From cf9b604fe43bade885b7102031aa56e684356b61 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 23 Jan 2019 11:20:18 -0600
Subject: [PATCH] update concat fpkm on ensid
---
genect_rnaseq/concat_fpkm.pl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/genect_rnaseq/concat_fpkm.pl b/genect_rnaseq/concat_fpkm.pl
index a0eebb1..9bda30a 100755
--- a/genect_rnaseq/concat_fpkm.pl
+++ b/genect_rnaseq/concat_fpkm.pl
@@ -15,7 +15,7 @@ while (my $line = <SYM>) {
chomp($line);
my ($chrom,$start,$end,$ensembl,$symbol,$type) = split(/\t/,$line);
$ensembl = (split(/\./,$ensembl))[0];
- $names{$symbol} = {ensembl=>$ensembl,type=>$type};
+ $names{$ensembl} = {symbol=>$symbol,type=>$type};
}
my @files = @ARGV;
@@ -32,7 +32,7 @@ foreach $file (@files) {
while (my $line = <IN>) {
chomp($line);
my ($ensid,$gene,$chr,$strand,$start,$end,$cov,$fpkm,$tmp) = split(/\t/,$line);
- $cts{$gene}{$sample} = $fpkm;
+ $cts{$ensid}{$sample} = $fpkm;
}
close IN;
}
@@ -57,7 +57,7 @@ foreach $gene (keys %cts) {
#next unless ($sortct[0] >= 1);
next if ($names{$gene}{type} eq 'rRNA');
next if ($exc{$gene});
- print OUT join("\t",$names{$gene}{ensembl},$gene,
+ print OUT join("\t",$gene,$names{$gene}{symbol},
$names{$gene}{type},@line),"\n";
}
close OUT;
--
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