From b92e058dc255a46fee7ad9d02be03ed2062ff663 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 21 Jul 2020 20:25:54 -0500
Subject: [PATCH] remove biohpc hardcoded path
---
genect_rnaseq/fpkm_subset_panel.pl | 4 ++--
genect_rnaseq/geneabundance.sh | 3 ++-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/genect_rnaseq/fpkm_subset_panel.pl b/genect_rnaseq/fpkm_subset_panel.pl
index 9b611ec..4c37da5 100755
--- a/genect_rnaseq/fpkm_subset_panel.pl
+++ b/genect_rnaseq/fpkm_subset_panel.pl
@@ -9,14 +9,14 @@ my ($genelist,$fpkm_file) = ("") x 2;
GetOptions( 'g|genes=s' => \$genelist,
'f|fpkm=s' => \$fpkm_file,
- 'i|refinfo=s'=> \$refinfo);
+ 'i|geneinfo=s'=> \$refinfo);
my $fpkm_out = $fpkm_file;
$fpkm_out =~ s/\.fpkm.+txt/\.fpkm.capture.txt/;
open OUT, ">$fpkm_out" or die $!;
#gene_info.human.txt file is required for gene alias information
-open GENEINFO, "<$refinfo/gene_info.human.txt" or die $!;
+open GENEINFO, "<$geneinfo" or die $!;
my %geneinfo;
while(my $gline = <GENEINFO>){
chomp $gline;
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index 7eb6d3f..8f6f6d7 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -19,6 +19,7 @@ do
p) pair_id=$OPTARG;;
s) stranded=$OPTARG;;
f) filter=$OPTARG;;
+ i) ginfo=$OPTARG;;
h) usage;;
esac
done
@@ -54,6 +55,6 @@ if [[ -f $filter ]]
then
cd ..
mv ${pair_id}.fpkm.txt ${prefix}.fpkm.ori.txt
- perl ${baseDir}/fpkm_subset_panel.pl -f ${prefix}.fpkm.ori.txt -g $filter
+ perl ${baseDir}/fpkm_subset_panel.pl -f ${prefix}.fpkm.ori.txt -g $filter -i $ginfo
mv ${prefix}.fpkm.capture.txt ${pair_id}.fpkm.txt
fi
--
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