Mercurial > repos > yufei-luo > s_mart

annotate 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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18
94ab73e8a190 Uploaded
m-zytnicki
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1 #!/bin/bash
94ab73e8a190 Uploaded
m-zytnicki
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2 python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/clusterize.py -f gff -i $1 -o intermedia.gff3 -c -d 150
94ab73e8a190 Uploaded
m-zytnicki
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3 awk '{if ($3!="exon") {print $0}}' intermedia.gff3 > intermedia.gff
94ab73e8a190 Uploaded
m-zytnicki
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4 #perl sortGff.pl -i intermedia.gff > $2
94ab73e8a190 Uploaded
m-zytnicki
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5 python $GALAXY_ROOT/tools/repet_pipe/SMART/Java/Python/CollapseReads.py -i intermedia.gff -f gff -o $2