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1 # Wrapper for MOSAiCS
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2 # Written by Dongjun Chung, Sep. 15, 2011
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3
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4 #!/usr/bin/env perl;
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5 use warnings;
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6 use strict;
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7 use File::Temp qw/tempfile/;
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8 use File::Temp qw/tempdir/;
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9 use File::Basename;
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10
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11 # parse command arguments
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12
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13 die "Usage: perl mosaics_wrapper.pl [chip_path] [control_path] [chip_file_format] [control_file_format] [peak_path] [peak_file_format] [analysis_type] [report_summary_path] [report_gof_path] [report_exploratory_path] [fdr_level] [frag_len] [bin_size] [capping] [signal_model] [d] [maxgap] [minsize] [thres] [n_core]" unless @ARGV == 20;
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14
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15 my ( $chip_path, $control_path, $chip_file_format, $control_file_format, $peak_path, $peak_file_format, $analysis_type, $report_summary_path, $report_gof_path, $report_exploratory_path, $fdr_level, $frag_len, $bin_size, $capping, $signal_model, $d, $maxgap, $minsize, $thres, $n_core ) = @ARGV;
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16
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17 # parse options: analysis type
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18
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19 if ( $analysis_type ne "IO" ) {
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20 print "Only 'IO' is supported for analysis type!\n";
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21 exit 1;
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22 }
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23
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24 # parse options: ChIP, control, peak
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25
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26 my ($chip_filename, $chip_dir) = fileparse($chip_path);
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27 my ($control_filename, $control_dir) = fileparse($control_path);
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28 my ($peak_filename, $peak_dir) = fileparse($peak_path);
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29
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30 # parse options: report summary
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31
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32 my $report_summary = "FALSE";
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33 my $summary_dir = "NULL";
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34 my $summary_filename = "NULL";
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35 if ( $report_summary_path ne "None" ) {
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36 $report_summary = "TRUE";
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37 ($summary_filename, $summary_dir) = fileparse($report_summary_path);
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38 }
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39
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40 # parse options: report GOF
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41
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42 my $report_gof = "FALSE";
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43 my $gof_dir = "NULL";
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44 my $gof_filename = "NULL";
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45 if ( $report_gof_path ne "None" ) {
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46 $report_gof = "TRUE";
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47 ($gof_filename, $gof_dir) = fileparse($report_gof_path);
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48 }
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49
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50 # parse options: report exploratory analysis
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51
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52 my $report_exploratory = "FALSE";
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53 my $exploratory_dir = "NULL";
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54 my $exploratory_filename = "NULL";
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55 if ( $report_exploratory_path ne "None" ) {
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56 $report_exploratory = "TRUE";
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57 ($exploratory_filename, $exploratory_dir) = fileparse($report_exploratory_path);
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58 }
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59
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60 # write a R scrip to run
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61
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62 my $tempdir_bin = tempdir();
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63
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64 my $cmd = qq|
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65 suppressPackageStartupMessages(library(mosaics))
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66 try( suppressPackageStartupMessages(library(rparallel)), silent=TRUE )
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67
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68 mosaicsRunAll(
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69 chipDir="$chip_dir",
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70 chipFileName="$chip_filename",
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71 chipFileFormat="$chip_file_format",
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72 controlDir="$control_dir",
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73 controlFileName="$control_filename",
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74 controlFileFormat="$control_file_format",
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75 binfileDir="$tempdir_bin",
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76 peakDir="$peak_dir",
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77 peakFileName="$peak_filename",
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78 peakFileFormat="$peak_file_format",
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79 reportSummary=$report_summary,
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80 summaryDir="$summary_dir",
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81 summaryFileName="$summary_filename",
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82 reportExploratory=$report_exploratory,
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83 exploratoryDir="$exploratory_dir",
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84 exploratoryFileName="$exploratory_filename",
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85 reportGOF=$report_gof,
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86 gofDir="$gof_dir",
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87 gofFileName="$gof_filename",
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88 FDR=$fdr_level,
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89 fragLen=$frag_len,
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90 binSize=$bin_size,
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91 capping=$capping,
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92 analysisType="$analysis_type",
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93 d=$d,
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94 signalModel="$signal_model",
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95 maxgap=$maxgap,
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96 minsize=$minsize,
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97 thres=$thres,
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98 nCore=$n_core )
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99
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100 q()
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101 |;
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102
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103 # run R
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104
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105 open( FT, "| R --slave --vanilla >& /dev/null" ) or die "Couldn't call R!\n";
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106 print FT $cmd, "\n";
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107 close FT or die "Couldn't finish R!\n";
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108
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109 exit;
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110
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111
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