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1 #!/usr/bin/perl
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2
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3 use File::Copy qw/ copy /;
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4
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5 $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";
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6
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7 $fastafile = $ARGV[0];
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8 $file_path = $ARGV[1];
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9 $output_file = $ARGV[2];
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10 $fastafile_text = $ARGV[3];
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11
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12 $output_basename = `basename $output_file`;
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13 chomp $output_basename;
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14 $filepath_basename = `basename $file_path`;
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15 chomp $filepath_basename;
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16
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17 $output_dir = $output_file;
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18 $output_dir =~ s/$output_basename/$filepath_basename/;
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19
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20 system ("mkdir -p $file_path");
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21 copy ($fastafile, $output_file);
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22 copy ($output_file, $file_path);
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23
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24 system ("bowtie-build $fastafile $file_path/$output_basename");
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25
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26 open (OUTPUT,">$output_file");
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27 print OUTPUT "<h1>Bowtie index on $fastafile_text</h1>\n";
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28 $dirout = `ls $file_path`;
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29
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30 foreach $file (split (/\n/, $dirout)) {
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31 print OUTPUT "<a href='$file'>$file</a><br/>\n";
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32 }
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33 close (OUTPUT);
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