Mercurial > repos > nikhil-joshi > mirdeep2_and_targetspy
view mirdeep2/mapper_wrapper.pl @ 0:5b9519f4b165
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author | nikhil-joshi |
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date | Mon, 19 Sep 2011 19:04:41 -0400 |
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#!/usr/bin/perl $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.";}