Added support for DE analysis on multiple conditions via running EBSeq

[rsem.git] / rsem-prepare-reference

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 055bef8c0bd7ff45b7aa494f100ef4eba1ca9dbd..8ff37c7ffc79dcc894cbbd2e3fb0b402fbb89570 100755 (executable)
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -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 $status;
 
 my $gtfF = "";
@@ -58,7 +61,7 @@ elsif ($subsetFile ne "") { $polyAChoice = 2; }
 
 if ($bowtie_path ne "") { $bowtie_path .= "/"; }
 
-my ($fn, $dir, $suf) = fileparse($0); 
+my $dir = "$FindBin::Bin/";
 my $command = "";
 
 if ($type == 0) {
@@ -93,20 +96,6 @@ if (!$no_bowtie) {
     &runCommand($command);
 }
 
-# command, {err_msg}
-sub runCommand {
-    print $_[0]."\n";
-    my $status = system($_[0]);
-    if ($status != 0) {
-        my $errmsg = "";
-        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
-        $errmsg .= "\"$_[0]\" failed! Please check if you provide correct parameters/options for the pipeline!\n";
-        print $errmsg;
-        exit(-1);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME
@@ -115,11 +104,7 @@ rsem-prepare-reference
 
 =head1 SYNOPSIS
 
-=over
-
- rsem-prepare-reference [options] reference_fasta_file(s) reference_name
-
-=back
+rsem-prepare-reference [options] reference_fasta_file(s) reference_name
 
 =head1 ARGUMENTS
 
@@ -164,7 +149,7 @@ If this option is off, then the mapping of isoforms to genes depends on whether
 
 =item B<--no-polyA>
 
-Do not add poly(A) tails to the end of reference isoforms. (Default: add poly(A) tails to all transcripts)
+Do not add poly(A) tails to the end of reference isoforms. (Default: adding poly(A) tails to all transcripts)
 
 =item B<--no-polyA-subset> <file>
 
@@ -207,7 +192,7 @@ This program will generate 'reference_name.grp', 'reference_name.ti', 'reference
 
 'reference_name.grp', 'reference_name.ti', 'reference_name.seq', 'reference_name.idx.fa', and 'reference_name.chrlist' are used by RSEM internally.
 
-B<'reference_name.transcripts.fa'> contains the extracted reference transcripts in FASTA format. Poly(A) tails are not added.
+B<'reference_name.transcripts.fa'> contains the extracted reference transcripts in FASTA format. Poly(A) tails are added unless '--no-polyA' is set.
 
 =head1 EXAMPLES