Modified the shebang line for perl scripts

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index ba75db8b6fd23ca22886dc07dc1db1ed94aada5c..c0776162e064ef7bec9eeefbdf0412be4a22f8ad 100755 (executable)
--- 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 260cd834972f663f9df143f10a74e35518074028..bf53b9bdbdbad65ddc5c3441e7679f04e1eacd64 100755 (executable)
--- 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 8a7ca0e45b6d58b7d1089bd98dceb306a9cf4d79..a9f26c9d47142988d4d7e2fd52022f673f2e2819 100755 (executable)
--- 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 65c57cbc866277fa772ba59760d59e5c696cbfec..eb8f3454b05579568877917f0c41972a94018f6c 100755 (executable)
--- 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 b1b4f63e9713babf3730565261f90c6738fdcdfe..f85156d0bf68e1aa3bd138da730de578f4594ba6 100755 (executable)
--- 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 68fe664e5dd69a9dae2ca8a20e91e9bf0bf8430e..dc874a916157576c5b8e5653e389b02765cb8576 100755 (executable)
--- 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 74076ec7d4acc2053bde04581a81bf514ae9c6f8..3aa7e359290b9cab8ef845f375da37a26c8208fe 100755 (executable)
--- 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 de4f061612d4b3a976147afe48e5a22594ae3f42..8050356e567e2b260457e0b7ba311fe63b9c3b1b 100755 (executable)
--- 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 4d424915f820b9b28e956e65f70629282f3cef9e..9693eeea13e550f63879514173a346c328dbc66d 100755 (executable)
--- 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 4321a45ab3df0b58c2e312567a90d7c054f02a69..6355f67a07f88fcf4207407325542644c2c5a454 100644 (file)
--- 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;