Mercurial > repos > nikhil-joshi > mirdeep2_and_targetspy
comparison mirdeep2/mirdeep2_wrapper.pl @ 0:5b9519f4b165
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author | nikhil-joshi |
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date | Mon, 19 Sep 2011 19:04:41 -0400 |
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-1:000000000000 | 0:5b9519f4b165 |
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1 #!/usr/bin/perl | |
2 | |
3 use File::Temp qw/ tempfile tempdir /; | |
4 use File::Copy qw/ copy /; | |
5 use Cwd; | |
6 | |
7 $collapsed_reads = $ARGV[0]; | |
8 $bowtie_index_name = $ARGV[1]; | |
9 $bowtie_files_path = $ARGV[2]; | |
10 $arf_file = $ARGV[3]; | |
11 $mirna_ref = $ARGV[4]; | |
12 $mirna_other = $ARGV[5]; | |
13 $precursors = $ARGV[6]; | |
14 $file_path = $ARGV[7]; | |
15 $input_name = $ARGV[8]; | |
16 | |
17 $csv_output = $ARGV[9]; | |
18 $html_output = $ARGV[10]; | |
19 $survey_output = $ARGV[11]; | |
20 $mrd_output = $ARGV[12]; | |
21 | |
22 # the rest are options | |
23 $options = join (" ", @ARGV[13..$#ARGV]); | |
24 | |
25 #point to correct bowtie index path | |
26 $basename = `basename $bowtie_index_name`; | |
27 chomp $basename; | |
28 | |
29 # create the path used to house the pdfs | |
30 chomp $file_path; | |
31 system ("mkdir -p $file_path"); | |
32 | |
33 # do all the dirty work in a temp directory | |
34 $cwd = cwd(); | |
35 $tempdir = tempdir(CLEANUP => 1); | |
36 chdir ($tempdir); | |
37 | |
38 if ($mirna_ref eq "None") {$mirna_ref="none";} | |
39 if ($mirna_other eq "None") {$mirna_other="none";} | |
40 if ($precursors eq "None") {$precursors="none";} | |
41 | |
42 $ret_mirdeep2 = `miRDeep2.pl $collapsed_reads $bowtie_files_path/$basename $arf_file $mirna_ref $mirna_other $precursors -v $options 2> /dev/null`; | |
43 system ("cp $tempdir/pdfs*/*.pdf $file_path"); | |
44 | |
45 $csv_file = `ls $tempdir/result*.csv`; | |
46 chomp $csv_file; | |
47 if ($csv_file eq "") {die "Error: Cannot find csv result file in dir $tempdir\n";} | |
48 | |
49 $html_file = `ls $tempdir/result*.html`; | |
50 chomp $html_file; | |
51 if ($html_file eq "") {die "Error: Cannot find html result file in dir $tempdir\n";} | |
52 | |
53 $survey_file = `ls $tempdir/mirdeep_runs/run*/survey.csv`; | |
54 chomp $survey_file; | |
55 if ($survey_file eq "") {die "Error: Cannot find survey result file in dir $tempdir\n";} | |
56 | |
57 $mrd_file = `ls $tempdir/mirdeep_runs/run*/output.mrd`; | |
58 chomp $mrd_file; | |
59 if ($mrd_file eq "") {die "Error: Cannot find hairpin result file in dir $tempdir\n";} | |
60 | |
61 # replacing mirdeep created links with relative links in galaxy | |
62 system ("sed -r -i 's/file:\\/\\/.+\\/(.+\\.pdf)/\\1/g' $html_file"); | |
63 | |
64 copy ($csv_file, $csv_output); | |
65 copy ($html_file, $html_output); | |
66 copy ($survey_file, $survey_output); | |
67 copy ($mrd_file, $mrd_output); | |
68 | |
69 chdir($cwd); |