Mercurial > repos > gandres > vcftools_filter_stats_diversity
view VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh @ 8:2b6bb9d5e4e9 draft
planemo upload
author | gandres |
---|---|
date | Tue, 12 Apr 2016 05:43:01 -0400 |
parents | ca045c1d5fa5 |
children | f494c8d22725 |
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#!/bin/bash tool_path=$(dirname $0) filein=$1 fileout_label=$(date "+%Y%m%d%H%M%S") window=$2 filelog=$3 fileout_taj=$4 fileout_tstv=$5 fileout_windowed=$6 fileout_snp=$7 group=$8 if [ "$group" != "none" ] then fileout_fst=${9} fileout_fst_marker=${10} fileout_taj_combined=${11} fileout_windowed_combined=${12} fileout_tstv_combined=${13} fileout_snp_combined=${14} fi cp $filein ${filein}.vcf if [ "$group" != "none" ] then if [ $(sort -k2,2 -t ';' -u $group | cut -f2 -d ';' |wc -l) -ge 3 ] then echo 'ERROR: it only works with 2 groups. There is too many groups in your file.' >&2 exit 1 else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window --group $group fi else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --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} paste ${fileout_label}.Pop1.TsTv ${fileout_label}.Pop2.TsTv | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{$3="Pop1";$4="Pop2"}1' > ${fileout_tstv_combined} paste ${fileout_label}.Pop1.snpden ${fileout_label}.Pop2.snpden | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{$3="Pop1";$4="Pop2"}1' > ${fileout_snp_combined} fi rm -f ${filein}.vcf ${filein}.vcf.*