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1 #!/bin/bash
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2
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3 # convert junctions file to input for circos to display links
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4 # usage: junctions2circos.sh <input file> <output file>
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5
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6 # output format: hs1 start end hs2 start end
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7
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8 infile=$1
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9 outfile=$2
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10 bedfile=$3
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11
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12 if [ $# -ne 3 ]
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13 then
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14 echo "error, unexpected number of arguments in $0"
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15 exit
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16 fi
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17
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18 ### convert junctions file
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19 echo "converting junctions files"
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20
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21 fname=`basename $infile`
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22
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23 echo "infile: $infile, outfile: $outfile, fname: $fname"
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24
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25 # remove header and 'chr'
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26 sed '1,13d' $infile > $fname
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27 sed -i 's/chr//g' $fname
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28
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29 # make output for links in circos
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30 awk 'BEGIN{
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31 FS="\t";
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32 OFS=" "
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33 }{
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34 if($2 != "M" && $6 != "M")
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35 print "hs"$2,$3,$3,"hs"$6,$7,$7;
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36 }END{}' $fname > $outfile
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37
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38
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39 #make bedfile to find impacted genes
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40 awk 'BEGIN{
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41 FS="\t";
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42 OFS="\t"
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43 }{
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44 if($2 != "M" && $6 != "M"){
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45 print "chr"$2,$3,$3; #left side
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46 print "chr"$6,$7,$7; #right side
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47 }
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48
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49 }END{}' $fname > $bedfile
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