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annotate 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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1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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1 #!/bin/bash
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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2 #we will search for isoforms of this contig
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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3 contig_to_search=$1;
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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4 reference=$2;
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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5 #including only putative isoforms
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
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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;