From a1e0f0f1ae2d7e1f90d6a0d448b1bedaa922cdb5 Mon Sep 17 00:00:00 2001
From: Daniel Sobral <ds19@sanger.ac.uk>
Date: Thu, 2 Jun 2011 14:21:22 +0000
Subject: [PATCH] Added extra biotype
---
misc-scripts/density_feature/seq_region_stats.pl | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/density_feature/seq_region_stats.pl b/misc-scripts/density_feature/seq_region_stats.pl
index 73a5886ec0..379a5b757e 100644
--- a/misc-scripts/density_feature/seq_region_stats.pl
+++ b/misc-scripts/density_feature/seq_region_stats.pl
@@ -35,6 +35,7 @@ my %attrib_codes = ( 'miRNA' => 'miRNA',
'Mt_tRNA' => 'MTtRNA',
'Mt_rRNA' => 'MTrRNA',
'ncRNA' => 'ncRNA',
+ '3prime_overlapping_ncrna' => 'ncRNA', # (v63)
'polymorphic_pseudogene' => 'pseudo',
'havana_pseudogene' => 'pseudo',
'processed_pseudogene' => 'pseudo',
@@ -158,12 +159,12 @@ foreach my $name (@dbnames) {
if($genes_present) {
my %counts;
- my $biotype;
my $genes = $slice->get_all_Genes();
while (my $gene = shift(@{$genes})) {
- $biotype = $gene->biotype();
+
+ my $biotype = $gene->biotype();
if( $biotype =~ /coding/i ) {
if($gene->is_known()) {
$biotype = "known ".$biotype;
@@ -173,6 +174,7 @@ foreach my $name (@dbnames) {
}
$counts{$biotype}++;
+
}
for my $biotype ( keys %counts ) {
@@ -181,6 +183,7 @@ foreach my $name (@dbnames) {
print STDERR "Unspecified biotype \"$biotype\" in database $name.\n";
next;
}
+
# not used:
# my $no_space = $biotype;
# $no_space =~ s/ /_/g;
--
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