WHAT_IS_NEW is updated

[rsem.git] / rsem-prepare-reference

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 81fd13ea74edab4b31dd147db9be502e62321167..a74d97d194fce454a99b8714284d67fbf2d3dcfc 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 = "";
@@ -24,8 +27,11 @@ my $bowtie2_path = "";
 my $quiet = 0;
 my $help = 0;
 
+my $alleleMappingF = "";
+
 GetOptions("gtf=s" => \$gtfF,
           "transcript-to-gene-map=s" => \$mappingF,
+          "allele-to-gene-map=s" => \$alleleMappingF,
           "no-polyA" => \$no_polyA, 
           "no-polyA-subset=s" => \$subsetFile,
           "polyA-length=i" => \$polyALen,
@@ -39,6 +45,8 @@ GetOptions("gtf=s" => \$gtfF,
 
 pod2usage(-verbose => 2) if ($help == 1);
 pod2usage(-msg => "Set --no-polyA & --no-polyA-subset at the same time!", -exitval => 2, -verbose => 2) if ($no_polyA == 1 && $subsetFile ne '');
+pod2usage(-msg => "--transcript-to-gene-map and --allele-to-gene-map are mutually exclusive!", -exitval => 2, -verbose => 2) if (($mappingF ne "") && ($alleleMappingF ne ""));
+pod2usage(-msg => "--gtf and --allele-to-gene-map are mutually exclusive!", -exitval => 2, -verbose => 2) if (($gtfF ne "") && ($alleleMappingF ne ""));
 pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 2);
 
 if ($bowtie2) { $no_bowtie = 1; $no_ntog = 1; }
@@ -70,12 +78,11 @@ elsif ($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"; }
     $command .= " @list";
@@ -83,14 +90,15 @@ if ($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"; } 
     $command .= " @list";
     &runCommand($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"; }
@@ -164,6 +172,19 @@ If this option is off, then the mapping of isoforms to genes depends on whether
 
 (Default: off)
 
+=item B<--allele-to-gene-map> <file>
+
+Use information from <file> to provide gene_id and transcript_id information for each allele-specific transcript.
+Each line of <file> should be of the form:
+
+gene_id transcript_id allele_id
+
+with the fields separated by a tab character.
+
+This option is designed for quantifying allele-specific expression. It is only valid if '--gtf' option is not specified. allele_id should be the sequence names presented in the FASTA-formatted files.  
+
+(Default: off) 
+
 =item B<--no-polyA>
 
 Do not add poly(A) tails to the end of reference isoforms. (Default: adding poly(A) tails to all transcripts)