view VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh @ 3:612066e3f57d draft

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#!/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.*