Skip to content
Snippets Groups Projects
Commit 47b225a3 authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

confounding symbols on multiple chrs

parent 77c74abb
Branches
Tags
No related merge requests found
......@@ -15,7 +15,7 @@ while (my $line = <SYM>) {
chomp($line);
my ($chrom,$start,$end,$ensembl,$symbol,$type) = split(/\t/,$line);
$ensembl = (split(/\./,$ensembl))[0];
$names{$ensembl} = {symbol=>$symbol,type=>$type};
$names{$ensembl} = {chr=>$chrom,symbol=>$symbol,type=>$type};
}
my @files = @ARGV;
......@@ -32,8 +32,13 @@ foreach $file (@files) {
while (my $line = <IN>) {
chomp($line);
my ($ensid,$gene,$chr,$strand,$start,$end,$cov,$fpkm,$tmp) = split(/\t/,$line);
my ($ens,$version) = split(/\./,$ensid);
$cts{$ens}{$sample} = $fpkm;
my $ens = $ensid;
$ens =~ s/\.\d+//;
if ($chr eq $names{$ens}{chr}) {
$cts{$ens}{$sample} = $fpkm;
}else {
warn "unable to map to genenames\n";
}
}
close IN;
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment