From 32fa063aa4f0c2cbed1e3042e69a5d821d635b9f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 15 Nov 2018 11:27:35 -0600
Subject: [PATCH] update genefusion parser
---
alignment/filter_genefusions.pl | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/alignment/filter_genefusions.pl b/alignment/filter_genefusions.pl
index 6dca268..8ea28ab 100755
--- a/alignment/filter_genefusions.pl
+++ b/alignment/filter_genefusions.pl
@@ -91,6 +91,7 @@ while (my $line = <FUSION>) {
$leftexon = $exonnuminfo{$key}{leftgene};
$rightexon = $exonnuminfo{$key}{rightgene};
}
+ $hash{PROT_FUSION_TYPE} = 'in-frame' if ($hash{PROT_FUSION_TYPE} eq 'INFRAME');
my ($dna_support,$rna_support)=("no") x 2;
if ($known{$fname2} && ($hash{SumRNAReads} >= 3)|| ($hash{SumRNAReads} >= 5)) {
$rna_support = "yes";
@@ -99,11 +100,11 @@ while (my $line = <FUSION>) {
$hash{RightStrand},$hash{SumRNAReads},0),"\n";
print OAS join("\t",$fname,$hash{LeftGene},$hash{LeftBreakpoint},$leftexon,$hash{LeftStrand},
$hash{RightGene},$hash{RightBreakpoint},$rightexon,$hash{RightStrand},
- $hash{SumRNAReads},0,$hash{PROT_FUSION_TYPE},$hash{annots}),"\n";
+ $hash{SumRNAReads},0,lc($hash{PROT_FUSION_TYPE}),$hash{annots}),"\n";
print OUTIR join("\t",$hash{LeftGene},$entrez{$hash{LeftGene}},"UTSW",$sname,$fname." fusion",
- $dna_support,$rna_support,"STAR Fusion","N/A"),"\n";
+ $dna_support,$rna_support,"STAR Fusion",lc($hash{PROT_FUSION_TYPE})),"\n";
print OUTIR join("\t",$hash{RightGene},$entrez{$hash{RightGene}},"UTSW",$sname,$fname." fusion",
- $dna_support,$rna_support,"STAR Fusion","N/A"),"\n";
+ $dna_support,$rna_support,"STAR Fusion",lc($hash{PROT_FUSION_TYPE})),"\n";
}
}
--
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