From 7e6448ca6511040a5244072f36cb5a301c224a89 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 27 Feb 2004 11:49:06 +0000
Subject: [PATCH] script to calculate some stats on chromosomes (gene counts)
---
.../density_feature/seq_region_stats.pl | 73 +++++++++++++++++++
1 file changed, 73 insertions(+)
create mode 100644 misc-scripts/density_feature/seq_region_stats.pl
diff --git a/misc-scripts/density_feature/seq_region_stats.pl b/misc-scripts/density_feature/seq_region_stats.pl
new file mode 100644
index 0000000000..d07f4d6262
--- /dev/null
+++ b/misc-scripts/density_feature/seq_region_stats.pl
@@ -0,0 +1,73 @@
+use strict;
+
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+
+
+my $host = 'ecs1g';
+my $user = '';
+my $pass = '';
+my $dbname = 'homo_sapiens_core_20_34';
+my $port = '3306';
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
+ -user => $user,
+ -port => $port,
+ -pass => $pass,
+ -dbname => $dbname);
+
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+
+my @chromosomes = @{$slice_adaptor->fetch_all('chromosome')};
+
+foreach my $chromosome (@chromosomes) {
+ my $num_known_genes = 0;
+ my $num_genes = 0;
+ my $num_pseudo_genes = 0;
+
+ print "Processing chromosome ", $chromosome->seq_region_name(), "\n";
+
+ my @genes = @{$chromosome->get_all_Genes()};
+
+ foreach my $gene (@genes) {
+ if($gene->type() eq 'pseudogene') {
+ $num_pseudo_genes++;
+ } else {
+ $num_genes++;
+ if($gene->is_known()) {
+ $num_known_genes++;
+ }
+ }
+ }
+
+ $slice_adaptor->set_seq_region_attrib($chromosome,
+ 'GeneCount', $num_genes);
+ $slice_adaptor->set_seq_region_attrib($chromosome,
+ 'KnownGeneCount', $num_known_genes);
+
+ $slice_adaptor->set_seq_region_attrib($chromosome,
+ 'PseudoGeneCount', $num_pseudo_genes);
+}
+
+
+print_chromo_stats(\@chromosomes);
+
+sub print_chromo_stats {
+ my $chromosomes = shift;
+
+ foreach my $chr (@$chromosomes) {
+ print "\nchromosome: ",$chr->seq_region_name(),"\n";
+ my ($num_genes) = $chr->get_attribute('GeneCount');
+ my ($num_known) = $chr->get_attribute('KnownGeneCount');
+ my ($num_pseudo) = $chr->get_attribute('PseudoGeneCount');
+ print "NumGenes: $num_genes\n";
+ print "NumKnown: $num_known\n";
+ print "NumPseudo: $num_pseudo\n";
+ }
+}
+
+
+1;
+
+
--
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