t299\t0.000307109\n+chr1\t650001\t850000\t295\t0.000293259\n+chr1\t700001\t900000\t230\t0.000219009\n+chr1\t750001\t950000\t155\t0.000140595\n+chr1\t800001\t1000000\t150\t0.000115318\n+chr1\t850001\t1050000\t100\t8.92489e-05\n+chr1\t900001\t1100000\t100\t8.92489e-05\n+chr1\t950001\t1150000\t103\t0.000100019\n+chr1\t1000001\t1200000\t98\t0.000129897\n+chr1\t1050001\t1250000\t191\t0.000295682\n+chr1\t1100001\t1300000\t271\t0.000407235\n+chr1\t1150001\t1350000\t333\t0.000509177\n+chr1\t1200001\t1400000\t248\t0.000398162\n+chr1\t1250001\t1450000\t234\t0.000338995\n+chr1\t1300001\t1500000\t169\t0.000241573\n+chr1\t1350001\t1550000\t303\t0.0004158\n+chr1\t1400001\t1600000\t361\t0.000519612\n+chr1\t1450001\t1650000\t386\t0.000561072\n+chr1\t1500001\t1700000\t371\t0.000546925\n+chr1\t1550001\t1750000\t164\t0.00025588\n+chr1\t1600001\t1800000\t312\t0.000425137\n+chr1\t1650001\t1850000\t251\t0.000330136\n+chr1\t1700001\t1900000\t297\t0.000398713\n+chr1\t1750001\t1950000\t413\t0.000607137\n+chr1\t1800001\t2000000\t205\t0.000330061\n+chr1\t1850001\t2050000\t172\t0.000286818\n+chr1\t1900001\t2100000\t243\t0.000366861\n+chr1\t1950001\t2150000\t220\t0.00029231\n+chr1\t2000001\t2200000\t445\t0.000581015\n+chr1\t2050001\t2250000\t454\t0.000592002\n+chr1\t2100001\t2300000\t338\t0.000444008\n+chr1\t2150001\t2350000\t338\t0.000445434\n+chr1\t2200001\t2400000\t172\t0.000214814\n+chr1\t2250001\t2450000\t232\t0.000293456\n+chr1\t2300001\t2500000\t231\t0.000292796\n+chr1\t2350001\t2550000\t223\t0.000261517\n+chr1\t2400001\t2600000\t238\t0.000311505\n+chr1\t2450001\t2650000\t200\t0.000265178\n+chr1\t2500001\t2700000\t289\t0.000365742\n+chr1\t2550001\t2750000\t209\t0.000263191\n+chr1\t2600001\t2800000\t135\t0.00015514\n+chr1\t2650001\t2850000\t145\t0.000158513\n+chr1\t2700001\t2900000\t56\t5.79756e-05\n+chr1\t2750001\t2950000\t84\t7.99616e-05\n+chr1\t2800001\t3000000\t142\t0.000170039\n+chr1\t2850001\t3050000\t91\t0.000113528\n+chr1\t2900001\t3100000\t266\t0.000319585\n+chr1\t2950001\t3150000\t353\t0.000420949\n+chr1\t3000001\t3200000\t410\t0.000458413\n+chr1\t3050001\t3250000\t410\t0.000458413\n+chr1\t3100001\t3300000\t274\t0.000289272\n+chr1\t3150001\t3350000\t303\t0.000428964\n+chr1\t3200001\t3400000\t205\t0.000314147\n+chr1\t3250001\t3450000\t205\t0.000314147\n+chr1\t3300001\t3500000\t166\t0.000277131\n+chr1\t3350001\t3550000\t31\t2.65952e-05\n+chr1\t3400001\t3600000\t41\t3.98383e-05\n+chr1\t3450001\t3650000\t51\t5.14876e-05\n+chr1\t3500001\t3700000\t121\t0.000146285\n+chr1\t3550001\t3750000\t248\t0.000283325\n+chr1\t3600001\t3800000\t249\t0.000297986\n+chr1\t3650001\t3850000\t239\t0.000286334\n+chr1\t3700001\t3900000\t169\t0.000191518\n+chr1\t3750001\t3950000\t141\t0.000204289\n+chr1\t3800001\t4000000\t157\t0.000222481\n+chr1\t3850001\t4050000\t157\t0.000222481\n+chr1\t3900001\t4100000\t171\t0.000242043\n+chr1\t3950001\t4150000\t120\t0.000132335\n+chr1\t4000001\t4200000\t165\t0.00017175\n+chr1\t4050001\t4250000\t219\t0.000215035\n+chr1\t4100001\t4300000\t306\t0.000335559\n+chr1\t4150001\t4350000\t244\t0.00028153\n+chr1\t4200001\t4400000\t221\t0.000251634\n+chr1\t4250001\t4450000\t362\t0.000508197\n+chr1\t4300001\t4500000\t279\t0.000394172\n+chr1\t4350001\t4550000\t305\t0.000429032\n+chr1\t4400001\t4600000\t248\t0.000378315\n+chr1\t4450001\t4650000\t94\t0.000139898\n+chr1\t4500001\t4700000\t76\t0.000113853\n+chr1\t4550001\t4750000\t56\t8.73635e-05\n+chr1\t4600001\t4800000\t115\t0.000153575\n+chr1\t4650001\t4850000\t119\t0.000154077\n+chr1\t4700001\t4900000\t184\t0.000264529\n+chr1\t4750001\t4950000\t189\t0.000265032\n+chr1\t4800001\t5000000\t125\t0.000184089\n+chr1\t4850001\t5050000\t80\t0.000122206\n+chr1\t4900001\t5100000\t15\t1.17588e-05\n+chr1\t4950001\t5150000\t83\t0.00013105\n+chr1\t5000001\t5200000\t79\t0.000128136\n+chr1\t5050001\t5250000\t98\t0.000143418\n+chr1\t5100001\t5300000\t98\t0.000143418\n+chr1\t5150001\t5350000\t32\t2.8353e-05\n+chr1\t5200001\t5400000\t67\t7.2589e-05\n+chr1\t5250001\t5450000\t1'..b'000\t70\t0.000106546\n+chr4\t22750001\t22950000\t44\t8.2638e-05\n+chr4\t22800001\t23000000\t13\t1.87363e-05\n+chr4\t22900001\t23100000\t5\t7.80224e-06\n+chr4\t22950001\t23150000\t44\t2.97844e-05\n+chr4\t23000001\t23200000\t72\t6.5561e-05\n+chr4\t23050001\t23250000\t72\t6.5561e-05\n+chr4\t23100001\t23300000\t67\t5.77571e-05\n+chr4\t23150001\t23350000\t29\t3.59355e-05\n+chr4\t23200001\t23400000\t11\t1.35165e-05\n+chr4\t23250001\t23450000\t11\t1.35165e-05\n+chr4\t23300001\t23500000\t11\t1.35165e-05\n+chr4\t23350001\t23550000\t10\t1.33516e-05\n+chr4\t23600001\t23800000\t283\t0.000380594\n+chr4\t23650001\t23850000\t291\t0.000391807\n+chr4\t23700001\t23900000\t291\t0.000391807\n+chr4\t23750001\t23950000\t291\t0.000391807\n+chr4\t23800001\t24000000\t11\t1.74176e-05\n+chr4\t23850001\t24050000\t20\t3.22527e-05\n+chr4\t23900001\t24100000\t20\t3.22527e-05\n+chr4\t23950001\t24150000\t37\t6.15385e-05\n+chr4\t24000001\t24200000\t38\t6.27473e-05\n+chr4\t24050001\t24250000\t43\t6.35167e-05\n+chr4\t24100001\t24300000\t43\t6.35167e-05\n+chr4\t24150001\t24350000\t26\t3.42309e-05\n+chr4\t24200001\t24400000\t22\t2.68133e-05\n+chr4\t24300001\t24500000\t27\t4.83524e-05\n+chr4\t24350001\t24550000\t75\t0.000122257\n+chr4\t24400001\t24600000\t186\t0.000286064\n+chr4\t24450001\t24650000\t209\t0.000315187\n+chr4\t24500001\t24700000\t248\t0.000329182\n+chr4\t24550001\t24750000\t256\t0.000320513\n+chr4\t24600001\t24800000\t145\t0.000156678\n+chr4\t24650001\t24850000\t134\t0.000140744\n+chr4\t24700001\t24900000\t73\t8.06673e-05\n+chr4\t24750001\t24950000\t17\t1.54402e-05\n+chr4\t24800001\t25000000\t37\t5.29143e-05\n+chr4\t24850001\t25050000\t25\t3.97261e-05\n+chr4\t24900001\t25100000\t76\t0.000110936\n+chr4\t24950001\t25150000\t183\t0.000262041\n+chr4\t25000001\t25200000\t184\t0.000246769\n+chr4\t25050001\t25250000\t203\t0.000276056\n+chr4\t25100001\t25300000\t161\t0.000221214\n+chr4\t25150001\t25350000\t105\t0.000173465\n+chr4\t25200001\t25400000\t116\t0.000184844\n+chr4\t25250001\t25450000\t100\t0.000156493\n+chr4\t25300001\t25500000\t104\t0.000162153\n+chr4\t25350001\t25550000\t108\t0.000123209\n+chr4\t25400001\t25600000\t120\t0.000133483\n+chr4\t25450001\t25650000\t117\t0.000132547\n+chr4\t25500001\t25700000\t100\t0.000108313\n+chr4\t25550001\t25750000\t131\t0.000162643\n+chr4\t25600001\t25800000\t224\t0.000310176\n+chr4\t25650001\t25850000\t338\t0.000499642\n+chr4\t25700001\t25900000\t433\t0.000660636\n+chr4\t25750001\t25950000\t347\t0.00054189\n+chr4\t25800001\t26000000\t331\t0.000542931\n+chr4\t25850001\t26050000\t280\t0.000447045\n+chr4\t25900001\t26100000\t258\t0.000413033\n+chr4\t25950001\t26150000\t412\t0.000653487\n+chr4\t26000001\t26200000\t364\t0.000557118\n+chr4\t26050001\t26250000\t301\t0.000463538\n+chr4\t26100001\t26300000\t227\t0.000336499\n+chr4\t26150001\t26350000\t79\t0.000110553\n+chr4\t26200001\t26400000\t31\t4.56055e-05\n+chr4\t26250001\t26450000\t51\t6.93423e-05\n+chr4\t26300001\t26500000\t70\t9.47846e-05\n+chr4\t26350001\t26550000\t65\t8.03338e-05\n+chr4\t26400001\t26600000\t40\t4.92321e-05\n+chr4\t26450001\t26650000\t44\t6.02216e-05\n+chr4\t26500001\t26700000\t25\t3.47805e-05\n+chr4\t26550001\t26750000\t42\t5.48353e-05\n+chr4\t26600001\t26800000\t81\t0.000100662\n+chr4\t26650001\t26850000\t78\t9.56621e-05\n+chr4\t26700001\t26900000\t78\t9.56621e-05\n+chr4\t26750001\t26950000\t90\t0.000120445\n+chr4\t26800001\t27000000\t100\t0.000156156\n+chr4\t26850001\t27050000\t88\t0.000138684\n+chr4\t26900001\t27100000\t93\t0.000143959\n+chr4\t26950001\t27150000\t95\t0.000148407\n+chr4\t27000001\t27200000\t69\t0.00010544\n+chr4\t27050001\t27250000\t177\t0.000270774\n+chr4\t27100001\t27300000\t200\t0.000303914\n+chr4\t27150001\t27350000\t264\t0.000373227\n+chr4\t27200001\t27400000\t243\t0.000335314\n+chr4\t27250001\t27450000\t130\t0.000159469\n+chr4\t27300001\t27500000\t142\t0.000188259\n+chr4\t27350001\t27550000\t85\t0.000119728\n+chr4\t27400001\t27600000\t172\t0.000254735\n+chr4\t27450001\t27650000\t235\t0.000357099\n+chr4\t27500001\t27700000\t195\t0.000289899\n+chr4\t27550001\t27750000\t213\t0.00029847\n+chr4\t27600001\t27800000\t154\t0.000198356\n+chr4\t27650001\t27850000\t87\t9.4232e-05\n+chr4\t27700001\t27900000\t87\t9.4232e-05\n+chr4\t27750001\t27950000\t30\t3.55499e-05\n+chr4\t27900001\t28100000\t13\t1.72527e-05\n+chr4\t27950001\t28150000\t141\t0.000208022\n+chr4\t28000001\t28200000\t243\t0.000363033\n+chr4\t28050001\t28250000\t243\t0.000363033\n+chr4\t28100001\t28300000\t230\t0.00034578\n+chr4\t28150001\t28350000\t102\t0.000155005\n' |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/sample.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/sample.vcf Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| b'@@ -0,0 +1,5000 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type'..b'm=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:20,22:42:99:726,0,669\n+chr1\t188266\t.\tA\tG\t878.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.261;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=3.8663;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.827;QD=15.69;ReadPosRankSum=0.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:28,27:56:99:907,0,965\n+chr1\t188270\t.\tA\tG\t850.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=4.8662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.692;QD=15.75;ReadPosRankSum=0.709;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:27,27:54:99:879,0,898\n+chr1\t188311\t.\tT\tG\t901.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=2.345;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.454;QD=17.01;ReadPosRankSum=0.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:25,28:53:99:930,0,831\n+chr1\t188357\t.\tC\tT\t1327.77\t.\tAC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t1/1:0,36:36:99:1356,105,0\n+chr1\t188364\t.\tG\tC\t578.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.285;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.585;QD=14.47;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:22,18:40:99:607,0,770\n+chr1\t188393\t.\tT\tC\t515.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-1.106;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.191;QD=12.28;ReadPosRankSum=-1.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:24,18:42:99:544,0,828\n+chr1\t188395\t.\tC\tG\t543.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.775;QD=13.26;ReadPosRankSum=-1.773;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:23,18:41:99:572,0,791\n+chr1\t188416\t.\tT\tC\t397.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=39;Dels=0.00;FS=1.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.893;QD=10.20;ReadPosRankSum=0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:25,14:39:99:426,0,821\n+chr1\t188438\t.\tC\tA\t930.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=2.123;DP=50;Dels=0.00;FS=5.900;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.020;QD=18.62;ReadPosRankSum=-0.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:21,29:50:99:959,0,659\n+chr1\t188621\t.\tG\tA\t704.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=49;Dels=0.00;FS=5.986;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.090;QD=14.38;ReadPosRankSum=-0.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:27,22:49:99:733,0,926\n' |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/test-data/sample_group.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/test-data/sample_group.vcf Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| b'@@ -0,0 +1,156288 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=PQ,Number=1,Type=Float,Description="Read-backed phasing quality">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">\n+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">\n+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">\n+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher\'s exact test to detect strand bias">\n+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">\n+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">\n+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">\n+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">\n+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">\n+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">\n+##INFO=<ID=PhasingInconsistent,Number=0,Type=Flag,Description="Are the reads significantly haplotype-inconsistent?">\n+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">\n+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">\n+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">\n+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">\n+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">\n+##ReadBackedPhasing="analysis_type=ReadBackedPhasing input_file=[/scratch/hueber-29030/merged_bams_file.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/coffea_cds.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals='..b'NYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E433D|Cc04_g17260|mRNA||GSCOCT00013576001|Exon_chr4_28172125_28173380)\tGT:AD:DP:GQ:PL:PQ\t0|0:240,4:242:99:0,547,6548\t0|0:241,1:242:99:0,596,7549\t1|0:92,130:214:99:2886,0,2050:1282.63\t0|0:247,0:247:99:0,692,8837\t0|0:242,2:244:99:0,585,8141\t0|0:242,1:243:99:0,593,7685\t0|0:246,0:246:99:0,650,8149\n+chr4\t28173081\t.\tT\tC\t3504.68\t.\tAC=1;AF=0.071;AN=14;BaseQRankSum=0.846;DP=1727;Dels=0.00;FS=1.442;HaplotypeScore=11.9112;MLEAC=1;MLEAF=0.071;MQ=59.70;GenePos=1358;MQ0=1;MQRankSum=-0.410;QD=14.36;ReadPosRankSum=-0.556;EFF=DOWNSTREAM(MODIFIER||||Cc04_g17250|mRNA||GSCOCT00013575001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K453R|Cc04_g17260|mRNA||GSCOCT00013576001|Exon_chr4_28172125_28173380)\tGT:AD:DP:GQ:PL:PQ\t0|0:235,1:230:99:0,599,7552\t0|0:248,0:242:99:0,569,7170\t1|0:114,129:232:99:3538,0,3373:333.84\t0|0:246,2:240:99:0,659,8315\t0|0:249,1:243:99:0,689,8781\t0|0:250,0:250:99:0,605,7696\t0|0:250,0:250:99:0,623,7841\n+chr4\t28173026\t.\tG\tA\t3182.68\t.\tAC=1;AF=0.071;AN=14;BaseQRankSum=0.423;DP=1729;Dels=0.00;FS=0.000;HaplotypeScore=8.5953;MLEAC=1;MLEAF=0.071;MQ=59.71;GenePos=1413;MQ0=0;MQRankSum=-0.668;QD=12.89;ReadPosRankSum=0.160;EFF=DOWNSTREAM(MODIFIER||||Cc04_g17250|mRNA||GSCOCT00013575001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L471|Cc04_g17260|mRNA||GSCOCT00013576001|Exon_chr4_28172125_28173380)\tGT:AD:DP:GQ:PL\t0/1:139,108:235:99:3216,0,3665\t0|0:247,1:247:99:0,653,8063\t0|0:235,0:235:99:0,620,7685\t0|0:250,0:250:99:0,698,8846\t0|0:248,0:248:99:0,704,8915\t0|0:250,0:250:99:0,671,8365\t0|0:248,0:248:99:0,656,8121\n+chr4\t28172930\t.\tG\tA\t10653.53\t.\tAC=3;AF=0.214;AN=14;BaseQRankSum=-2.302;DP=1665;Dels=0.00;FS=10.594;HaplotypeScore=8.8246;MLEAC=3;MLEAF=0.214;MQ=59.61;GenePos=1509;MQ0=0;MQRankSum=1.573;QD=23.78;ReadPosRankSum=4.957;EFF=DOWNSTREAM(MODIFIER||||Cc04_g17250|mRNA||GSCOCT00013575001|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P503|Cc04_g17260|mRNA||GSCOCT00013576001|Exon_chr4_28172125_28173380)\tGT:AD:DP:GQ:PL\t1|1:3,195:195:99:7195,572,0\t0|0:250,0:250:99:0,731,9415\t0|0:216,1:216:99:0,641,8224\t0|0:250,0:250:99:0,728,9470\t0/1:139,111:238:99:3506,0,4026\t0|0:249,0:249:99:0,734,9502\t0|0:250,0:250:99:0,725,9355\n+chr4\t28172890\t.\tC\tT\t51135.68\t.\tAC=13;AF=0.929;AN=14;BaseQRankSum=-2.272;DP=1598;Dels=0.00;FS=0.000;HaplotypeScore=5.7927;MLEAC=13;MLEAF=0.929;MQ=59.46;GenePos=1549;MQ0=1;MQRankSum=-1.034;QD=32.00;ReadPosRankSum=-2.491;EFF=DOWNSTREAM(MODIFIER||||Cc04_g17240|mRNA||GSCOCT00013574001|),DOWNSTREAM(MODIFIER||||Cc04_g17250|mRNA||GSCOCT00013575001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D517N|Cc04_g17260|mRNA||GSCOCT00013576001|Exon_chr4_28172125_28173380)\tGT:AD:DP:GQ:PL\t1|1:2,167:167:99:5859,466,0\t1|1:4,241:241:99:7876,650,0\t1|1:0,182:182:99:6500,520,0\t0/1:122,126:242:99:3892,0,3876\t1|1:0,250:250:99:9467,731,0\t1|1:1,245:246:99:8558,645,0\t1|1:0,247:247:99:9017,701,0\n+chr4\t28185676\t.\tG\tC\t788.5\t.\tAC=12;AF=0.857;AN=14;BaseQRankSum=-2.373;DP=39;Dels=0.00;FS=29.609;HaplotypeScore=0.0000;MLEAC=12;MLEAF=0.857;MQ=56.35;GenePos=131;MQ0=0;MQRankSum=-0.231;QD=20.22;ReadPosRankSum=-1.197;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R44P|Cc04_g17270|mRNA||GSCOCT00013577001|Exon_chr4_28185546_28186106),UPSTREAM(MODIFIER||||Cc04_g17260|mRNA||GSCOCT00013576001|)\tGT:AD:DP:GQ:PL\t1|1:1,3:4:9:111,9,0\t1|1:0,5:5:12:137,12,0\t1|1:0,1:1:3:38,3,0\t0/1:3,4:7:46:46,0,106\t0/1:1,12:13:10:245,0,10\t1|1:0,4:4:12:138,12,0\t1|1:0,5:5:9:109,9,0\n+chr4\t28185711\t.\tC\tG\t3757.55\t.\tAC=3;AF=0.214;AN=14;BaseQRankSum=2.697;DP=390;Dels=0.00;FS=10.697;HaplotypeScore=1.0825;MLEAC=3;MLEAF=0.214;MQ=57.38;GenePos=166;MQ0=0;MQRankSum=1.973;QD=17.72;ReadPosRankSum=3.637;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Ggc|R56G|Cc04_g17270|mRNA||GSCOCT00013577001|Exon_chr4_28185546_28186106),UPSTREAM(MODIFIER||||Cc04_g17260|mRNA||GSCOCT00013576001|)\tGT:AD:DP:GQ:PL:PQ\t0|0:31,0:31:93:0,93,1165\t0|0:50,0:50:99:0,150,1866\t0/1:20,19:38:99:609,0,640\t0|1:27,42:66:99:1324,0,852:71.58\t0/1:43,61:99:99:1866,0,1350\t0|0:48,0:48:99:0,141,1778\t0|0:49,0:49:99:0,144,1853\n' |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| @@ -0,0 +1,43 @@ +#!/bin/bash + +tool_path=$(dirname $0) + +filein=$1 +fileout_label=$(date "+%Y%m%d%H%M%S") +step=$2 +window=$3 +filelog=$4 +fileout_taj=$5 +fileout_tstv=$6 +fileout_windowed=$7 +fileout_snp=$8 +group=$9 +if [ "$group" != "none" ] +then fileout_fst=${10} + fileout_fst_marker=${11} + fileout_taj_combined=${12} + fileout_windowed_combined=${13} +fi + + +cp $filein ${filein}.vcf +if [ "$group" != "none" ] +then perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window --group $group +else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window +fi + +mv ${fileout_label}.vcftools.log $filelog +mv ${fileout_label}.Tajima.D ${fileout_taj} +mv ${fileout_label}.TsTv ${fileout_tstv} +mv ${fileout_label}.windowed.pi ${fileout_windowed} +mv ${fileout_label}.snpden ${fileout_snp} + +if [ "$group" != "none" ] +then mv ${fileout_label}.fst.txt ${fileout_fst} +mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker} +mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined} +mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined} +fi + +rm -f ${filein}.vcf ${filein}.vcf.* + |
| b |
| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml --- a/VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="sniplay_vcftoolsslidingwindow" name="VCF tools SlidingWindow" version="1.0.0"> +<tool id="sniplay_vcftoolsslidingwindow" name="VCF tools SlidingWindow" version="1.1.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Make diversity computation with sliding window </description> @@ -9,16 +9,21 @@ <requirement type="package" version="0.1.12b">vcftools</requirement> </requirements> - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + <!-- [REQUIRED] The command to execute --> - <command interpreter="perl"> - VCFToolsSlidingWindow.pl --input $filein --out $fileout_label --step $step --window $window && mv ${fileout_label}.vcftools.log $filelog && mv ${fileout_label}.Tajima.D ${fileout_taj} && mv ${fileout_label}.TsTv ${fileout_tstv} && mv ${fileout_label}.windowed.pi ${fileout_windowed} && mv ${fileout_label}.snpden ${fileout_snp} + <command interpreter="bash"> + vcfToolsSlidingWindow.sh ${filein} $step $window $filelog ${fileout_taj} ${fileout_tstv} ${fileout_windowed} ${fileout_snp} + #if $group : + $group ${fileout_fst} ${fileout_fst_marker} ${fileout_taj_combined} ${fileout_windowed_combined} + #else : + "none" + #end if </command> <!-- [REQUIRED] Input files and tool parameters --> @@ -27,6 +32,7 @@ <param name="fileout_label" type="text" value="snp_density" optional="false" label="Output file basename"/> <param name="window" type="integer" value="200000" optional="false" label="Window size (in bp)"/> <param name="step" type="integer" value="50000" optional="false" label="Step size (in bp)"/> + <param name="group" type="data" format="tab" optional="True" label="(optionnal) Groups" help="Each line of the file should be : Indiv;Pop" /> </inputs> <!-- [REQUIRED] Output files --> @@ -36,24 +42,41 @@ <data name="fileout_tstv" format="tabular" label="${fileout_label}.TsTv" /> <data name="fileout_windowed" format="tabular" label="${fileout_label}.windowed.pi" /> <data name="filelog" format="txt" label="${fileout_label}.log" /> + <data name="fileout_fst" format="txt" label="${fileout_label}.fst.txt"> + <filter>(group != None)</filter> + </data> + <data name="fileout_fst_marker" format="txt" label="${fileout_label}.fst.by_marker.genes.txt"> + <filter>(group != None)</filter> + </data> + <data name="fileout_windowed_combined" format="tabular" label="${fileout_label}.combined.pi.txt" > + <filter>(group != None)</filter> + </data> + <data name="fileout_taj_combined" format="tabular" label="${fileout_label}.combined.dtajima.txt" > + <filter>(group != None)</filter> + </data> </outputs> - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> - <test> + <test> + <param name="filein" value="sample_group.vcf" /> + <param name="group" value="groups.txt" /> + <output name="fileout_snp" file="result2.snpden" /> + <output name="fileout_taj" file="result2.Tajima.D" /> + <output name="fileout_tstv" file="result2.TsTv" /> + <output name="fileout_windowed" file="result2.windowed.pi" /> + <output name="fileout_fst" file="result2.fst.txt" /> + <output name="fileout_fst_marker" file="result2.fst.by_marker.genes.txt" /> + <output name="fileout_taj_combined" file="result2.combined.dtajima.txt" /> + <output name="fileout_windowed_combined" file="result2.combined.pi.txt" /> + </test> + <test> <param name="filein" value="sample.vcf" /> - <output name="fileout_annot" file="result.annotation" /> - <output name="fileout_het" file="result.het" /> - <output name="fileout_imiss" file="result.imiss" /> - <output name="fileout_sum" file="result.TsTv.summary" /> - <output name="filelog" file="result.log" /> + <output name="fileout_snp" file="result.snpden" /> + <output name="fileout_taj" file="result.Tajima.D" /> + <output name="fileout_tstv" file="result.TsTv" /> + <output name="fileout_windowed" file="result.windowed.pi" /> </test> </tests> |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsStats/VCFToolsStats.pl --- a/VCFToolsStats/VCFToolsStats.pl Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolsStats/VCFToolsStats.pl Mon Nov 09 05:18:45 2015 -0500 |
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| @@ -2,7 +2,6 @@ #!/usr/bin/perl use strict; -use Switch; use Getopt::Long; use Bio::SeqIO; |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsStats/test-data/result.log --- a/VCFToolsStats/test-data/result.log Fri Jul 10 04:16:17 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,44 +0,0 @@ - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --het - --out vcf_stats - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting Individual Heterozygosity - Individual Heterozygosity: Only using biallelic SNPs. -After filtering, kept 4813 out of a possible 4955 Sites -Run Time = 0.00 seconds - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --out vcf_stats - --TsTv-summary - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting Ts/Tv summary -Ts/Tv ratio: 1.883 -After filtering, kept 4813 out of a possible 4955 Sites -Run Time = 0.00 seconds - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --missing-indv - --out vcf_stats - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting Individual Missingness -After filtering, kept 4813 out of a possible 4955 Sites -Run Time = 0.00 seconds |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsStats/vcfToolsStats.sh --- a/VCFToolsStats/vcfToolsStats.sh Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolsStats/vcfToolsStats.sh Mon Nov 09 05:18:45 2015 -0500 |
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| @@ -3,12 +3,12 @@ tool_path=$(dirname $0) filein=$1 -fileout_label=$2 -fileout_annot=$3 -fileout_het=$4 -fileout_imiss=$5 -fileout_sum=$6 -filelog=$7 +fileout_label=$(date "+%Y%m%d%H%M%S") +fileout_annot=$2 +fileout_het=$3 +fileout_imiss=$4 +fileout_sum=$5 +filelog=$6 |
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| diff -r ac7c9e40d601 -r 612066e3f57d VCFToolsStats/vcfToolsStats.xml --- a/VCFToolsStats/vcfToolsStats.xml Fri Jul 10 04:16:17 2015 -0400 +++ b/VCFToolsStats/vcfToolsStats.xml Mon Nov 09 05:18:45 2015 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.0.0"> +<tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.1.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> </description> @@ -9,16 +9,15 @@ <requirement type="package" version="0.1.12b">vcftools</requirement> </requirements> - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> <!-- [REQUIRED] The command to execute --> <command interpreter="perl"> - vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog + vcfToolsStats.sh $filein $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog </command> <!-- [REQUIRED] Input files and tool parameters --> @@ -36,12 +35,6 @@ <data name="filelog" format="txt" label="${fileout_label}.log" /> </outputs> - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> @@ -51,7 +44,6 @@ <output name="fileout_het" file="result.het" /> <output name="fileout_imiss" file="result.imiss" /> <output name="fileout_sum" file="result.TsTv.summary" /> - <output name="filelog" file="result.log" /> </test> </tests> |
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| diff -r ac7c9e40d601 -r 612066e3f57d tool_dependencies.xml --- a/tool_dependencies.xml Fri Jul 10 04:16:17 2015 -0400 +++ b/tool_dependencies.xml Mon Nov 09 05:18:45 2015 -0500 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="vcftools" version="0.1.12b"> - <repository changeset_revision="a655cb1dfc58" name="package_vcftools_0_1_12b" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="a655cb1dfc58" name="package_vcftools_0_1_12b" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |