Mercurial > repos > saskia-hiltemann > file_manipulation
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chrprefix.sh Thu Oct 22 09:18:30 2015 -0400 @@ -0,0 +1,52 @@ +#!/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