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author jgarbe
date Wed, 27 Nov 2013 14:44:13 -0500
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1 #!/usr/bin/perl -w
2
3 ###########################################################
4 # rgttable.pl
5 # John Garbe
6 # October 2013
7 #
8 # Read in a cuffdiff output file (any read_group_tracking file) and print out a file with
9 # tab-delimited columns: featureID, group1-sample1 fpkm, group1-sample2 fpkm, group2-sample1 fpkm, ...
10 #
11 ###########################################################
12
13 =head1 NAME
14
15 rgttable.pl - Read in a cuffdiff output file (any read_group_tracking file) and print out a file with
16 tab-delimited columns: featureID, group1-rep1 fpkm, group1-rep2 fpkm, group2-rep1 fpkm, group2-rep2 fpkm, etc.
17
18 =head1 SYNOPSIS
19
20 rgttable.pl [-c column] genes.read_group_tracking [output.txt]
21
22 =head1 DESCRIPTION
23
24 This script converts read group tracking files produced by Cuffdiff into a format useful
25 for importing into other programs. This works with the isoforms, genes, cds, and tss_groups
26 read group tracking files generated by cuffdiff
27
28 =cut
29
30 use Getopt::Std;
31
32 $usage = "USAGE: rgttable.pl [-c column_number] genes.read_group_tracking [output.txt]\n";
33
34 die $usage if ($#ARGV < 0);
35
36 # parameters
37 getopts('c:', \%opts) or die "$usage\n";
38 $column = $opts{'c'} || 7; # column to extract
39 $column--; # convert from 1-based index to 0-based index
40
41 # open up input file
42 open IFILE, "<$ARGV[0]" or die "cannot open input file $ARGV[0]\n";
43 if ($#ARGV == 1) {
44 open OFILE, ">$ARGV[1]" or die "cannot open outputfile $ARGV[1]\n";
45 } else {
46 open OFILE, ">-" or die "cannot open stdout\n";
47 }
48
49 # open up output files - don't use this, write to STDOUT instead
50 # open OFILE, ">$ARGV[0].txt" or die "cannot open $ARGV[0].out\n";
51
52 # run through the input file, which has these columns:
53 # tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status
54 $header = <IFILE>;
55 @line = split /\t/, $header;
56 # if an output file is specified, write to stdout for Galaxy compatibility
57 if ($#ARGV == 1) {
58 print STDOUT "Extracting column " . ($column+1) . ": $line[$column]\n";
59 } else {
60 print STDERR "Extracting column " . ($column+1) . ": $line[$column]\n";
61 }
62 while ($line = <IFILE>) {
63 chomp $line;
64 # $linecount++;
65 @line = split /\t/, $line;
66 $data{$line[0]}{$line[1]}{$line[2]} = $line[$column];
67 }
68
69 $header = 1;
70 # print out the data
71 for $feature (sort keys %data) {
72 if ($header) {
73 print OFILE "tracking_id";
74 } else {
75 print OFILE "$feature";
76 }
77 for $condition (sort keys %{ $data{$feature} }) {
78 for $replicate (sort keys %{ $data{$feature}{$condition} }) {
79 if ($header) {
80 print OFILE "\t$condition-$replicate";
81 } else {
82 print OFILE "\t$data{$feature}{$condition}{$replicate}";
83 }
84 }
85 }
86 print OFILE "\n";
87 $header = 0;
88 }