Mercurial > repos > saskia-hiltemann > cgtag_circos
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/junctions2circos.sh Tue Sep 17 11:29:11 2013 -0400 @@ -0,0 +1,49 @@ +#!/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