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rsem-generate-data-matrix5
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rsem-generate-data-matrix5
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#!/usr/bin/env perl
#This is a modified version of rsem-generate-data-matrix, a function that comes with the RSEM package (https://github.com/deweylab/RSEM).
use strict;
if (scalar(@ARGV) == 0) {
print "Usage: rsem-generate-data-matrix sampleA.[alleles/genes/isoforms].results sampleB.[alleles/genes/isoforms].results ... > output_nam
e.matrix\n";
print "All result files should have the same file type. The 'expected_count' columns of every result file are extracted to form the data m
atrix.\n";
exit(-1);
}
my $offsite = 5; # for new file formats
if ($ARGV[0] =~ /alleles.results$/) { $offsite = 5; }
my $line;
my $n = scalar(@ARGV);
my $M = -1;
my @matrix = ();
# 0, file_name; 1, reference of expected count array; 2, reference of transcript_id/gene_id array
sub loadData {
open(INPUT, $_[0]);
my $line = <INPUT>; # The first line contains only column names
while ($line = <INPUT>) {
chomp($line);
my @fields = split(/\t/, $line);
push(@{$_[2]}, "\"$fields[0]\"");
push(@{$_[1]}, $fields[$offsite]);
}
close(INPUT);
if (scalar(@{$_[1]}) == 0) {
print STDERR "Nothing is detected! $_[0] may not exist or is empty.\n";
exit(-1);
}
}
#0, M; 1, reference of @ids_arr; 2, reference of @ids
sub check {
my $size = $_[0];
for (my $i = 0; $i < $size; $i++) {
if ($_[1]->[$i] ne $_[2]->[$i]) {
return 0;
}
}
return 1;
}
my @ids_arr = ();
for (my $i = 0; $i < $n; $i++) {
my (@ids, @ecs) = ();
&loadData($ARGV[$i], \@ecs, \@ids);
if ($M < 0) {
$M = scalar(@ids);
@ids_arr = @ids;
}
elsif (!&check($M, \@ids_arr, \@ids)) {
print STDERR "Number of lines among samples are not equal!\n";
exit(-1);
}
my $colname;
if (substr($ARGV[$i], 0, 2) eq "./") { $colname = substr($ARGV[$i], 2); }
else { $colname = $ARGV[$i]; }
$colname = "\"$colname\"";
@ecs = ($colname, @ecs);
push(@matrix, \@ecs);
}
@ids_arr = ("", @ids_arr);
@matrix = (\@ids_arr, @matrix);
for (my $i = 0; $i <= $M; $i++) {
for (my $j = 0; $j < $n; $j++) { print "$matrix[$j][$i]\t"; }
print "$matrix[$n][$i]\n";
}