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cbioportal

Merged Chelsea Raulerson requested to merge phg_workflow_ps into master
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@@ -5,7 +5,6 @@ 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 $!;
my $headline = <ENT>;
@@ -36,7 +35,7 @@ print OUT join("\t","FusionName","LeftGene","RightGene","LefttBreakpoint",
print OUTIR join("\t","Hugo_Symbol","Entrez_Gene_Id","Center","Tumor_Sample_Barcode",
"Fusion","DNA_support","RNA_support","Method","Frame"),"\n";
my $sname = (split(/_DNA_panel1385/,$opt{prefix}))[0];
my $sname = $opt{prefix};
open FUSION, "<$opt{fusion}" or die $!;
my $header = <FUSION>;
@@ -62,15 +61,16 @@ while (my $line = <FUSION>) {
$hash{SumRNAReads} += $hash{JunctionReadCount}+$hash{SpanningFragCount};
my $fname = join("--",$hash{LeftGene},$hash{RightGene});
my $fname2 = join("--",sort {$a cmp $b} $hash{LeftGene},$hash{RightGene});
my $ename = join("--",$entrez{$hash{LeftGene}},$entrez{$hash{RightGene}});
my ($dna_support,$rna_support)=("no","no");
my ($dna_support,$rna_support)=("no") x 2;
if ($known{$fname2} && ($hash{SumRNAReads} >= 3)|| ($hash{SumRNAReads} >= 5)) {
$rna_support = "yes";
print OUT join("\t",$fname,$hash{LeftGene},$hash{RightGene},
$hash{LeftBreakpoint},$hash{RightBreakpoint},$hash{LeftStrand},
$hash{RightStrand},$hash{SumRNAReads},0),"\n";
print OUTIR join("\t",$fname,$ename,"UTSW NGS Clinical Sequencing Lab",$sname,$fname." fusion",
0,$rna_support,"STAR 2.5.2b","N/A"),"\n";
print OUTIR join("\t",$hash{LeftGene},$entrez{$hash{LeftGene}},"UTSW",$sname,$fname." fusion",
$dna_support,$rna_support,"STAR Fusion","N/A"),"\n";
print OUTIR join("\t",$hash{RightGene},$entrez{$hash{RightGene}},"UTSW",$sname,$fname." fusion",
$dna_support,$rna_support,"STAR Fusion","N/A"),"\n";
}
}