Mercurial > repos > david-hoover > mirdeep2_and_targetspy_dh
annotate 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 |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/perl |
| 2 | |
| 3 $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"; | |
| 4 | |
| 5 $bowtie_index_name = $ARGV[0]; | |
| 6 $output_arf = $ARGV[1]; | |
| 7 $bowtie_files_path = $ARGV[2]; | |
| 8 $options = join (" ", @ARGV[3..$#ARGV]); | |
| 9 | |
| 10 $basename = `basename $bowtie_index_name`; | |
| 11 chomp $basename; | |
| 12 | |
| 13 system ("mapper.pl $options -p $bowtie_files_path/$basename -t $output_arf 2> /dev/null"); | |
| 14 | |
| 15 if (-s $output_arf == 0) {die "No reads aligned to the reference.";} |