Added support for DE analysis on multiple conditions via running EBSeq

[rsem.git] / rsem-plot-transcript-wiggles

diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 25e8b355dae5992cfd003bb3a659a0d28662f29a..efe00ba91863d7125268d0e492d602ae6b9cbeb7 100755 (executable)
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -2,9 +2,12 @@
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
 use strict;
 
+use rsem_perl_utils;
+
 my $gene_list = 0; # default is 0, means input is a transcript list; 1 means input is a gene list
 my $show_unique = 0; # 0, default value, means do not show unique transcript wiggles; 1 means show unique transcript wiggles
 my $help = 0;
@@ -16,7 +19,7 @@ GetOptions("gene-list" => \$gene_list,
 pod2usage(-verbose => 2) if ($help == 1);
 pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3);
 
-my ($fn, $dir, $suf) = fileparse($0);
+my $dir = "$FindBin::Bin/";
 my $command = "";
 
 unless (-e "$ARGV[0].transcript.sorted.bam") {
@@ -46,20 +49,6 @@ if ($show_unique) {
 $command = $dir."rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $gene_list $show_unique $ARGV[2]";
 &runCommand($command);
 
-# command, {err_msg}
-sub runCommand {
-    print $_[0]."\n";
-    my $status = system($_[0]);
-    if ($status != 0) { 
-       my $errmsg;
-       if (scalar(@_) > 1) { $errmsg = $_[1]; }
-       else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
-       print $errmsg."\n";
-       exit(-1);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME
@@ -68,11 +57,7 @@ rsem-plot-transcript-wiggles
 
 =head1 SYNOPSIS
 
-=over
-
- rsem-plot-transcript-wiggles [options] sample_name input_list output_plot_file
-
-=back
+rsem-plot-transcript-wiggles [options] sample_name input_list output_plot_file
 
 =head1 ARGUMENTS