Mercurial > repos > saskia-hiltemann > file_manipulation
view chrprefix.sh @ 0:e77c9484b2d0 draft default tip
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author | saskia-hiltemann |
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date | Thu, 22 Oct 2015 09:18:30 -0400 |
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#!/bin/bash inputfile=$1 col=$2 addremove=$3 outputfile=$4 echo "args: $@" echo "inputfile: $inputfile" echo "column: $column" echo "addremove: $addremove" echo "outputfile: $outputfile" #get column number column=`expr match "$col" '\([0-9]*\)'` echo "colnumber: $column" if [ $addremove == "add" ] then echo "adding prefix to column $column" awk 'BEGIN{ FS="\t" OFS="\t" c="'"$column"'" }{ if (index($0,"#")!=1){ $c="chr"$c } print $0 }END{}' $inputfile > $outputfile else #remove prefix echo "removing prefix from column $column" awk 'BEGIN{ FS="\t" OFS="\t" c="'"$column"'" }{ if (FNR>1 && index($0,"#")!=1){ $c=substr($c,4) } print $0 }END{}' $inputfile > $outputfile fi echo "inputfile: " head -5 $inputfile echo "outputfile: " head -5 $outputfile