Commits (2)
......@@ -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);
......@@ -29,6 +29,8 @@ while (my $line = <OM>) {
my @exonfiles = `ls */*.exons.txt`;
foreach $efile (@exonfiles) {
chomp($efile);
my @leftexons;
my @rightexons;
my ($dir,$pair,@etc) = split(/\/|\./,$efile);
open EFILE, "<$efile" or die $!;
my $header = <EFILE>;
......
......@@ -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/3.0.2
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
......
......@@ -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;
......