From e5d968a41e922d285548db9ae166388d4f55627e Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Thu, 24 Nov 2005 14:27:17 +0000
Subject: [PATCH] new gene counts by biotype
---
.../density_feature/seq_region_stats.pl | 68 ++++++++++++-------
1 file changed, 42 insertions(+), 26 deletions(-)
diff --git a/misc-scripts/density_feature/seq_region_stats.pl b/misc-scripts/density_feature/seq_region_stats.pl
index 0ab7b04eca..9925eb1ea4 100644
--- a/misc-scripts/density_feature/seq_region_stats.pl
+++ b/misc-scripts/density_feature/seq_region_stats.pl
@@ -22,6 +22,22 @@ my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
-dbname => $dbname);
+my %attrib_codes = ( 'miRNA' => 'miRNA',
+ 'snRNA' => 'snRNA',
+ 'snoRNA' => 'snoRNA',
+ 'rRNA' => 'rRNA',
+ 'tRNA' => 'tRNA',
+ 'known protein_coding' => 'knwCod',
+ 'misc_RNA' => 'mscRNA',
+ 'novel protein_coding' => 'novCod',
+ 'pseudogene' => 'pseudo',
+ 'scRNA' => 'scRNA',
+ 'Mt-tRNA' => 'MTtRNA',
+ 'Mt-rRNA' => 'MTrRNA');
+
+
+
+
# do both genestats and snpstats by default
$genestats = $snpstats = 1 if(!$genestats && !$snpstats);
@@ -69,39 +85,39 @@ foreach my $slice (@$top_slices) {
my @attribs;
if($genes_present) {
- my $num_known_genes = 0;
- my $num_genes = 0;
- my $num_pseudo_genes = 0;
+ my %counts;
+ my $biotype;
my @genes = @{$slice->get_all_Genes()};
-
+
foreach my $gene (@genes) {
- if($gene->type() =~ /pseudogene/i) {
- $num_pseudo_genes++;
- } else {
- $num_genes++;
+ $biotype = $gene->biotype();
+ if( $biotype =~ /coding/i ) {
if($gene->is_known()) {
- $num_known_genes++;
- }
+ $biotype = "known ".$biotype;
+ } else {
+ $biotype = "novel ".$biotype;
+ }
}
- }
- push @attribs, Bio::EnsEMBL::Attribute->new
- (-NAME => 'Gene Count',
- -CODE => 'GeneCount',
- -VALUE => $num_genes,
- -DESCRIPTION => 'Total Number of Genes');
- push @attribs, Bio::EnsEMBL::Attribute->new
- (-NAME => 'Known Gene Count',
- -CODE => 'KnownGeneCount',
- -VALUE => $num_known_genes,
- -DESCRIPTION => 'Total Number of Known Genes');
+ $counts{$biotype}++;
+ }
- push @attribs, Bio::EnsEMBL::Attribute->new
- (-NAME => 'PseudoGene Count',
- -CODE => 'PseudoGeneCount',
- -VALUE => $num_pseudo_genes,
- -DESCRIPTION => 'Total Number of PseudoGenes');
+ for my $biotype ( keys %counts ) {
+ my $attrib_code = $attrib_codes{$biotype};
+ if( !$attrib_code ) {
+ print STDERR "Unspecified biotype \"$biotype\".\n";
+ next;
+ }
+ my $no_space = $biotype;
+ $no_space =~ s/ /_/g;
+
+ push @attribs, Bio::EnsEMBL::Attribute->new
+ (-NAME => $biotype.' Gene Count',
+ -CODE => 'GeneNo_'.$attrib_code,
+ -VALUE => $counts{$biotype},
+ -DESCRIPTION => 'Number of '.$biotype.' Genes');
+ }
}
if( $snps_present ) {
--
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