Mercurial > repos > david-hoover > mirdeep2_and_targetspy_dh

comparison mirdeep2_wrapper.pl @ 0:17e442abb3de draft default tip

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author david-hoover
date Wed, 23 Jul 2014 10:27:07 -0400
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-1:000000000000 0:17e442abb3de
1 #!/usr/bin/perl
2
3 use File::Temp qw/ tempfile tempdir /;
4 use File::Copy qw/ copy /;
5 use Cwd;
6
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";
8
9 $collapsed_reads = $ARGV[0];
10 $bowtie_index_name = $ARGV[1];
11 $bowtie_files_path = $ARGV[2];
12 $arf_file = $ARGV[3];
13 $mirna_ref = $ARGV[4];
14 $mirna_other = $ARGV[5];
15 $precursors = $ARGV[6];
16 $file_path = $ARGV[7];
17 $input_name = $ARGV[8];
18
19 $csv_output = $ARGV[9];
20 $html_output = $ARGV[10];
21 $survey_output = $ARGV[11];
22 $mrd_output = $ARGV[12];
23
24 # the rest are options
25 $options = join (" ", @ARGV[13..$#ARGV]);
26
27 #point to correct bowtie index path
28 $basename = `basename $bowtie_index_name`;
29 chomp $basename;
30
31 # create the path used to house the pdfs
32 chomp $file_path;
33 system ("mkdir -p $file_path");
34
35 # do all the dirty work in a temp directory
36 $cwd = cwd();
37 $tempdir = tempdir(CLEANUP => 1);
38 chdir ($tempdir);
39
40 if ($mirna_ref eq "None") {$mirna_ref="none";}
41 if ($mirna_other eq "None") {$mirna_other="none";}
42 if ($precursors eq "None") {$precursors="none";}
43
44 $ret_mirdeep2 = `miRDeep2.pl $collapsed_reads $bowtie_files_path/$basename $arf_file $mirna_ref $mirna_other $precursors -v $options 2> /dev/null`;
45 system ("cp $tempdir/pdfs*/*.pdf $file_path");
46
47 $csv_file = `ls $tempdir/result*.csv`;
48 chomp $csv_file;
49 if ($csv_file eq "") {die "Error: Cannot find csv result file in dir $tempdir\n";}
50
51 $html_file = `ls $tempdir/result*.html`;
52 chomp $html_file;
53 if ($html_file eq "") {die "Error: Cannot find html result file in dir $tempdir\n";}
54
55 $survey_file = `ls $tempdir/mirdeep_runs/run*/survey.csv`;
56 chomp $survey_file;
57 if ($survey_file eq "") {die "Error: Cannot find survey result file in dir $tempdir\n";}
58
59 $mrd_file = `ls $tempdir/mirdeep_runs/run*/output.mrd`;
60 chomp $mrd_file;
61 if ($mrd_file eq "") {die "Error: Cannot find hairpin result file in dir $tempdir\n";}
62
63 # replacing mirdeep created links with relative links in galaxy
64 system ("sed -r -i 's/file:\\/\\/.+\\/(.+\\.pdf)/\\1/g' $html_file");
65
66 copy ($csv_file, $csv_output);
67 copy ($html_file, $html_output);
68 copy ($survey_file, $survey_output);
69 copy ($mrd_file, $mrd_output);
70
71 chdir($cwd);