#!/usr/bin/perl

use strict;

if (scalar(@ARGV) == 0) {
    print "Usage: rsem-form-counts-matrix sampleA.[genes/isoforms].results sampleB.[genes/isoforms].results ... > output_name.counts.matrix\n";
    print "Results files should be either all .genes.results or all .isoforms.results.\n";
    exit(-1);
}

my $line;
my $n = scalar(@ARGV);
my $M = -1;
my @matrix = ();

for (my $i = 0; $i < $n; $i++) {
    my @sample = ();
    open(INPUT, $ARGV[$i]);
    while ($line = <INPUT>) {
	chomp($line); 
	my @fields = split(/\t/, $line);
	push(@sample, $fields[1]);
    }
    close(INPUT);
    if (scalar(@sample) == 0) {
	print STDERR "No transcript is detected! Please check if $ARGV[$i] exists.\n";
	exit(-1);
    }
    if ($M < 0) { $M = scalar(@sample); }
    elsif ($M != scalar(@sample)) { 
	print STDERR "Number of transcripts among samples are not equal!\n"; 
	exit(-1); 
    }
    push(@matrix, \@sample);
}

for (my $i = 0; $i < $M; $i++) {
    for (my $j = 0; $j < $n - 1; $j++) { print "$matrix[$j][$i]\t"; }
    print "$matrix[$n - 1][$i]\n";
}