Mercurial > repos > dereeper > sniplay

diff ped2bed/ped2bed.sh @ 1:420b57c3c185 draft

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author dereeper
date Fri, 10 Jul 2015 04:39:30 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ped2bed/ped2bed.sh	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,20 @@
+#!/bin/bash
+ped=$1
+map=$2
+bed=$3
+fam=$4
+bim=$5
+logs=$6
+
+directory=`dirname $0`
+mkdir tmpdir$$
+cp -rf $ped tmpdir$$/input.ped
+cp -rf $map tmpdir$$/input.map
+ 
+plink --file tmpdir$$/input --out tmpdir$$/out --make-bed --noweb >>$logs 2>&1
+
+mv tmpdir$$/out.bed $bed
+mv tmpdir$$/out.fam $fam
+mv tmpdir$$/out.bim $bim
+
+