Mercurial > repos > nikhil-joshi > mirdeep2_and_targetspy

comparison mirdeep2/mapper_wrapper.pl @ 0:5b9519f4b165

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author nikhil-joshi
date Mon, 19 Sep 2011 19:04:41 -0400
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-1:000000000000 0:5b9519f4b165
1 #!/usr/bin/perl
2
3 $bowtie_index_name = $ARGV[0];
4 $output_arf = $ARGV[1];
5 $bowtie_files_path = $ARGV[2];
6 $options = join (" ", @ARGV[3..$#ARGV]);
7
8 $basename = `basename $bowtie_index_name`;
9 chomp $basename;
10
11 system ("mapper.pl $options -p $bowtie_files_path/$basename -t $output_arf 2> /dev/null");
12
13 if (-s $output_arf == 0) {die "No reads aligned to the reference.";}