Mercurial > repos > david-hoover > mirdeep2_and_targetspy_dh
diff mapper_wrapper.pl @ 0:17e442abb3de draft default tip
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| author | david-hoover |
|---|---|
| date | Wed, 23 Jul 2014 10:27:07 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mapper_wrapper.pl Wed Jul 23 10:27:07 2014 -0400 @@ -0,0 +1,15 @@ +#!/usr/bin/perl + +$ENV{PATH} .= ":/usr/local/apps/mirdeep2/2.0.0.5:/usr/local/apps/bowtie/0.12.9:/usr/local/apps/viennarna/current/bin:/usr/local/randfold-2.0/bin"; + +$bowtie_index_name = $ARGV[0]; +$output_arf = $ARGV[1]; +$bowtie_files_path = $ARGV[2]; +$options = join (" ", @ARGV[3..$#ARGV]); + +$basename = `basename $bowtie_index_name`; +chomp $basename; + +system ("mapper.pl $options -p $bowtie_files_path/$basename -t $output_arf 2> /dev/null"); + +if (-s $output_arf == 0) {die "No reads aligned to the reference.";}