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1 #!/usr/bin/perl
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2
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3 use File::Temp qw/ tempfile tempdir /;
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4 use File::Copy qw/ copy /;
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5 use Cwd;
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6
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7 $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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8
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9 $collapsed_reads = $ARGV[0];
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10 $bowtie_index_name = $ARGV[1];
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11 $bowtie_files_path = $ARGV[2];
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12 $arf_file = $ARGV[3];
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13 $mirna_ref = $ARGV[4];
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14 $mirna_other = $ARGV[5];
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15 $precursors = $ARGV[6];
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16 $file_path = $ARGV[7];
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17 $input_name = $ARGV[8];
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18
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19 $csv_output = $ARGV[9];
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20 $html_output = $ARGV[10];
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21 $survey_output = $ARGV[11];
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22 $mrd_output = $ARGV[12];
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23
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24 # the rest are options
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25 $options = join (" ", @ARGV[13..$#ARGV]);
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26
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27 #point to correct bowtie index path
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28 $basename = `basename $bowtie_index_name`;
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29 chomp $basename;
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30
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31 # create the path used to house the pdfs
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32 chomp $file_path;
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33 system ("mkdir -p $file_path");
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34
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35 # do all the dirty work in a temp directory
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36 $cwd = cwd();
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37 $tempdir = tempdir(CLEANUP => 1);
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38 chdir ($tempdir);
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39
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40 if ($mirna_ref eq "None") {$mirna_ref="none";}
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41 if ($mirna_other eq "None") {$mirna_other="none";}
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42 if ($precursors eq "None") {$precursors="none";}
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43
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44 $ret_mirdeep2 = `miRDeep2.pl $collapsed_reads $bowtie_files_path/$basename $arf_file $mirna_ref $mirna_other $precursors -v $options 2> /dev/null`;
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45 system ("cp $tempdir/pdfs*/*.pdf $file_path");
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46
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47 $csv_file = `ls $tempdir/result*.csv`;
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48 chomp $csv_file;
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49 if ($csv_file eq "") {die "Error: Cannot find csv result file in dir $tempdir\n";}
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50
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51 $html_file = `ls $tempdir/result*.html`;
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52 chomp $html_file;
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53 if ($html_file eq "") {die "Error: Cannot find html result file in dir $tempdir\n";}
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54
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55 $survey_file = `ls $tempdir/mirdeep_runs/run*/survey.csv`;
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56 chomp $survey_file;
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57 if ($survey_file eq "") {die "Error: Cannot find survey result file in dir $tempdir\n";}
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58
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59 $mrd_file = `ls $tempdir/mirdeep_runs/run*/output.mrd`;
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60 chomp $mrd_file;
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61 if ($mrd_file eq "") {die "Error: Cannot find hairpin result file in dir $tempdir\n";}
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62
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63 # replacing mirdeep created links with relative links in galaxy
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64 system ("sed -r -i 's/file:\\/\\/.+\\/(.+\\.pdf)/\\1/g' $html_file");
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65
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66 copy ($csv_file, $csv_output);
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67 copy ($html_file, $html_output);
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68 copy ($survey_file, $survey_output);
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69 copy ($mrd_file, $mrd_output);
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70
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71 chdir($cwd);
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