| Previous changeset 5:ec22fcacb66c (2016-02-15) Next changeset 7:24336e3d3dd8 (2016-06-15) |
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Commit message:
planemo upload |
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modified:
test-data/SNPden-result.txt test-data/SNPden-result_bysample.txt tool_dependencies.xml |
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added:
AnnotationStatsFromVCF/AnnotationStatsFromVCF.pl AnnotationStatsFromVCF/annotationStatsFromVCF AnnotationStatsFromVCF/annotationStatsFromVCF.effect AnnotationStatsFromVCF/annotationStatsFromVCF.location AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml GetHaplotypesFromPhasedVCF/GetHaplotypesFromPhasedVCF.pl GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml SNP_density/CalculateSlidingWindowsSNPdensitiesFromVCF.pl SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF.sh SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml test-data/getHaplotypesFromPhasedVCF-input.vcf test-data/getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt test-data/getHaplotypesFromPhasedVCF-result.haplo.fas |
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removed:
SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 AnnotationStatsFromVCF/AnnotationStatsFromVCF.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotationStatsFromVCF/AnnotationStatsFromVCF.pl Mon May 23 17:49:17 2016 -0400 |
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| @@ -0,0 +1,127 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use Bio::SeqIO; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -v, --vcf <VCF input> + -o, --out <output> + -s, --step <step (in bp)> +~; +$usage .= "\n"; + +my ($vcf,$out,$step,$min_depth); +$min_depth = 5; + +GetOptions( + "vcf=s" => \$vcf, + "out=s" => \$out, + "min_depth=s"=> \$min_depth, + "step=s" => \$step, +); + + +die $usage + if ( !$vcf || !$step || !$out ); + +if ($step =~/^(\d+)\s*$/){ + $step = $1; +} +else{ + die "Error: step size must be an integer\n"; +} + + +my $VCFTOOLS_EXE = "vcftools"; + +my %max; +my %counts_ns; +my %counts_s; +my $nb_gene = 0; +my $nb_intergenic = 0; +my $nb_exon = 0; +my $nb_intron = 0; +my $nb_UTR = 0; +my $nb_syn = 0; +my $nb_nsyn = 0; +if ($vcf =~/\.bcf/){ + system("$VCFTOOLS_EXE --bcf $vcf --recode --recode-INFO-all --out $out"); + $vcf = "$out.recode.vcf"; +} +open(my $VCF,$vcf); +while(<$VCF>) +{ + my @infos = split(/\t/,$_); + if (scalar @infos > 8 && !/#CHROM/) + { + my $chrom = $infos[0]; + my $position = $infos[1]; + my $id = $infos[2]; + + + my $classe_position = int($position/$step); + if (/=NON_SYNONYMOUS_CODING/){ + $counts_ns{$chrom}{$classe_position}++; + $nb_nsyn++; + } + if (/=SYNONYMOUS_CODING/){ + $counts_s{$chrom}{$classe_position}++; + $nb_syn++; + } + if (/INTERGENIC/){ + $nb_intergenic++; + } + elsif (/EFF=/){ + $nb_gene++; + } + if (/CODING/){ + } + elsif (/UTR/){ + $nb_UTR++; + } + elsif (/INTRON/){ + $nb_intron++; + } + $max{$chrom} = $classe_position; + } +} +my $nb_exon = $nb_gene - $nb_intron - $nb_UTR; + +open(my $OUT,">$out"); +#print $OUT "Chrom Bin Nb synonymous SNPs Nb non-synonymous SNPs dN/dS ratio\n"; +print $OUT "Chrom Bin dN/dS ratio\n"; +foreach my $chrom(sort keys(%counts_s)) +{ + my $maximum = $max{$chrom}; + for(my $i=1;$i<=$maximum;$i++) + { + my $classe_position = $i; + my $nb_s = 0; + my $nb_ns = 0; + my $ratio = 0; + if ($counts_s{$chrom}{$classe_position}){$nb_s = $counts_s{$chrom}{$classe_position};} + if ($counts_ns{$chrom}{$classe_position}){$nb_ns = $counts_ns{$chrom}{$classe_position};} + if ($nb_s){$ratio = $nb_ns/$nb_s;} + my $bin = $classe_position * $step; + #print $OUT "$chrom $classe_position $nb_s $nb_ns $ratio\n"; + print $OUT "$chrom $bin $ratio\n"; + } +} +close($OUT); + + + +open(my $A2, ">$out.location"); +print $A2 "Intergenic $nb_intergenic Intergenic:$nb_intergenic\n"; +print $A2 "Genic $nb_gene Exon:$nb_exon Intron:$nb_intron UTR:$nb_UTR\n"; +close($A2); + +open(my $A2, ">$out.effect"); +print $A2 "Intron $nb_intron Intron:$nb_intron\n"; +print $A2 "UTR $nb_UTR UTR:$nb_UTR\n"; +print $A2 "Exon $nb_exon Synonym:$nb_syn Non-syn:$nb_nsyn\n"; +close($A2); + |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 AnnotationStatsFromVCF/annotationStatsFromVCF --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotationStatsFromVCF/annotationStatsFromVCF Mon May 23 17:49:17 2016 -0400 |
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| @@ -0,0 +1,10 @@ +Chrom Bin dN/dS ratio +chr1 20000 0.606060606060606 +chr1 40000 0 +chr1 60000 5.5 +chr1 80000 0.363636363636364 +chr1 100000 0.764705882352941 +chr1 120000 1 +chr1 140000 1.11111111111111 +chr1 160000 7 +chr1 180000 2 |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 AnnotationStatsFromVCF/annotationStatsFromVCF.effect --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotationStatsFromVCF/annotationStatsFromVCF.effect Mon May 23 17:49:17 2016 -0400 |
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| @@ -0,0 +1,3 @@ +Intron 960 Intron:960 +UTR 281 UTR:281 +Exon 3248 Synonym:124 Non-syn:120 |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 AnnotationStatsFromVCF/annotationStatsFromVCF.location --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotationStatsFromVCF/annotationStatsFromVCF.location Mon May 23 17:49:17 2016 -0400 |
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| @@ -0,0 +1,2 @@ +Intergenic 466 Intergenic:466 +Genic 4489 Exon:3248 Intron:960 UTR:281 |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml Mon May 23 17:49:17 2016 -0400 |
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| @@ -0,0 +1,175 @@ +<tool id="annotationStatsFromVCF" name="Get annotation statistics" version="1.0.0"> + <description> from VCF file </description> + <requirements> + <requirement type="binary">perl</requirement> + <requirement type="package" version="0.1.12b">vcftools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="perl"> + AnnotationStatsFromVCF.pl -v $input -o $output_label -s $step && mv ${output_label} $output_count && mv ${output_label}.effect $output_stats_effect && mv ${output_label}.location $output_stats_location + </command> + <inputs> + <param type="data" name="input" format="vcf" label="VCF file" /> + <param type="text" name="output_label" label="Output_label" value='VCF_stats' /> + </inputs> + <outputs> + <data name="output_count" format="txt" label="${output_label}."/> + <data name="output_stats_effect" format="txt" label="${output_label}."/> + <data name="output_stats_location" format="txt" label="${output_label}."/> + </outputs> + <tests> + <test> + <param name="input" value="vcf2fastaAndHapmap-sample.vcf"/> + <output name="output_count" file=".txt"/> + <output name="output_stats_effect" file=""/> + <output name="output_stats_location" file=""/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + +============================== +Get Haplotypes From Phased VCF +============================== + +----------- +Description +----------- + + | Get Haplotype from phased VCF + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ========================== ======= +Name output file(s) format +=============== ========================== ======= +Beagle Phased VCF file VCF +=============== ========================== ======= + + +**Downstream tool** + +=============== ========================== =========== +Name input file(s) format +=============== ========================== =========== +=============== ========================== =========== + + +---------- +Input file +---------- + +VCF file + Phased VCF file + +---------- +Parameters +---------- + +Output file basename + Prefix for the output VCF file + +------------ +Output files +------------ + + +Text file + File describing haplotypes + +Fasta file + Fasta file with haplotypes + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +VCF file +--------- + +:: + + #fileformat=VCFv4.1 + #FILTER=<ID=LowQual,Description="Low quality"> + #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> + [...] + CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA + Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0 + + +Parameters +========== + +Output name -> haplotypes + + +Output files +============ + +haplotypes.distinct_haplotypes.txt +---------------------------------- + +:: + + ===Chr10=== + haplo1:2:CIRAD403_1,CIRAD403_2, + TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT + haplo2:2:MAHAE_1,MAHAE_2, + TAAATCTTGGTGCTGATCTGATATTTAATGCGT + + +haplotypes.haplo.fas +-------------------- + +:: + + >Chr10_AZUCENA_1 + TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT + >Chr10_AZUCENA_2 + TAAATCTTGGTGCTGATCTGATATTTAATGCGT + + ]]></help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, + author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, + title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, + year = {2015}, + doi = {10.1093/nar/gkv351}, + abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, + URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, + eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, + journal = {Nucleic Acids Research} + } + + }</citation> + + </citations> + +</tool> |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 GetHaplotypesFromPhasedVCF/GetHaplotypesFromPhasedVCF.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GetHaplotypesFromPhasedVCF/GetHaplotypesFromPhasedVCF.pl Mon May 23 17:49:17 2016 -0400 |
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| @@ -0,0 +1,108 @@ +#!/usr/bin/perl + +use strict; + +my $vcf = $ARGV[0]; +my $out = $ARGV[1]; + +open(O1,">$out.haplo.fas"); +open(O2,">$out.distinct_haplotypes.txt"); + +my %indiv; +my %genes; +my $nb_cols = 0; +my %phasing; +open(my $V,$vcf); +while(<$V>){ + my $line = $_; + $line =~s/\n//g; + $line =~s/\r//g; + my @infos = split(/\t/,$line); + if (/#CHROM/){ + for (my $i = 9; $i <= $#infos; $i++){ + $indiv{$i} = $infos[$i]; + } + } + else{ + my $gene = $infos[0]; + my $ref = $infos[3]; + my $alt = $infos[4]; + $nb_cols = $#infos; + for (my $i = 9; $i <= $#infos; $i++){ + my ($alleles,$depth) = split(":",$infos[$i]); + $alleles =~s/0/$ref/g; + $alleles =~s/1/$alt/g; + my $ind = $indiv{$i}; + #if ($alleles =~/\// && $genes{$gene}){next;} + $phasing{$gene}{$i}.= $alleles ." "; + } + $genes{$gene} = 1; + } +} +close($V); + +my %haplos; +my $gene_ok = 0; +my $gene_shared = 0; +my $gene_all_shared = 0; +my $nb_gene = 0; +my %haplotypes2; +foreach my $gene(keys(%phasing)) +{ + my $list = ""; + my $ok = 0; + my %haplotypes; + for (my $i=9;$i <= $nb_cols;$i++){ + + my $alleles = $phasing{$gene}{$i}; + if ($alleles eq "" or $alleles =~ /\./ or $alleles =~/ \w+\//){next;} + my @snps = split(" ",$alleles); + if (scalar @snps < 2){next;} + $alleles =~s/\//\|/g; + my @al = split(" ",$alleles); + my $haplo1 = ""; + my $haplo2 = ""; + foreach my $a(@al){ + my ($a1,$a2) = split(/\|/,$a); + $haplo1.= $a1; + $haplo2.= $a2; + } + $haplotypes{$haplo1}++; + $haplotypes{$haplo2}++; + my $ind = $indiv{$i}; + $haplotypes2{$gene}{$haplo1}.=$ind."_1,"; + $haplotypes2{$gene}{$haplo2}.=$ind."_2,"; + $haplos{$gene}{$haplo1}++; + $haplos{$gene}{$haplo2}++; + $list .= ">".$gene."_".$ind."_1\n$haplo1\n"; + $list .= ">".$gene."_".$ind."_2\n$haplo2\n"; + $ok++; + } + #print "$gene $nb_cols $ok\n"; + #if ($ok > 13 && $found_M1_M2 == 2){ + if ($ok == ($nb_cols - 8)){ + $nb_gene++; + print O1 $list; + } +} +foreach my $gene(sort {$a<=>$b} keys(%haplos)){ + print O2 "===$gene===\n"; + my $ref_hash = $haplos{$gene}; + my %hash = %$ref_hash; + my $num_haplo = 0; + foreach my $haplo(keys(%hash)){ + $num_haplo++; + my $haplo_name = "haplo".$num_haplo; + my $nb = $haplos{$gene}{$haplo}; + my $ind = $haplotypes2{$gene}{$haplo}; + print O2 $haplo_name.":$nb:".$haplotypes2{$gene}{$haplo}."\n".$haplo."\n"; + if ($nb > 1){ + #print "$nb \n"; + } + } +} + +close(O1); +close(O1); +#print scalar keys(%haplos); + |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml Mon May 23 17:49:17 2016 -0400 |
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| @@ -0,0 +1,171 @@ +<tool id="getHaplotypesFromPhasedVCF" name="Get Haplotypes From Phased VCF" version="1.0.0"> + <requirements> + <requirement type="binary">perl</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="perl"> + GetHaplotypesFromPhasedVCF.pl $input $output_label && mv ${output_label}.distinct_haplotypes.txt $output_distinct && mv ${output_label}.haplo.fas $output_haplo + </command> + <inputs> + <param type="data" name="input" format="vcf" label="Phased VCF" /> + <param type="text" name="output_label" label="Output_label" value='Haplotypes' /> + </inputs> + <outputs> + <data name="output_distinct" format="txt" label="${output_label}.distinct_haplotypes.txt"/> + <data name="output_haplo" format="fasta" label="${output_label}.haplo.fas"/> + </outputs> + <tests> + <test> + <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/> + <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt"/> + <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + +============================== +Get Haplotypes From Phased VCF +============================== + +----------- +Description +----------- + + | Get Haplotype from phased VCF + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ========================== ======= +Name output file(s) format +=============== ========================== ======= +Beagle Phased VCF file VCF +=============== ========================== ======= + + +**Downstream tool** + +=============== ========================== =========== +Name input file(s) format +=============== ========================== =========== +=============== ========================== =========== + + +---------- +Input file +---------- + +VCF file + Phased VCF file + +---------- +Parameters +---------- + +Output file basename + Prefix for the output VCF file + +------------ +Output files +------------ + + +Text file + File describing haplotypes + +Fasta file + Fasta file with haplotypes + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +VCF file +--------- + +:: + + #fileformat=VCFv4.1 + #FILTER=<ID=LowQual,Description="Low quality"> + #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> + [...] + CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA + Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0 + + +Parameters +========== + +Output name -> haplotypes + + +Output files +============ + +haplotypes.distinct_haplotypes.txt +---------------------------------- + +:: + + ===Chr10=== + haplo1:2:CIRAD403_1,CIRAD403_2, + TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT + haplo2:2:MAHAE_1,MAHAE_2, + TAAATCTTGGTGCTGATCTGATATTTAATGCGT + + +haplotypes.haplo.fas +-------------------- + +:: + + >Chr10_AZUCENA_1 + TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT + >Chr10_AZUCENA_2 + TAAATCTTGGTGCTGATCTGATATTTAATGCGT + + ]]></help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, + author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, + title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, + year = {2015}, + doi = {10.1093/nar/gkv351}, + abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, + URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, + eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, + journal = {Nucleic Acids Research} + } + + }</citation> + + </citations> + +</tool> |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl --- a/SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl Mon Feb 15 10:26:18 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,124 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --input <Hapmap input> - -o, --out <output in tabular format> - -s, --step <step (in bp)> -~; -$usage .= "\n"; - -my ($input,$out,$step); - -GetOptions( - "input=s" => \$input, - "out=s" => \$out, - "step=s" => \$step, -); - - -die $usage - if ( !$input || !$step || !$out ); - -my $max_chr_num = 100; - -my %counts; -my %counts_by_ind; -open(my $HAPMAP,$input); -my $headers= <$HAPMAP>; -$headers=~s/\n//g; -$headers=~s/\r//g; -my @ind_names = split(/\t/,$headers); -my @individual_names; -for (my $i = 12; $i <= $#ind_names; $i++) -{ - push(@individual_names,$ind_names[$i]); -} -my %maximums; -while(<$HAPMAP>) -{ - my $line = $_; - $line=~s/\n//g; - $line=~s/\r//g; - my @infos = split(/\t/,$line); - my $chrom = $infos[2]; - my $position = $infos[3]; - if ($position > $maximums{$chrom}){$maximums{$chrom}=$position;} - my $classe_position = int($position/$step); - $counts{$chrom}{$classe_position}++; - - my $ref_allele = $infos[11]; - for (my $i = 12; $i <= $#infos; $i++) - { - if (!$counts_by_ind{$chrom}{$classe_position}{$i}){$counts_by_ind{$chrom}{$classe_position}{$i} = 0;} - if ($infos[$i] ne $ref_allele) - { - $counts_by_ind{$chrom}{$classe_position}{$i}++; - } - } -} -close($HAPMAP); - -####################################################### -# global -####################################################### -open(my $OUT,">$out"); -print $OUT "Chromosome Position SNPs\n"; -my $chr_num = 0; -foreach my $chrom(sort keys(%counts)) -{ - $chr_num++; - my $ref_counts = $counts{$chrom}; - my %final_counts = %$ref_counts; - my $x = 0; - #foreach my $classe_position(sort {$a<=>$b} keys(%final_counts)) - for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) - { - my $nb = 0; - if ($counts{$chrom}{$classe_position}) - { - $nb = $counts{$chrom}{$classe_position}; - } - $x += $step; - print $OUT "$chrom $x $nb\n"; - } - if ($chr_num >= $max_chr_num){last;} -} -close($OUT); - -####################################################### -# For each individual -####################################################### -open(my $OUT2,">$out.by_sample"); -$chr_num = 0; -print $OUT2 "Chromosome ".join("\t",@individual_names) . "\n"; -foreach my $chrom(sort keys(%counts_by_ind)) -{ - $chr_num++; - my $ref_counts = $counts_by_ind{$chrom}; - my %final_counts = %$ref_counts; - for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) - { - print $OUT2 "$chrom"; - my $num_ind = 12; - foreach my $indiv(@individual_names) - { - my $val = 0; - - if ($counts_by_ind{$chrom}{$classe_position}{$num_ind}) - { - $val = $counts_by_ind{$chrom}{$classe_position}{$num_ind}; - } - print $OUT2 " $val"; - $num_ind++; - } - print $OUT2 "\n"; - } - if ($chr_num >= $max_chr_num){last;} -} -close($OUT2); |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 SNP_density/CalculateSlidingWindowsSNPdensitiesFromVCF.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/CalculateSlidingWindowsSNPdensitiesFromVCF.pl Mon May 23 17:49:17 2016 -0400 |
| [ |
| @@ -0,0 +1,159 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use Bio::SeqIO; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --input <VCF/Hapmap input> + -o, --out <output in tabular format> + -s, --step <step (in bp)> +~; +$usage .= "\n"; + +my ($input,$out,$step); + +GetOptions( + "input=s" => \$input, + "out=s" => \$out, + "step=s" => \$step, +); + + +die $usage + if ( !$input || !$step || !$out ); + +my $max_chr_num = 100; + +my %counts; +my %counts_by_ind; + +my $VCFTOOLS_EXE = "vcftools"; + +my $is_vcf = `head -4000 $input | grep -c CHROM`; +my $is_bcf = 0; +if ($input =~/\.bcf/){ + $is_bcf = 1; +} + + +my $IN; +my $headers; +my $start_indiv_retrieval = 12; +my $chrom_retrieval = 2; +my $pos_retrieval = 3; +if ($is_vcf or $is_bcf){ + $start_indiv_retrieval = 9; + $chrom_retrieval = 0; + $pos_retrieval = 1; + if ($is_vcf){ + $headers = `grep '#CHROM' $input`; + open($IN,$input); + } + elsif ($is_bcf){ + my $cmd = "$VCFTOOLS_EXE --bcf $input --stdout --recode | head -4000 | grep CHROM"; + $headers = `$cmd`; + my $cmd2 = "$VCFTOOLS_EXE --bcf $input --stdout --recode"; + open $IN, '-|' , "$cmd2" or die "Can not run Vcftools"; + } +} +else{ + $headers= <$IN>; + open($IN,$input); +} +$headers=~s/\n//g; +$headers=~s/\r//g; +my @ind_names = split(/\t/,$headers); +my @individual_names; +for (my $i = $start_indiv_retrieval; $i <= $#ind_names; $i++) +{ + push(@individual_names,$ind_names[$i]); +} +my %maximums; +while(<$IN>) +{ + my $line = $_; + $line=~s/\n//g; + $line=~s/\r//g; + my @infos = split(/\t/,$line); + if (scalar @infos > 8 && !/#CHROM/){ + my $chrom = $infos[$chrom_retrieval]; + my $position = $infos[$pos_retrieval]; + if ($position > $maximums{$chrom}){$maximums{$chrom}=$position;} + my $classe_position = int($position/$step); + $counts{$chrom}{$classe_position}++; + + my $ref_allele = $infos[11]; + if ($is_vcf or $is_bcf){ + $ref_allele = "0/0"; + } + for (my $i = $start_indiv_retrieval; $i <= $#infos; $i++){ + if (!$counts_by_ind{$chrom}{$classe_position}{$i}){$counts_by_ind{$chrom}{$classe_position}{$i} = 0;} + if ($infos[$i] ne $ref_allele){ + $counts_by_ind{$chrom}{$classe_position}{$i}++; + } + } + } +} +close($IN); + +####################################################### +# global +####################################################### +open(my $OUT,">$out"); +print $OUT "Chromosome Position SNPs\n"; +my $chr_num = 0; +foreach my $chrom(sort keys(%counts)) +{ + $chr_num++; + my $ref_counts = $counts{$chrom}; + my %final_counts = %$ref_counts; + my $x = 0; + #foreach my $classe_position(sort {$a<=>$b} keys(%final_counts)) + for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) + { + my $nb = 0; + if ($counts{$chrom}{$classe_position}) + { + $nb = $counts{$chrom}{$classe_position}; + } + $x += $step; + print $OUT "$chrom $x $nb\n"; + } + if ($chr_num >= $max_chr_num){last;} +} +close($OUT); + +####################################################### +# For each individual +####################################################### +open(my $OUT2,">$out.by_sample"); +$chr_num = 0; +print $OUT2 "Chromosome ".join("\t",@individual_names) . "\n"; +foreach my $chrom(sort keys(%counts_by_ind)) +{ + $chr_num++; + my $ref_counts = $counts_by_ind{$chrom}; + my %final_counts = %$ref_counts; + for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) + { + print $OUT2 "$chrom"; + my $num_ind = $start_indiv_retrieval; + foreach my $indiv(@individual_names) + { + my $val = 0; + + if ($counts_by_ind{$chrom}{$classe_position}{$num_ind}) + { + $val = $counts_by_ind{$chrom}{$classe_position}{$num_ind}; + } + print $OUT2 " $val"; + $num_ind++; + } + print $OUT2 "\n"; + } + if ($chr_num >= $max_chr_num){last;} +} +close($OUT2); |
| b |
| diff -r ec22fcacb66c -r ebb0ac9b6fa9 SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml --- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml Mon Feb 15 10:26:18 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,205 +0,0 @@ -<tool id="sniplay_density" name="SNP density" version="1.4.0"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Calculate SNP densities along chromosome from HapMap</description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - </requirements> - - <!-- [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] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="bash"> - calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" /> - <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> - <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout" type="data" format="txt" label="${fileout_label}" /> - <data name="fileout_bysample" type="data" format="txt" label="${fileout_label}.by_sample" /> - </outputs> - - <tests> - <test> - <param name="filein" value="SNPden-hapmap" /> - <param name="step" value="200000" /> - <output name="fileout" file="SNPden-result.txt" /> - <output name="fileout_bysample" file="SNPden-result_bysample.txt" /> - </test> - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - -.. class:: infomark - -**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform - - | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr - ---------------------------------------------------- - - - -============= -SNP densities -============= - ------------ -Description ------------ - - Calculate SNP densities along chromosome from HapMap - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Hapmap file hapmap -=============== ====================== =========== - - ----------- -Input file ----------- - -Hapmap file - File with SNPs - - ----------- -Parameters ----------- - -Step - Step in bp for the window to calculate SNP density - -Output name - Output base name for the two ouput files - - ------------- -Output files ------------- - -Output_name - Tabular file with SNP density in each postion - -Output_name.by_sample - Tabular file with SNP density for each sample - - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -hapmap file ------------ - -:: - - rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54 - chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT - chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA - chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC - chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG - chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG - chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT - -Parameters -========== - -Step -> 200000 - -Output name -> densities - - -Output files -============ - -densities ---------- - -:: - - Chromosome Position SNPs - chr1 200000 355 - chr1 400000 228 - chr1 600000 63 - chr1 800000 191 - - -densities.by_sample -------------------- - -:: - - Chromosome BA58 BA59 BD54 - chr1 220 197 225 - chr1 130 119 133 - chr1 43 43 40 - chr1 139 167 141 - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> -</tool> |
| b |
| diff -r ec22fcacb66c -r ebb0ac9b6fa9 SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh --- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh Mon Feb 15 10:26:18 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -#!/bin/bash - -tool_path=$(dirname $0) -hapmap=$1 -fileout=$2 -fileout_bysample=$3 -step=$4 - -perl $tool_path/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl -i $hapmap -o $fileout -s $step - -cp $fileout.by_sample $fileout_bysample -rm $fileout.by_sample - |
| b |
| diff -r ec22fcacb66c -r ebb0ac9b6fa9 SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF.sh Mon May 23 17:49:17 2016 -0400 |
| b |
| @@ -0,0 +1,13 @@ +#!/bin/bash + +tool_path=$(dirname $0) +input=$1 +fileout=$2 +fileout_bysample=$3 +step=$4 + +perl $tool_path/CalculateSlidingWindowsSNPdensitiesFromVCF.pl -i $input -o $fileout -s $step + +cp $fileout.by_sample $fileout_bysample +rm $fileout.by_sample + |
| b |
| diff -r ec22fcacb66c -r ebb0ac9b6fa9 SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml Mon May 23 17:49:17 2016 -0400 |
| [ |
| @@ -0,0 +1,204 @@ +<tool id="sniplay_density" name="SNP density" version="2.0.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Calculate SNP densities along chromosome from a VCF input</description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + <requirement type="package" version="0.1.12b">vcftools</requirement> + </requirements> + + <!-- [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] Command to be executed to get the tool's version string --> + <version_command> +<!-- + tool_binary -v +--> + </version_command> + + <!-- [REQUIRED] The command to execute --> + <command interpreter="bash"> + calculateSlidingWindowsSNPdensitiesFromVCF.sh $filein $fileout $fileout_bysample $step + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> + <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> + <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout" type="data" format="txt" label="${fileout_label}" /> + <data name="fileout_bysample" type="data" format="txt" label="${fileout_label}.by_sample" /> + </outputs> + + <tests> + <test> + <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" /> + <param name="step" value="20000" /> + <output name="fileout" file="SNPden-result.txt" /> + <output name="fileout_bysample" file="SNPden-result_bysample.txt" /> + </test> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + + + +============= +SNP densities +============= + +----------- +Description +----------- + + Calculate SNP densities along chromosome from a VCF file + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +=============== ====================== =========== + + +---------- +Input file +---------- + +VCF file + File with SNPs + + +---------- +Parameters +---------- + +Step + Step in bp for the window to calculate SNP density + +Output name + Output base name for the two ouput files + + +------------ +Output files +------------ + +Output_name + Tabular file with SNP density in each postion + +Output_name.by_sample + Tabular file with SNP density for each sample + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +vcf file +----------- + +:: + + #fileformat=VCFv4.1 + #FILTER=<ID=LowQual,Description="Low quality"> + #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> + [...] + CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 + chr1 2209 . G T 213.84 . AC=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|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 + +Parameters +========== + +Step -> 200000 + +Output name -> densities + + +Output files +============ + +densities +--------- + +:: + + Chromosome Position SNPs + chr1 200000 355 + chr1 400000 228 + chr1 600000 63 + chr1 800000 191 + + +densities.by_sample +------------------- + +:: + + Chromosome BA58 BA59 BD54 + chr1 220 197 225 + chr1 130 119 133 + chr1 43 43 40 + chr1 139 167 141 + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool> |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 test-data/SNPden-result.txt --- a/test-data/SNPden-result.txt Mon Feb 15 10:26:18 2016 -0500 +++ b/test-data/SNPden-result.txt Mon May 23 17:49:17 2016 -0400 |
| b |
| @@ -1,21 +1,11 @@ Chromosome Position SNPs -chr1 200000 355 -chr1 400000 228 -chr1 600000 63 -chr1 800000 191 -chr1 1000000 88 -chr1 1200000 90 -chr1 1400000 190 -chr1 1600000 267 -chr1 1800000 226 -chr1 2000000 163 -chr1 2200000 357 -chr1 2400000 132 -chr1 2600000 158 -chr1 2800000 104 -chr1 3000000 146 -chr1 3200000 331 -chr1 3400000 181 -chr1 3600000 36 -chr1 3800000 167 -chr1 4000000 110 +chr1 20000 188 +chr1 40000 544 +chr1 60000 746 +chr1 80000 412 +chr1 100000 356 +chr1 120000 625 +chr1 140000 769 +chr1 160000 512 +chr1 180000 510 +chr1 200000 293 |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 test-data/SNPden-result_bysample.txt --- a/test-data/SNPden-result_bysample.txt Mon Feb 15 10:26:18 2016 -0500 +++ b/test-data/SNPden-result_bysample.txt Mon May 23 17:49:17 2016 -0400 |
| b |
| @@ -1,21 +1,11 @@ -Chromosome BA58 BA59 BD54 -chr1 197 220 225 -chr1 119 130 133 -chr1 43 43 40 -chr1 167 139 141 -chr1 72 62 78 -chr1 76 35 38 -chr1 123 98 82 -chr1 205 133 135 -chr1 141 94 151 -chr1 116 112 117 -chr1 238 228 204 -chr1 95 86 96 -chr1 106 60 82 -chr1 74 60 64 -chr1 112 106 115 -chr1 220 199 228 -chr1 94 151 64 -chr1 32 18 27 -chr1 90 87 100 -chr1 75 54 47 +Chromosome CATB1 +chr1 188 +chr1 544 +chr1 746 +chr1 412 +chr1 356 +chr1 625 +chr1 769 +chr1 512 +chr1 510 +chr1 293 |
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| diff -r ec22fcacb66c -r ebb0ac9b6fa9 test-data/getHaplotypesFromPhasedVCF-input.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/getHaplotypesFromPhasedVCF-input.vcf Mon May 23 17:49:17 2016 -0400 |
| [ |
| b'@@ -0,0 +1,16055 @@\n+##fileformat=VCFv4.1\n+##filedate=20160411\n+##source="beagle.jar (r1399)"\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated Allele Frequencies">\n+##INFO=<ID=AR2,Number=1,Type=Float,Description="Allelic R-Squared: estimated correlation between most probable ALT dose and true ALT dose">\n+##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated correlation between estimated ALT dose [P(RA) + 2*P(AA)] and true ALT dose">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=DS,Number=1,Type=Float,Description="estimated ALT dose [P(RA) + P(AA)]">\n+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Estimated Genotype 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|
| b |
| diff -r ec22fcacb66c -r ebb0ac9b6fa9 test-data/getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt Mon May 23 17:49:17 2016 -0400 |
| b |
| b'@@ -0,0 +1,3992 @@\n+===Chr10===\n+haplo1:2:CIRAD403_1,CIRAD403_2,\n+TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACATAATTTACAATTACATAGAATTTAACCTTATAAATAATTTAAATCTGAATTGTTAGGAACAATTTCAATTCTCAAACTACATGTCAAAATGCCACTATATCTAATATTGTATAGATATATTATAACTTTAACTTTAAACATCTATAAACATCTTCATGTTCTTAAAAATAAATCTTATAAATTACCTGTTCAATTTTTAATACACTAATACGATTATATCTTATCCATTATATGATGTATATCATTAAGTGATTATATTTATAACTTAGCTTCATGTATATATAATTAATATAAAAAGTTAATTTCGCTAAAATATATATTATTTACTCATATTTAGGGTGGCGGATAACATAATCTGTTTGTATCTACTATATATTAATTTTACTCAATTTGTAGAACCATTACATACTTACTGTGTTGCTTACAAAATTTGAACATCTAATTATTTCTTGAAACCATATATTCACCCTGTTTAATTGTATACTTAGATAAATAGTTATATTATAATTAAAAGCATATAGGATCTTAAAATTCACCTTGCAGGTAGGACTACGTAGTCTGAAAAATCTTTCCTAAAATAATCTAAATTATTTAATGAGATTAATACGCTCTTAATTAAATTATAAATTTCCTTGAATAATATATAAATCTTGATTATTAGTATATTATAGATTCTATCATTAATCGCTTGTTTATACTTAAATTAAAACCAATTATCTGAAATAATAAAAAACTATCTATATAAGATAGATATATCAATGGACAAGGAGTACTATTTATTATAGGTTATATATACGCATTAATAAATATCCAAGAGCGTGTTTAATTACAATTATTATTGTATTCTACATTTAAATTATTTTGGCTTCAGCCATTTTACTCTTAATATAAATTTATTATTAGTGTTAATTATCAATTAATTCAGATATAACAGAAACGGATAATTATACTAATATGTATTTCAAATGATTACAATTTAGCTTTCATTTACTATTGTACACTAATCTCCTGGTATATCCATAATTCGAGATTGAC\n+haplo2:2:MAHAE_1,MAHAE_2,\n+TAAATCTTGGTGCTGATCTGATATTTAATGCGTTTCTGTTTTTTATTAAATCAATTACATAGAATTTAACCTTATAAATAATTTAAATCTGAATTGTTAATAACAATTTCAATTCTCAAACTACATATCAAAATGGCACAATATATTTATAACAATTAATTTTTTTTAACCCCATCCTTAATAATCTATAAACATCTTCATGTTCTTAAAAATAAATCGTTATTTATACCCGTTCAATATAATTATCTCTAATACGATTATATCTAATCCATTATATGATGAGCATAATTAAGTGAAATAAAAATAATCTAAGATTAATGATCGGTATTAATTATATTTTTGCTAATTTCGCTAAAATTAATATTATTCACTATATAAATTGGCGGCAATAAGTATAATCTGTATGTATATTCTTATTATGAATTATTTTCATATCGTAAAATCTTATTATTCTTTGTAAAATGCATACATTATTCGAACACATAATTATTTCTTTCTTCCATATATTCACCCAATATATAACAATGCTTACTATTTTAGTTATATTATAATTAAAAGCATATAGGATCTCAAAAAATGCTTAGCTAAGAGTATATAAATGAATTATGCTATACAGTCCCGTATTCTATTATTATATAATGAGATTAATACGCTCTTAATTATACACAGGGCTATTTACGTATTCTATATTTAAAAGTAATAATCATATAATAGTTAACCTAACTCATATGCTAGTAAAAACTTTTAAAATTACCTTAATCCTGGTAATTATATGTTCTTACATATTATGATAATACTTATAACCGTCTCGGAGATTAACAATTATATGGTAATGTTATCACATTAATTAGTTTTCTACAATGTGTTTAATTATGAATATATATAATACTGGTTATTTGGCATAGAATTTACTTGTCAAAAGGAAGAATTCTATTTAAATAATTATACTAATTAATATTTCATTAATTGAATAGACAGAAATAATTTTTATAGAGTTAATGTAATTCAAATGATTACAATTTAGCTTACATTTACTTTTGCAAACTTATCTCCTGGATTATCCATAATTCGAGATTGAC\n+haplo3:2:CHUAN4_1,CHUAN4_2,\n+TAAATCTTGGTGCTGATCTGATATTTAATGCGATTCTGTTTTTTATTAAATCAATTACATAGAATTTAACCTTATAAATAATTTAAATCTGAATTGTTAGGAGCAATTATATTAGTCTAAATTCATGTTAAAATGGCTCATAATATTTATAACAATTAATTTTTTTTAACCCCAACCTTAAACAAGTATAAACATCTTCATGTTCTTTAGAAATAATCGAATAAATTATCCATATAAAATAATATACACATGAACGGTTTATATATTACGATTTATTGTTGAGTAACGTTAAGTGAAATAAAAATAATCTAAGATTAATGATCGGTATTAATTATATTTTTGCTAATTTCGCTAAAATTAATATTATTCACTATATAAATTGGCGGCAATAAGTATAATCTGAATGTATATTCTTATTATGAATTATTTTCATATCGTAAAATGTTAATAATCTTTCTGTGATGCTCATATTAATCGAACACATAATTATTTCTATCTTCCATATATTCACCCAATATATAACAATGCTTACTATTAGATTAAACAATATTATCTGTGCTAATTAATACCTATTATTCACCTTGCAGGTAGTATATAAATGAATTATGCTATACAGTCCCGTATTCTTAAATCGCACATAGTAATATAATCTTATCAAATTAAATTATAAATTTCCTTGAATAATATATAAATCTTGTTTATTAGTATTTTATAGATACTATCATTAATTATCTGAAAAAACTTTTAAATTAATCAAAATTACTGAATAATAAAGTACCATGTAATATTGATTGTAATATCAATGGACTCGTATTATTTCATACAATAAGTTATATATACAGTTCTACTAGTAACCTGCGGCGTATAATCAAATGAATATATATAATACTGGTTATTTGGCAATGAATTTACTTGTCAAAAGGAAGAATTCTATTTAAATAATTATACTAATTAATATTTCATTAATTGAATAGGCAGAAATAATATTTATAGCGTTAATGTAATTCAAATGATTACAATTTAGCTTACATTTACTTTTGCAAACTTAACACCTGGATTATCCATAATTCGAGATTGAC\n+haplo4:2:ARROZCEBADA_1,ARROZCEBADA_2,\n+TTTGAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACATAATTTACAATTACATAGAATTTAACCTTATAAATAATTTAAATCTGAATTGTTAAGAACAATTTCAATTCTCTTTCATCTAGACTTATACGCACAATATCTAATATTGTATAGATATATTATAACTTTAACTTTAAACATCTATAAACATCTTCATGTTCCTACGTGAAAATCGATATTTAAACCTGTACAATTTTTAATACACTAATACGATTATATCTTATCCATTATATGATGTATTACATTAAGTGATTATATTTATAACTTAGCTTCATGTATATATAATTAATATAAAAAGTTAATTTCGCTAAAATATATATTATTTACTCATATTTAGGGTGGCGGATAACATAATCTGTTTATATCTACAATATATTAATTTTACTCAATTTGTAGAACCATTACATACTTACTGTGTTGCTTACAAAATTTGAACATCTAATTATTTCTTGAAACCATATATTCACCCTGTTTAATTGTATACTTAGATAATTAGTTATATTATAATTAAAAGCATATAGGATCTTAAAATTCACCTTGCAGGTAGGACT'..b'AATCTTAAATATTTAAATTATATATGTAATATATAAATTATTTCCTATTATATATATTTAAATAAAAAATAATCATTATTATATTTATATATAATAAAATAATTATAATTTATTATTTAAAAATTTATATTAAATAATTAATTTTATATCGAATAAAATTGTAATTAAAT\n+haplo165:2:DINORADO_1,DINORADO_2,\n+AAACGCATATATTAAGTCAAACTACATAATCCATGCCCTATACATACTTATTACCTACTATATAATTAAAAACTGGCCAATATATTAGAAGAGACTTGATTTTGTTTAGTATAGAGTCTTATGAAGAAAACATTTAAGTATACGATATATTAAAAAATATATACATCATTAATTTTATATAATATAATAATAATATATATAGTAATATAATAGTAAATATATTATTACTACTTATGTAATTTAAATGTGATTAATATAATATCTCAAATTATTTTATCTATGAGTAAGTAACTCCTCATATATTTGAAGTCTATAAATTATTATATACCAAATAAAATTTTAATTTCTATAAAATTTTTCTGTACGAAAAAATTTATAATATAATATTATAGTATATATAATATGAATTTAATTAATAAAATTATATTAGTCTTCAATAGTTAATTCCTATTAAATGTGTACATACTGAAATTTCTAGGGCTGTACTGTCTACTAGATTAGAATGTTATTATATATAAATTTGTAAGCATTTAATTTACTACATGTTGTCTGATAAAATATAGTATTAAATAATAAATGATATGGTTTTTAATTAAAAATTTTAATGAATTACATTCTATCGATAAAAATTTGAAAATTTCTCGAATACAACTATTATAATTAACTTAAGTCTGAATTACAAGAATATTTTAGCTTGAAGGCAACGCAATAATAGTTATTTATTTTTTGGTTTCATTGTATTCCAGTATTTAACTCGTTTCATATCTGCAAAGATACTTATTCGTAGTTTAAAGCAAAAATATAGATTATAATTCTAAATATTATTGCCTTGAATTAATTATACCGCTTGTATCACTTATTTGCTTTAAAATCAATTTTAGGACTTTAATAAAAGAAATGTGAAGACGAATGATTTCTAATTATTTTTCTTGAATGATAATTAAACTACTTTAGATTAGCTTTTATTAAATATTGTTAAATACTGTAATATATATTTGTATTATTAGTTGTATCGAGTAATTAGTCACTATAATGTATATAGAAATAAGTATTATATTATAAGAATTAAAATATTAATTAAGGTGATAGTGAAATATTAATTGATAAATTAAAAGATTTATTACATAATAAAAAGCTATCAAATCCATATCATACTATTATACTTAATTAATTTAATATGTAAATTTAAGCTATACTATCAATCATAATATTAAAGGTAAAAATTAGTATATATTAATAGTATACTTATTTTGTAAAAAATATTAAATTTCTTACTTTATATTACATCTAATTTACAATATAAGATTTATTATATAATATTAGAAAAAATTATGGTAATACAATCTGACTAACAATAACATACAAATTTATATATTTTAGCAATTAATCATATCATTATTATTTAAGATGGAAATATATTATATTTATATTTTTATTATATTCTTTTATAACAGAGATACTAATAAGGTTTGATTGATCATCTAATAATATTTATTTATTCATACATTAAACCATGACAATCGATGTTATGTGTTATGAGGCATATTGATAAAAAAATAATTTTTTTTTAGATAAGAATCTTTTCTAAATATTATTTGTTTTAATATTTATTAAGTTATTTAATTTTTATTATAATATTTTAGTTTCTGTACAAAAATATACGAATTAAATTTGTACTAAAAAATCAAATTATGGTAAATATATAATATTTTAAATTTTTATAATAAAAAAATAAATTATCATCGTTAAATAAATTATTTTTAATATAATAATCATTATTATATTTATATTATTATAATCTTAATTATAAAATATTATAAATTATTATATTAAATAATTAATTTTATATCGAATAAAATTGTAATTAAAT\n+haplo166:2:KINANDANGPATONG_1,KINANDANGPATONG_2,\n+AAACGCATATATTAAGTCAAACTACATAATCCATGCCCTATACATACTATTCTCTATCTATAAAATTAAATACTGGCCAATATATTAGAAGAGACTTGATTTTGTTTAGAATAGAGTCTTATGAAGAAAACATTTAAGTATACGATATATTAAAAAATATATACATCATTAATTTTATATAATATAATAATAATATATATAGTAATATAATAGTAAATATATTATTACTACTTATGTAATTTAAATAAGTATTTAATTAAGAATCTTAAATATAATTCCAGAAAAAAGAATGTCTATGCATGTTAGTAGTATATATTAATTAAAAATCAAAATATTAATTATTATTCTATAAAATTTTTCTGTACGAAAAAATTTATAATATAATATTATAGTATATATAATATGAATTTAATTAATAAAATTATATTAGTCTTCAATAGTTAATTCCTATAAAATGTGTACATACTGAAATTTCTAGGGCTGTACTGTCTACTAGATGAGAATGTTATTATATATAAATTTGTAAGCATTTAATTTACTACATGTTGTCTGATAAAATATAGTATTAAATAATAAATGATATGGTTTTTAATTAAAAATTTTAAAGAATTACATTCTATCGATAAAAATTTGAAAATTTCTCGATTACAACTATTATTATTAACTTAAGTCTGAATTACAGGAATATTTTAGCTTGAAGGCAACGCAATAATAGTTATTTATTTTTTGGTTTCATTGAATTCCAGTATTTAACTCGTTTCATATCTGCAAAGATACTTATTCGTAGTTTAAAGCAAAAATATAGATTATAATTCTAAATATTATTGCCTTGAATTAATTTAATTACAACTTTCACATATGAGCTATTAAGACTTAAAATGGACTATGATAATAGAAATGTGAAGACGAATGATTTCTAATTATTTTTCTTGAATGATAATTAAACTACTTTAGATTAGCTATTATTATATACAGTTAAATACTGTAATATATATTTGTTTTAATAGTTGTATCGAGTAATTAGTCACTATAATGTATATAGAAATAAGTATTATATTATAAGAATTAAAATAATAAAATAAGTGATACTACTAATAATTAAGTTAAACTAAGAATATTAATATATAATAAAAAGCTATCAAATCCATATCATACTATTATACTTAATTAATTTTATATGTATATTTATTTATATAGGATTTATTAATATAATTAATATTTATTATGATATATAATATTGTATACTTATTTAGTTTAATATATATTATTTCTTATAAATAATTACATTTAATTATCGATATAAGATATATATATATTATATTGTGTTATAAATGCTAATACAAGCTGATTAACTTATATTTAATTTAAATATATAACTAGATGTTTTTCGTATCATTTAATATTATGGTGGAATAATATTATATTTAATAAATAATTTCATACTTTTACAACAAAGATATATATATGGAATGTATGATCATCTATTAATATTTATTTATTCTTACTAAAAGAGATCACATACCATCTTATGTACTCTGAGGCAAATTGAAATATAATATATTTAGAACATACGTACTAACATTACTAAATATTAATTGCTATTTCTCTTTAAAAGAAATTTTTTAAATAATATTAATTTTGCATTACTGTATTTTTTTTGGCGATAAATTTATTTATTAAATAATCTTATAATGAATTTAAATCTTAAATATTTAAATTATATATGTAATATATAAATTATTTCCTATTATATATATTTAAATAAAAAATAATCATTATTATATTTATATATAATAAAATAATTATAATTTATTATTTAAAAATTTATATTAAATAATTAATTTTATATCGAATAAAATTGTAATTAAAT\n' |
| b |
| diff -r ec22fcacb66c -r ebb0ac9b6fa9 test-data/getHaplotypesFromPhasedVCF-result.haplo.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/getHaplotypesFromPhasedVCF-result.haplo.fas Mon May 23 17:49:17 2016 -0400 |
| b |
| b'@@ -0,0 +1,8016 @@\n+>Chr10_AZUCENA_1\n+TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACATAATTTACAATTACATAGAATTTAACCTTATAAATAATTTAAATCTGAATTGTTAAGAACAATTTCAATTCTCAAACTACATGTCAAAATGCCACTATATCTAATATTGTATAGATATATTATAACTTTAACTTTAAACATCTATAAACATCTTCATGTTCTTAAAAATATATCTTATAAATTACCCGATCAATATAATTATCTCTAATACGATTATATCTTATCCATTATATGATATGCATAATTAAGTGAAATAAAAATAATCTAAGATTAATGAACGGTATTAATTATATTTTTGCTAGCTTCGCTAGATAATTTATTATTTACTAATTAAATTCGTATTAAAAGGCTTATTTTGTATGTATATTCTAATCATGTATAATACTTATATTATTGAACGAAATTTTAACTTCTGTGACTGTTACTATTTTCGTTTTCCTTAAAACTACTAGAAACCTATATTATGCCCTGTTTAATTGTATACTTAGATAAATAGTTATATTATAATTAAAAGCATATAGGATCTCAAAAAATGCTTAGCTAAGAGTATATAAATGAATTATGCTATACAGTCCCGTATTCTATTATCGCTCATAGTAATTATTACGCTCTTAATTAAATTATAAATTTCCTTGAATAATATATAAATCTTGTTTATTAGTATATTTTAGATTCTATCATTAATTATCTGTTTATACTTAAATTAAAACCAATTATCTGAAATAATAAAAAACTATCTATATAAGATAGATATATCAATGGACAAGGAGTACTATTTATTATAGGATTAGTTATAAGATCTACTAGTAACCTGCGGCGTATAATCAAATGAATATATATGTATCTTACATTTAAATTATTTTGGCTTCAGCCATTTTACTCTTAATATAAATTTATTATTAGTGTTAATTATCAATTAATTCAGATATAACATCGTCGGATAATTATGAGTTAATGTATTTCAAATGATTACAATTTAGCTTTCATTTACTTTTGCAAACTTATCTCCTGGATTATCCATAATTCGAGATTGAC\n+>Chr10_AZUCENA_2\n+TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACATAATTTACAATTACATAGAATTTAACCTTATAAATAATTTAAATCTGAATTGTTAAGAACAATTTCAATTCTCAAACTACATGTCAAAATGCCACTATATCTAATATTGTATAGATATATTATAACTTTAACTTTAAACATCTATAAACATCTTCATGTTCTTAAAAATATATCTTATAAATTACCCGATCAATATAATTATCTCTAATACGATTATATCTTATCCATTATATGATATGCATAATTAAGTGAAATAAAAATAATCTAAGATTAATGAACGGTATTAATTATATTTTTGCTAGCTTCGCTAGATAATTTATTATTTACTAATTAAATTCGTATTAAAAGGCTTATTTTGTATGTATATTCTAATCATGTATAATACTTATATTATTGAACGAAATTTTAACTTCTGTGACTGTTACTATTTTCGTTTTCCTTAAAACTACTAGAAACCTATATTATGCCCTGTTTAATTGTATACTTAGATAAATAGTTATATTATAATTAAAAGCATATAGGATCTCAAAAAATGCTTAGCTAAGAGTATATAAATGAATTATGCTATACAGTCCCGTATTCTATTATCGCTCATAGTAATTATTACGCTCTTAATTAAATTATAAATTTCCTTGAATAATATATAAATCTTGTTTATTAGTATATTTTAGATTCTATCATTAATTATCTGTTTATACTTAAATTAAAACCAATTATCTGAAATAATAAAAAACTATCTATATAAGATAGATATATCAATGGACAAGGAGTACTATTTATTATAGGATTAGTTATAAGATCTACTAGTAACCTGCGGCGTATAATCAAATGAATATATATGTATCTTACATTTAAATTATTTTGGCTTCAGCCATTTTACTCTTAATATAAATTTATTATTAGTGTTAATTATCAATTAATTCAGATATAACATCGTCGGATAATTATGAGTTAATGTATTTCAAATGATTACAATTTAGCTTTCATTTACTTTTGCAAACTTATCTCCTGGATTATCCATAATTCGAGATTGAC\n+>Chr10_BULUPANDAK_1\n+TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACATAATTTACAGAATCTATATTTAATTCTTAATTTTTTTAAATAATTAGTTAAAATAAGAACAATTTCAATTCTCAAACTACATGTCAAAATGCCACTATATCTAATATTGTATAGATATATTATAACTTTAACTTTAAACATCTATAAACATCTTCATGTTCTTAAAAATAAATCGTTATTTATACCCGTTCTTTTAAAAATATTATTGTATTACTATATCTAAACCATTTAATGTTGTGTTTAAATAAAGAATTATATTAATTACAATGCATCGTAATTGTATATAATTATTTTTTAACATGCTATGGTAAAATTAATATTATTCACTATATAAATTGGCGGCAATAAGTATAATCAGAATGTATATTCTTATTATGAATTATTTTCATATCGTAAAATCTTATTATTCTTTGTAAAATGCATACATTATTCGTACTCCTTAAAACTACTAGAAACCTATATTATGCCCTGTTTAATTGTATACTTAGATAAATAGTTATATTATAATTAAAAGCATATAGGATCTCAAAAAATGCTTAGCTAAGAGTATATAAATGAATTATGCTATACAGTCCCGTATTCTATTATCGCACATAGTAATATAATATTATCAAATTAAATTATAAATTTCCTTGAATAATATATAAATCTTGTTTATTAGTATATTATAGATTCTATCATTAATCGCTTGTTTATACTTTTAAATTAATCAAAATTACTGAATAATAAAGTACCATGTAATATTGATTGTAATTACCACCAACAAGGAGTACTATTTATTATAGGATTAGTTATAACAATATTTGGAATCTTGCAGCGAAAATAATATCGTACTAATAAAATACTGGTTATTTGGCATAGAATTTACTTGTCAAAAGGAAGAATTCTATTTAAATAATTATACTAATTAATATTTCATTAATTGAATAGACAGAAATAATTTTTATAGAGTTAATGTAATTCAAATGATTACAATTTAGCTTTCATAACTAATCTCTATTAAATTTCTAATTAAAAATGATCGCGATACTACGT\n+>Chr10_BULUPANDAK_2\n+TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACATAATTTACAGAATCTATATTTAATTCTTAATTTTTTTAAATAATTAGTTAAAATAAGAACAATTTCAATTCTCAAACTACATGTCAAAATGCCACTATATCTAATATTGTATAGATATATTATAACTTTAACTTTAAACATCTATAAACATCTTCATGTTCTTAAAAATAAATCGTTATTTATACCCGTTCTTTTAAAAATATTATTGTATTACTATATCTAAACCATTTAATGTTGTGTTTAAATAAAGAATTATATTAATTACAATGCATCGTAATTGTATATAATTATTTTTTAACATGCTATGGTAAAATTAATATTATTCACTATATAAATTGGCGGCAATAAGTATAATCAGAATGTATATTCTTATTATGAATTATTTTCATATCGTAAAATCTTATTATTCTTTGTAAAATGCATACATTATTCGTACTCCTTAAAACTACTAGAAACCTATATTATGCCCTGTTTAATTGTATACTTAGATAAATAGTTATATTATAATTAAAAGCATATAGGATCTCAAAAAATGCTTAGCTAAGAGTATATAAATGAATTATGCTATACAGTCCCGTATTCTATTATCGCACATAGTAATATAATATTATCAA'..b'TTTATTAAATAATTATTTAATGGTATAATATCTTAAATATTTATAAAATATTTAAAATTAATAAAAATCATCGTTAAATAAATTATTTTTAATATAAATTACTATTAAAATACATATATTTTATTTACTTAATATAAATATTATTTATATTTAATTATTAATTAATTAATTTTTTAACGAATAAAATTGTAATTAAAT\n+>Chr11_EARLYMUTANTIAC165_1\n+AAACGCATATATTAAGTCAAACTACATAATCCATGCCCTATACATACTATACTCTATCTATAAAATTAAATACTGGCCAATATATTAGAAGAGACTTGATTTTTTTTAGAATAGAGTCTTATGAAGAAAACATTAAGGATATCAATATATTAAAAAATATATACATCATTAATTTCATATCATATAATAATAATATATATAGTAATATAATAGTAAATATATTATTACTACTTATGTAATTTAAATAAGTATTTAATTAAGAATCTTAAATATAATTTCAGAAAAAAGAATGTCTATGCATGTTAGTAGTATATATTAATTAAAAATCAAAATATTAATTATTATTCTATAAAATTTTTCTGTACGAAAAAATTTAAAATATAATATTATAGTATATATAATATGAATTTAATTAATAAAATTATATTAGTCTTCAATAGTTAATTCCTATTAAATGTGTACAATTGATGTGCCCTAGCGCTGTACTGTCTACTAGATTAGATTGTTATTATATATAAATCTGTAAGCATTTAATTTACTACATTTTATCTGATAAAATATAGTATTAAATAATAAATGATATGGTTTTTAATTAAAAATTTTAAAGAATTACATTCTATCGATAAAAATTTGAAAATTTCTCGATTACAACTATTATTATTAACTTAAGTCTGAATTACAGGAATATTTTAGCTTGAAGGCAACGCAATAATAGTTATTTATTTTTTGGTTTCATTGAATTCCAGTATTTAACTCGTTTCATATCTGCAAAGATACTTATTCGTAGATATAAGAATAAATATAGATTATAATTCTAAATATTATTGCCTTGAATTAATTTAATTACAACTTTCACATATGAGCTATTAAGACTTAAAATGGACTATGATACTAGAGTTGTGTAAACACTAGTAAACATTAAAGAGTTCTTGAATGATAATATTAAGATTTATGAATAGCTTTTATTATATACAGTTAAATACTGAAACTCATTATTATTTTAATAGTTGTATCGAGTAATTAGTCACTATAATGTATATAGAAATAAGTATTATATTATAAGAATTAAAATATTAATTAAGGTGATAGTGAAATATTAATTGATAATTTAAAAGATTTATTACATAATAAAAAGCTATCAATTCCATATCAAACTATTATACTTAATTAATTTTATATGTAAATTTAAGCTATACTATCAATCATAATATTAAAGGTAAAAATTTGTATATATTAATAATATACTTATTTTGTTAAAAATATATTATTTCTTATAAATAATTACATTTAATTATCGATATAAGATTTATATATATTATATTGTGTTATAAATGCTAATACAAGCTGATTAACTTATATTAAATTTAAATATATAACTAGATGTTTTTCATATTATATTTATATATGACGATGTATATAAATAAATTAATTATTGCTATTATTAAATACTACAGAGATCCTATAATGGATTGTATGATCTAGATAAAATATTTATTTTTTCTAACTTTAAACCACGACTATTCTAGTTATTTGTTAAGAGGTATATTTATAAAAAAATAATTTATTTTTAGATTTCAGATAATACATTTATAATATAGTAACATTTCTTATTAAGAAATTTAATTTTTTTATAATTAAAATAGTTACTGTATTTTTTTTGGCGTTAAATTTATTTATTAAATAATCTTATAATGAATTTAAATCTTAAATATTTAAATTATATATATATAAATAAAAAATCATCGTTTAATAATATAAATTTATAGATAAAATCATTATTATATTTATATTATTATAATCTTAATTATAAAATATTATAAATTATTATATTAAATAATTAATTTTATATCGAATAAAATTGTAATTAAAT\n+>Chr11_EARLYMUTANTIAC165_2\n+AAACGCATATATTAAGTCAAACTACATAATCCATGCCCTATACATACTATACTCTATCTATAAAATTAAATACTGGCCAATATATTAGAAGAGACTTGATTTTTTTTAGAATAGAGTCTTATGAAGAAAACATTAAGGATATCAATATATTAAAAAATATATACATCATTAATTTCATATCATATAATAATAATATATATAGTAATATAATAGTAAATATATTATTACTACTTATGTAATTTAAATAAGTATTTAATTAAGAATCTTAAATATAATTTCAGAAAAAAGAATGTCTATGCATGTTAGTAGTATATATTAATTAAAAATCAAAATATTAATTATTATTCTATAAAATTTTTCTGTACGAAAAAATTTAAAATATAATATTATAGTATATATAATATGAATTTAATTAATAAAATTATATTAGTCTTCAATAGTTAATTCCTATTAAATGTGTACAATTGATGTGCCCTAGCGCTGTACTGTCTACTAGATTAGATTGTTATTATATATAAATCTGTAAGCATTTAATTTACTACATTTTATCTGATAAAATATAGTATTAAATAATAAATGATATGGTTTTTAATTAAAAATTTTAAAGAATTACATTCTATCGATAAAAATTTGAAAATTTCTCGATTACAACTATTATTATTAACTTAAGTCTGAATTACAGGAATATTTTAGCTTGAAGGCAACGCAATAATAGTTATTTATTTTTTGGTTTCATTGAATTCCAGTATTTAACTCGTTTCATATCTGCAAAGATACTTATTCGTAGATATAAGAATAAATATAGATTATAATTCTAAATATTATTGCCTTGAATTAATTTAATTACAACTTTCACATATGAGCTATTAAGACTTAAAATGGACTATGATACTAGAGTTGTGTAAACACTAGTAAACATTAAAGAGTTCTTGAATGATAATATTAAGATTTATGAATAGCTTTTATTATATACAGTTAAATACTGAAACTCATTATTATTTTAATAGTTGTATCGAGTAATTAGTCACTATAATGTATATAGAAATAAGTATTATATTATAAGAATTAAAATATTAATTAAGGTGATAGTGAAATATTAATTGATAATTTAAAAGATTTATTACATAATAAAAAGCTATCAATTCCATATCAAACTATTATACTTAATTAATTTTATATGTAAATTTAAGCTATACTATCAATCATAATATTAAAGGTAAAAATTTGTATATATTAATAATATACTTATTTTGTTAAAAATATATTATTTCTTATAAATAATTACATTTAATTATCGATATAAGATTTATATATATTATATTGTGTTATAAATGCTAATACAAGCTGATTAACTTATATTAAATTTAAATATATAACTAGATGTTTTTCATATTATATTTATATATGACGATGTATATAAATAAATTAATTATTGCTATTATTAAATACTACAGAGATCCTATAATGGATTGTATGATCTAGATAAAATATTTATTTTTTCTAACTTTAAACCACGACTATTCTAGTTATTTGTTAAGAGGTATATTTATAAAAAAATAATTTATTTTTAGATTTCAGATAATACATTTATAATATAGTAACATTTCTTATTAAGAAATTTAATTTTTTTATAATTAAAATAGTTACTGTATTTTTTTTGGCGTTAAATTTATTTATTAAATAATCTTATAATGAATTTAAATCTTAAATATTTAAATTATATATATATAAATAAAAAATCATCGTTTAATAATATAAATTTATAGATAAAATCATTATTATATTTATATTATTATAATCTTAATTATAAAATATTATAAATTATTATATTAAATAATTAATTTTATATCGAATAAAATTGTAATTAAAT\n' |
| b |
| diff -r ec22fcacb66c -r ebb0ac9b6fa9 tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 15 10:26:18 2016 -0500 +++ b/tool_dependencies.xml Mon May 23 17:49:17 2016 -0400 |
| b |
| @@ -3,4 +3,7 @@ <package name="plink" version="1.07"> <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> + <package name="vcftools" version="0.1.12b"> + <repository changeset_revision="a655cb1dfc58" name="package_vcftools_0_1_12b" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> </tool_dependency> |