From 1e078e990dfaa9dfbd276a5044977e2707d624fc Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sun, 10 Feb 2019 19:45:59 -0600
Subject: [PATCH] file name locations
---
alignment/filter_genefusions.pl | 2 +-
alignment/starfusion.sh | 2 +-
genect_rnaseq/cBioPortal_documents.pl | 4 ++--
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/alignment/filter_genefusions.pl b/alignment/filter_genefusions.pl
index 8ea28ab..44b4453 100755
--- a/alignment/filter_genefusions.pl
+++ b/alignment/filter_genefusions.pl
@@ -6,7 +6,7 @@ use Getopt::Long qw(:config no_ignore_case no_auto_abbrev);
my %opt = ();
my $results = GetOptions (\%opt,'fusion|f=s','prefix|p=s','help|h');
my %entrez;
-open ENT, "</project/shared/bicf_workflow_ref/gene_info.human.txt" or die $!;
+open ENT, "</project/shared/bicf_workflow_ref/human/gene_info.human.txt" or die $!;
my $headline = <ENT>;
while (my $line = <ENT>) {
chomp($line);
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 619569c..73599fb 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -60,7 +60,7 @@ else
cp ${pair_id}_star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
fi
-module load singularity/2.6.0
+module load singularity/2.6.1
export PYENSEMBL_CACHE_DIR="/project/shared/bicf_workflow_ref/singularity_images"
cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "singularity exec /project/shared/bicf_workflow_ref/singularity_images/agfusion.simg agfusion annotate -db /project/shared/bicf_workflow_ref/singularity_images/pyensembl/GRCh38/ensembl92/agfusion.homo_sapiens.92.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
diff --git a/genect_rnaseq/cBioPortal_documents.pl b/genect_rnaseq/cBioPortal_documents.pl
index fd0a8ba..25a816e 100644
--- a/genect_rnaseq/cBioPortal_documents.pl
+++ b/genect_rnaseq/cBioPortal_documents.pl
@@ -6,7 +6,7 @@ use File::Basename;
my $results= GetOptions (\%opt,'fpkm|f=s','logcpm|l=s','cnv|c=s','prefix|p=s','help|h');
-open ENT_ENS, "</project/shared/bicf_workflow_ref/gene_info.human.txt" or die $!;
+open ENT_ENS, "</project/shared/bicf_workflow_ref/human/gene_info.human.txt" or die $!;
my %entrez;
my $ent_header = <ENT_ENS>;
while (my $line = <ENT_ENS>){
@@ -24,7 +24,7 @@ while (my $line = <ENT_ENS>){
$entrez{$row[3]}=$entrez{$row[4]};
}
close ENT_ENS;
-open ENT_ENS, "</project/shared/bicf_workflow_ref/gene2ensembl.human.txt" or die $!;
+open ENT_ENS, "</project/shared/bicf_workflow_ref/human/gene2ensembl.human.txt" or die $!;
my $ens_header = <ENT_ENS>;
while (my $line = <ENT_ENS>){
chomp $line;
--
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