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annotate scripts/isoform_exists.sh @ 1:4c5de3a2c54e

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toolshed2
author biomonika <biomonika@psu.edu>
date Sun, 07 Sep 2014 23:12:26 -0400
parents 05c27700e5ca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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biomonika <biomonika@psu.edu>
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1 #!/bin/bash
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biomonika <biomonika@psu.edu>
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2 #we will search for isoforms of this contig
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biomonika <biomonika@psu.edu>
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3 contig_to_search=$1;
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biomonika <biomonika@psu.edu>
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4 reference=$2;
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biomonika <biomonika@psu.edu>
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5 #including only putative isoforms
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biomonika <biomonika@psu.edu>
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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;