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comparison testing_cgatools-982e19c29ec0/cgatools/tools/cgatools_1.6/mkvcf_wrapper.pl @ 0:ef23f9cd599b draft default tip

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author devteam
date Thu, 27 Sep 2012 13:37:59 -0400
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-1:000000000000 0:ef23f9cd599b
1 #!/usr/bin/perl
2 use strict;
3 use Getopt::Long;
4 use vars qw($opt_reference $opt_output @opt_input $opt_genomes $opt_source $opt_datasource $opt_fields $opt_nocalls $opt_calibration $opt_jctscore $opt_jctside $opt_jctdistance $opt_jctlength $opt_jctpriority $opt_jcttumor);
5 $| = 1; # set autoflush to screen
6
7 # This is a wrapper for the cgatools mkvcf function to run cgatools mkvcf in Galaxy.
8 # written 8-10-2012 by bcrain@completegenomics.com
9
10 #print join("\n", @ARGV), "\n";
11 &GetOptions("reference=s", "output=s", "input=s@", "genomes=i", "source=s", "datasource=s", "fields=s", "nocalls", "calibration:s", "jctscore=i", "jctside=i", "jctdistance=i", "jctlength=i", "jctpriority", "jcttumor");
12
13 my $command = "cgatools mkvcf --beta --reference $opt_reference --output $opt_output --source-names $opt_source";
14
15 if ($opt_datasource eq 'in')
16 {
17 foreach my $file (@opt_input)
18 {
19 if ($opt_source eq 'masterVar') {$command .= " --master-var ";}
20 elsif ($opt_source eq 'SV') {$command .= " --junction-file ";}
21 else {die "there is an error in the logic: wrong source $opt_source for datasource $opt_datasource.\n";}
22 $command .= $file
23 }
24 }
25 elsif ($opt_datasource eq 'out')
26 {
27 if ($opt_genomes == 1)
28 {
29 if ($opt_input[0] =~ m/masterVar/ and $opt_source eq 'masterVar')
30 {
31 -f $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
32 $command .= " --master-var $opt_input[0]";
33 }
34 elsif ($opt_input[0] =~ m/Junctions/ and $opt_source eq 'SV')
35 {
36 -f $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
37 $command .= " --junction-file $opt_input[0]";
38 }
39 else
40 {
41 $opt_input[0] =~ s/\/$//;
42 -d $opt_input[0] or die "$opt_input[0] is not a valid directory.\n";
43 $command .= " --genome-root $opt_input[0]";
44 }
45 }
46 else
47 {
48 -T $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
49 my $count = 0;
50 foreach my $file (split /\s+/, `cat $opt_input[0]`)
51 {
52 $count ++;
53 ($opt_genomes == 2 and $count > 2) and die "The number of inputs in your list file cannot be greater than the number of genomes selected.\n";
54 if ($file =~ m/masterVar/ and $opt_source eq 'masterVar')
55 {
56 -f $file or die "$file is not a valid file.\n";
57 $command .= " --master-var ";
58 }
59 elsif ($file =~ m/Junctions/ and $opt_source eq 'SV')
60 {
61 -f $file or die "$file is not a valid file.\n";
62 $command .= " --junction-file ";
63 }
64 else
65 {
66 -d $file or die "$file is not a valid directory.\n";
67 $command .= " --genome-root ";
68 }
69 $command .= $file
70 }
71 }
72 }
73 else
74 {die "there is an error in the logic: wrong datasource $opt_datasource.\n";}
75
76 if ($opt_calibration)
77 {
78 (-r "$opt_calibration/0.0.0/metrics.tsv" or -r "$opt_calibration/version0.0.0/metrics.tsv") or die "This folder does not contain the calibration data\n";
79 $command .= " --calibration-root $opt_calibration";
80 }
81
82 $opt_fields eq 'all' or $command .= " --field-names $opt_fields";
83 $opt_nocalls and $command .= " --include-no-calls";
84 $opt_jctscore and $command .= " --junction-score-threshold $opt_jctscore";
85 $opt_jctside and $command .= " --junction-side-length-threshold $opt_jctside";
86 $opt_jctdistance and $command .= " --junction-distance-tolerance $opt_jctdistance";
87 $opt_jctlength and $command .= " --junction-length-threshold $opt_jctlength";
88 $opt_jctpriority and $command .= " --junction-normal-priority";
89 $opt_jcttumor and $command .= " --junction-tumor-hc";
90
91 my $version = `cgatools | head -1`;
92 print "$version\n";
93 print "$command \n";
94
95 `$command`;