Mercurial > repos > yufei-luo > s_mart

diff SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.sh @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/bacteriaRegulatoryRegion_Detection/prepareAnnot.sh	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,5 @@
+#!/bin/bash
+python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/clusterize.py -f gff -i $1 -o intermedia.gff3 -c -d 150
+awk '{if ($3!="exon") {print $0}}' intermedia.gff3 > intermedia.gff
+#perl sortGff.pl -i intermedia.gff > $2
+python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/CollapseReads.py -i intermedia.gff -f gff -o $2