From f054dfb3f9bb35d4043534ea88e1f5fa8e7eb2ea Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Fri, 21 Mar 2014 15:05:03 -0500
Subject: [PATCH] Modified the shebang line for perl scripts

---
 convert-sam-for-rsem                        | 2 +-
 extract-transcript-to-gene-map-from-trinity | 2 +-
 rsem-calculate-expression                   | 2 +-
 rsem-control-fdr                            | 2 +-
 rsem-generate-data-matrix                   | 7 ++++---
 rsem-generate-ngvector                      | 2 +-
 rsem-plot-transcript-wiggles                | 2 +-
 rsem-prepare-reference                      | 2 +-
 rsem-run-ebseq                              | 2 +-
 rsem_perl_utils.pm                          | 2 +-
 10 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index ba75db8..c077616 100755
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
diff --git a/extract-transcript-to-gene-map-from-trinity b/extract-transcript-to-gene-map-from-trinity
index 260cd83..bf53b9b 100755
--- a/extract-transcript-to-gene-map-from-trinity
+++ b/extract-transcript-to-gene-map-from-trinity
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use strict;
 
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 8a7ca0e..a9f26c9 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
diff --git a/rsem-control-fdr b/rsem-control-fdr
index 65c57cb..eb8f345 100755
--- a/rsem-control-fdr
+++ b/rsem-control-fdr
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
diff --git a/rsem-generate-data-matrix b/rsem-generate-data-matrix
index b1b4f63..f85156d 100755
--- a/rsem-generate-data-matrix
+++ b/rsem-generate-data-matrix
@@ -1,14 +1,15 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use strict;
 
 if (scalar(@ARGV) == 0) {
-    print "Usage: rsem-generate-data-matrix sampleA.[genes/isoforms].results sampleB.[genes/isoforms].results ... > output_name.matrix\n";
-    print "Results files should be either all .genes.results or all .isoforms.results.\n";
+    print "Usage: rsem-generate-data-matrix sampleA.[alleles/genes/isoforms].results sampleB.[alleles/genes/isoforms].results ... > output_name.matrix\n";
+    print "All result files should have the same file type. The 'TPM' columns of every result file are extracted to form the data matrix.\n";
     exit(-1);
 }
 
 my $offsite = 4; # for new file formats
+if ($ARGV[0] =~ /alleles.results$/) { $offsite = 5; }
 
 my $line;
 my $n = scalar(@ARGV);
diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index 68fe664..dc874a9 100755
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 74076ec..3aa7e35 100755
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index de4f061..8050356 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;	
diff --git a/rsem-run-ebseq b/rsem-run-ebseq
index 4d42491..9693eee 100755
--- a/rsem-run-ebseq
+++ b/rsem-run-ebseq
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
diff --git a/rsem_perl_utils.pm b/rsem_perl_utils.pm
index 4321a45..6355f67 100644
--- a/rsem_perl_utils.pm
+++ b/rsem_perl_utils.pm
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 package rsem_perl_utils;
 
-- 
2.39.2