Added a script, 'rsem-find-DE', to run EBSeq automatically

[rsem.git] / rsem-form-counts-matrix

diff --git a/rsem-form-counts-matrix b/rsem-form-counts-matrix
deleted file mode 100755 (executable)
index d275d6e..0000000
--- a/rsem-form-counts-matrix
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/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 $offsite = 4; # for new file formats
-
-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, $fields[$offsite]);
-    }
-    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";
-}