Mercurial > repos > saskia-hiltemann > cgtag_circos
view scripts/junctions2circos.sh @ 0:46f7f689b929 draft default tip
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author | saskia-hiltemann |
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date | Tue, 17 Sep 2013 11:29:11 -0400 |
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#!/bin/bash # convert junctions file to input for circos to display links # usage: junctions2circos.sh <input file> <output file> # output format: hs1 start end hs2 start end infile=$1 outfile=$2 bedfile=$3 if [ $# -ne 3 ] then echo "error, unexpected number of arguments in $0" exit fi ### convert junctions file echo "converting junctions files" fname=`basename $infile` echo "infile: $infile, outfile: $outfile, fname: $fname" # remove header and 'chr' sed '1,13d' $infile > $fname sed -i 's/chr//g' $fname # make output for links in circos awk 'BEGIN{ FS="\t"; OFS=" " }{ if($2 != "M" && $6 != "M") print "hs"$2,$3,$3,"hs"$6,$7,$7; }END{}' $fname > $outfile #make bedfile to find impacted genes awk 'BEGIN{ FS="\t"; OFS="\t" }{ if($2 != "M" && $6 != "M"){ print "chr"$2,$3,$3; #left side print "chr"$6,$7,$7; #right side } }END{}' $fname > $bedfile