diff scripts/SNParray2circos.sh @ 0:46f7f689b929 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/SNParray2circos.sh	Tue Sep 17 11:29:11 2013 -0400
@@ -0,0 +1,38 @@
+#! /bin/bash
+
+# usage: $0 <probes file> <snps file> <probes_out> <snps_out>
+
+if [ $# -ne 4 ]
+then
+	echo "error, unexpected number of arguments in $0"
+	exit
+fi
+
+probes=$1
+snps=$2
+probes_out=$3
+snps_out=$4
+
+echo ""
+echo "$0: "
+echo "probes: $probes, snps: $snps, probes_out: $probes_out, snps_out: $snps_out"
+echo ""
+
+# convert probes file	
+sed '1,1d' $probes > $probes_out.tmp
+sed -i "s/chr/hs/g" $probes_out.tmp
+sed -i '/NaN/d' $probes_out.tmp
+sed -i '/hsMT/d' $probes_out.tmp
+sed -i '/hsM/d' $probes_out.tmp
+cut  -f1,2,3,4 $probes_out.tmp > $probes_out
+
+
+# convert snps file
+sed '1,1d' $snps > $snps_out
+sed -i "s/chr/hs/g" $snps_out
+sed -i '/NaN/d' $snps_out
+sed -i '/hsMT/d' $snps_out
+sed -i '/hsM/d' $snps_out
+
+
+