annotate mirdeep2/mapper_wrapper.pl @ 1:798fe7ba8b5e
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nikhil-joshi |
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Mon, 19 Sep 2011 19:07:09 -0400 |
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5b9519f4b165 |
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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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10
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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.";}
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