Mercurial > repos > nikhil-joshi > mirdeep2_and_targetspy

annotate 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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5b9519f4b165 Upload first commmit
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1 #!/usr/bin/perl
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2
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3 $bowtie_index_name = $ARGV[0];
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4 $output_arf = $ARGV[1];
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5 $bowtie_files_path = $ARGV[2];
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6 $options = join (" ", @ARGV[3..$#ARGV]);
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7
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8 $basename = `basename $bowtie_index_name`;
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9 chomp $basename;
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11 system ("mapper.pl $options -p $bowtie_files_path/$basename -t $output_arf 2> /dev/null");
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12
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13 if (-s $output_arf == 0) {die "No reads aligned to the reference.";}