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#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
my $usage = <<__EOUSAGE__;
############################################################################################
#
# Required:
#
# --rsem_files <string> file containing a list of RSEM output files.
# (note, should be isoform or gene.results files, dont mix)
#
# --mode <string> counts|fpkm|tpm
#
# Optional:
#
# --trans_mode_bundle_gene_id specify the transcript identifier as 'gene|trans'
#
############################################################################################
__EOUSAGE__
;
my $rsem_files_list_file;
my $mode;
my $trans_mode_bundle_gene_id = 0;
my $help_flag;
&GetOptions( 'help|h' => \$help_flag,
'rsem_files=s' => \$rsem_files_list_file,
'mode=s' => \$mode,
'trans_mode_bundle_gene_id' => \$trans_mode_bundle_gene_id,
);
if ($help_flag) {
die $usage;
}
unless ($rsem_files_list_file && $mode) {
die $usage;
}
unless ($mode =~ /^(counts|fpkm|tpm)$/i) {
die "Error, mode $mode not recognized";
}
=header_format
0 transcript_id
1 gene_id
2 length
3 effective_length
4 expected_count
5 TPM
6 FPKM
7 IsoPct
=cut
main: {
unless (-f $rsem_files_list_file) { die "$usage\nError: cannot open file $rsem_files_list_file"; }
my @rsem_files = `cat $rsem_files_list_file`;
chomp @rsem_files;
my %data;
foreach my $file (@rsem_files) {
print STDERR "-capturing $mode from file: $file\n";
open (my $fh, $file) or die "Error, cannot open file $file";
my $header = <$fh>; # ignore it
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $acc = $x[0];
if ($trans_mode_bundle_gene_id) {
my $gene = $x[1];
$acc = "$gene|$acc";
}
my $count = $x[4];
my $tpm = $x[5];
my $fpkm = $x[6];
$data{$acc}->{$file} = ($mode =~ /counts/i) ? $count : ($mode =~ /fpkm/) ? $fpkm : $tpm;
}
close $fh;
}
print STDERR "\n\n* done parsing files. Now outputting matrix.\n\n";
my @filenames = @rsem_files;
foreach my $file (@filenames) {
$file = basename($file);
$file =~ s/-/_/g; # R doesn't like '-' in column headers
$file =~ s/\.(genes|isoforms)\.results//;
}
print join("\t", "", @filenames) . "\n";
foreach my $acc (keys %data) {
print "$acc";
foreach my $file (@rsem_files) {
my $count = $data{$acc}->{$file};
unless (defined $count) {
$count = "NA";
}
print "\t$count";
}
print "\n";
}
exit(0);
}
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