From 9dd921b126f99b0ac330cfef1210cebed7e6a411 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Tue, 2 Mar 2004 09:26:48 +0000
Subject: [PATCH] updated for changes related to seq_region_attribs
---
.../density_feature/seq_region_stats.pl | 42 ++++++++++++-------
1 file changed, 27 insertions(+), 15 deletions(-)
diff --git a/misc-scripts/density_feature/seq_region_stats.pl b/misc-scripts/density_feature/seq_region_stats.pl
index d07f4d6262..535784c2d6 100644
--- a/misc-scripts/density_feature/seq_region_stats.pl
+++ b/misc-scripts/density_feature/seq_region_stats.pl
@@ -1,12 +1,12 @@
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
-
+use Bio::EnsEMBL::Attribute;
my $host = 'ecs1g';
-my $user = '';
-my $pass = '';
+my $user = 'ensadmin';
+my $pass = 'ensembl';
my $dbname = 'homo_sapiens_core_20_34';
my $port = '3306';
@@ -18,6 +18,7 @@ my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
my $slice_adaptor = $db->get_SliceAdaptor();
+my $attrib_adaptor = $db->get_AttributeAdaptor();
my @chromosomes = @{$slice_adaptor->fetch_all('chromosome')};
@@ -41,13 +42,27 @@ foreach my $chromosome (@chromosomes) {
}
}
- $slice_adaptor->set_seq_region_attrib($chromosome,
- 'GeneCount', $num_genes);
- $slice_adaptor->set_seq_region_attrib($chromosome,
- 'KnownGeneCount', $num_known_genes);
+ my @attribs;
+
+ 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');
- $slice_adaptor->set_seq_region_attrib($chromosome,
- 'PseudoGeneCount', $num_pseudo_genes);
+ push @attribs, Bio::EnsEMBL::Attribute->new
+ (-NAME => 'PseudoGene Count',
+ -CODE => 'PseudoGeneCount',
+ -VALUE => $num_pseudo_genes,
+ -DESCRIPTION => 'Total Number of PseudoGenes');
+
+ $attrib_adaptor->store_on_Slice($chromosome, \@attribs);
}
@@ -58,12 +73,9 @@ sub print_chromo_stats {
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";
+ foreach my $attrib (@{$chr->get_all_Attributes()}) {
+ print " ", $attrib->name(), ": ", $attrib->value(), "\n";
+ }
}
}
--
GitLab