From 91b0ea397517c36f58cb7f61ea8a06946c65e6f7 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 21 Jul 2020 20:01:57 -0500
Subject: [PATCH] full path in fpkm subset
---
genect_rnaseq/fpkm_subset_panel.pl | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/genect_rnaseq/fpkm_subset_panel.pl b/genect_rnaseq/fpkm_subset_panel.pl
index baa830a..9b611ec 100755
--- a/genect_rnaseq/fpkm_subset_panel.pl
+++ b/genect_rnaseq/fpkm_subset_panel.pl
@@ -8,14 +8,15 @@ use Getopt::Long;
my ($genelist,$fpkm_file) = ("") x 2;
GetOptions( 'g|genes=s' => \$genelist,
- 'f|fpkm=s' => \$fpkm_file);
+ 'f|fpkm=s' => \$fpkm_file,
+ 'i|refinfo=s'=> \$refinfo);
my $fpkm_out = $fpkm_file;
$fpkm_out =~ s/\.fpkm.+txt/\.fpkm.capture.txt/;
open OUT, ">$fpkm_out" or die $!;
#gene_info.human.txt file is required for gene alias information
-open GENEINFO, "</project/shared/bicf_workflow_ref/human/gene_info.human.txt" or die $!;
+open GENEINFO, "<$refinfo/gene_info.human.txt" or die $!;
my %geneinfo;
while(my $gline = <GENEINFO>){
chomp $gline;
--
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