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author dongjun
date Thu, 10 Jan 2013 17:33:09 -0500
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11:002dc17c9824 12:ce96e302ee92
1 # Wrapper for MOSAiCS
2 # Written by Dongjun Chung, Jan. 15, 2013
3
4 #!/usr/bin/env perl;
5 use warnings;
6 use strict;
7 use File::Temp qw/tempfile/;
8 use File::Temp qw/tempdir/;
9 use File::Basename;
10
11 # parse command arguments
12 # inactive arguments: useChrfile, chrfile, excludeChr
13 # meaningless argument: analysisType (for later use)
14
15 die "Usage: perl mosaics_wrapper.pl [chip_path] [chip_file_format] [control_path] [control_file_format] [peak_path] [peak_file_format] [analysis_type] [report_summary_path] [report_gof_path] [report_exploratory_path] [PET?] [chromosome-wise?] [fdr_level] [frag_len] [bin_size] [capping] [signal_model] [bg_est_method] [d] [maxgap] [minsize] [thres] [parallel] [n_core]" unless @ARGV == 24;
16
17 my ( $chip_path, $chip_file_format, $control_path, $control_file_format, $peak_path, $peak_file_format, $analysis_type, $report_summary_path, $report_gof_path, $report_exploratory_path, $pet, $by_chr, $fdr_level, $frag_len, $bin_size, $capping, $signal_model, $bg_est_method, $d, $maxgap, $minsize, $thres, $parallel, $n_core ) = @ARGV;
18
19 # parse options: analysis type
20
21 if ( $analysis_type ne "IO" ) {
22 print "Only 'IO' is supported for analysis type!\n";
23 exit 1;
24 }
25
26
27 # parse options: report summary
28
29 my $report_summary = "FALSE";
30 if ( $report_summary_path ne "None" ) {
31 $report_summary = "TRUE";
32 }
33
34 # parse options: report GOF
35
36 my $report_gof = "FALSE";
37 if ( $report_gof_path ne "None" ) {
38 $report_gof = "TRUE";
39 }
40
41 # parse options: report exploratory analysis
42
43 my $report_exploratory = "FALSE";
44 if ( $report_exploratory_path ne "None" ) {
45 $report_exploratory = "TRUE";
46 }
47
48 # write a R scrip to run
49
50 my $tempdir_bin = tempdir();
51
52 my $cmd = qq|
53 suppressPackageStartupMessages(library(mosaics))
54 try( suppressPackageStartupMessages(library(parallel)), silent=TRUE )
55
56 mosaicsRunAll(
57 chipFile="$chip_path",
58 chipFileFormat="$chip_file_format",
59 controlFile="$control_path",
60 controlFileFormat="$control_file_format",
61 binfileDir="$tempdir_bin",
62 peakFile="$peak_path",
63 peakFileFormat="$peak_file_format",
64 reportSummary=$report_summary,
65 summaryFile="$report_summary_path",
66 reportExploratory=$report_exploratory,
67 exploratoryFile="$report_exploratory_path",
68 reportGOF=$report_gof,
69 gofFile="$report_gof_path",
70 PET=$pet,
71 byChr=$by_chr,
72 useChrfile=FALSE,
73 chrfile=NULL,
74 excludeChr=NULL,
75 FDR=$fdr_level,
76 fragLen=$frag_len,
77 binSize=$bin_size,
78 capping=$capping,
79 bgEst="$bg_est_method",
80 d=$d,
81 signalModel="$signal_model",
82 maxgap=$maxgap,
83 minsize=$minsize,
84 thres=$thres,
85 parallel=$parallel,
86 nCore=$n_core )
87
88 q()
89 |;
90
91 # run R
92
93 open( FT, "| R --slave --vanilla >& /dev/null" ) or die "Couldn't call R!\n";
94 print FT $cmd, "\n";
95 close FT or die "Couldn't finish R!\n";
96
97 exit;
98
99