Mercurial > repos > biomonika > linkyx

diff scripts/isoform_exists.sh @ 22:7997c93ee479

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last attempt to install perl as part of linkyx
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 19:40:01 -0400
parents 1955f03f092e
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/isoform_exists.sh	Thu Sep 11 19:40:01 2014 -0400
@@ -0,0 +1,6 @@
+#!/bin/bash
+#we will search for isoforms of this contig
+contig_to_search=$1;
+reference=$2;
+#including only putative isoforms
+part=`echo $contig_to_search | sed -n "s/^\(.*\_c[0-9]\+\)\_seq[0-9]\+/\1/p"`; egrep "$part\_" $reference | grep -v $contig_to_search;
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