Mercurial > repos > biomonika > linkyx

annotate scripts/isoform_exists.sh @ 2:0d8315be76b7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author biomonika
date Tue, 17 Feb 2015 21:59:51 -0500
parents 05c27700e5ca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
1 #!/bin/bash
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 #we will search for isoforms of this contig
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 contig_to_search=$1;
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
4 reference=$2;
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
5 #including only putative isoforms
05c27700e5ca initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
6 part=`echo $contig_to_search | sed -n "s/^\(.*\_c[0-9]\+\)\_seq[0-9]\+/\1/p"`; egrep "$part\_" $reference | grep -v $contig_to_search;