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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 rsem.file eXpress.file count|FPKM\n\n";
my $rsem_file = $ARGV[0] or die $usage;
my $express_file = $ARGV[1] or die $usage;
my $method = $ARGV[2] or die $usage;
unless ($method =~ /^(count|FPKM)$/) {
die $usage;
}
main: {
my %data;
&add_RSEM_data(\%data, $rsem_file, $method);
&add_eXpress_data(\%data, $express_file, $method);
print join("\t", "", "RSEM", "eXpress") . "\n";
foreach my $id (keys %data) {
my $rsem_val = $data{$id}->{RSEM};
unless (defined $rsem_val) {
$rsem_val = -1;
}
my $express_val = $data{$id}->{eXpress};
unless (defined $express_val) {
$express_val = -1;
}
if ($rsem_val > 0 && $express_val > 0) {
$rsem_val = "NA" if $rsem_val < 0;
$express_val = "NA" if $express_val < 0;
print join("\t", $id, $rsem_val, $express_val) . "\n";
}
}
exit(0);
}
####
sub add_RSEM_data {
my ($data_href, $rsem_file, $method) = @_;
my $data_field = ($method eq 'count') ? 4 : 6;
open (my $fh, $rsem_file) or die "Error, cannot open file $rsem_file";
my $header = <$fh>;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $id = $x[0];
my $val = $x[$data_field];
$data_href->{$id}->{RSEM} = $val;
}
close $fh;
return;
}
####
sub add_eXpress_data {
my ($data_href, $express_file, $method) = @_;
my $data_field = ($method eq 'count') ? 7 : 10;
open (my $fh, $express_file) or die "Error, cannot open file $express_file";
my $header = <$fh>;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $id = $x[1];
my $val = $x[$data_field];
$data_href->{$id}->{eXpress} = $val;
}
close $fh;
return;
}
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