Generated two index multi-Fasta files instead, one without 'N' converted to 'G' and...

[rsem.git] / rsem-prepare-reference

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index de4f061612d4b3a976147afe48e5a22594ae3f42..177cc43c83e35fa8e3f4bc3dbd475cc964a6016f 100755 (executable)
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -1,13 +1,16 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;        
 use FindBin;
-use lib $FindBin::Bin;
-use strict;
-
+use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
+use Env qw(@PATH);
+push(@PATH, $FindBin::RealBin);
+
+use strict;
+
 my $status;
 
 my $gtfF = "";
@@ -16,9 +19,9 @@ my $polyAChoice = 0; # 0, default, pad polyA tails for all isoforms; 1, --no-pol
 my $no_polyA = 0; # for option --no-polyA 
 my $subsetFile = "";
 my $polyALen = 125;
+my $ntog = 0; 
+my $bowtie = 0;
 my $bowtie_path = "";
-my $no_bowtie = 0;
-my $no_ntog = 0; 
 my $bowtie2 = 0;
 my $bowtie2_path = "";
 my $quiet = 0;
@@ -32,9 +35,9 @@ GetOptions("gtf=s" => \$gtfF,
           "no-polyA" => \$no_polyA, 
           "no-polyA-subset=s" => \$subsetFile,
           "polyA-length=i" => \$polyALen,
+          "ntog" => \$no_ntog,
+          "bowtie" => \$bowtie,
           "bowtie-path=s" => \$bowtie_path,
-          "no-bowtie" => \$no_bowtie,
-          "no-ntog" => \$no_ntog,
           "bowtie2" => \$bowtie2,
           "bowtie2-path=s" => \$bowtie2_path,
           "q|quiet" => \$quiet,
@@ -46,12 +49,8 @@ pod2usage(-msg => "--transcript-to-gene-map and --allele-to-gene-map are mutuall
 pod2usage(-msg => "--gtf and --allele-to-gene-map are mutually exclusive!", -exitval => 2, -verbose => 2) if (($gtfF ne "") && ($alleleMappingF ne ""));
 pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 2);
 
-if ($bowtie2) { $no_bowtie = 1; $no_ntog = 1; }
-
-pod2usage(-msg => "If bowtie is used, --no-ntog cannot be set!", -exitval => 2, -verbose => 2) if (!$no_bowtie && $no_ntog);
-
-if ($no_bowtie && ($bowtie_path ne "")) { print "Warning: If bowtie is not used, no need to set --bowtie-path option!\n"; }
-if (!$bowtie2 && ($bowtie2_path ne "")) { print "Warning: If bowtie2 is not used, no need to set --bowtie2-path option!\n"; }
+if (!$bowtie && ($bowtie_path ne "")) { print "Warning: If Bowtie is not used, no need to set --bowtie-path option!\n"; }
+if (!$bowtie2 && ($bowtie2_path ne "")) { print "Warning: If Bowtie 2 is not used, no need to set --bowtie2-path option!\n"; }
  
 my $type;
 
@@ -75,12 +74,11 @@ elsif ($subsetFile ne "") { $polyAChoice = 2; }
 if ($bowtie_path ne "") { $bowtie_path .= "/"; }
 if ($bowtie2_path ne "") { $bowtie2_path .= "/"; }
 
-my $dir = "$FindBin::Bin/";
 my $command = "";
 
 if ($type == 0) {
     $"=" ";
-    $command = $dir."rsem-extract-reference-transcripts $ARGV[1] $quiet $gtfF";
+    $command = "rsem-extract-reference-transcripts $ARGV[1] $quiet $gtfF";
     if ($mappingF ne "") { $command .= " 1 $mappingF"; }
     else { $command .= " 0"; }
     $command .= " @list";
@@ -88,7 +86,7 @@ if ($type == 0) {
 }
 else {
     $"=" ";
-    $command = $dir."rsem-synthesis-reference-transcripts $ARGV[1] $quiet";
+    $command = "rsem-synthesis-reference-transcripts $ARGV[1] $quiet";
     if ($mappingF ne "") { $command .= " 1 $mappingF"; }
     elsif ($alleleMappingF ne "") { $command .= " 2 $alleleMappingF"; }
     else { $command .= " 0"; } 
@@ -96,7 +94,7 @@ else {
     &runCommand($command);
 }
 
-$command = $dir."rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1] -l $polyALen";
+$command = "rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1] -l $polyALen";
 if ($polyAChoice == 2) { $command .= " -f $subsetFile"; }
 if ($no_ntog) { $command .= " --no-ntog"; }
 if ($quiet) { $command .= " -q"; }