From 07a64ab8b2b0a6fb6a1afc4b0401e2466f08c2c1 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 9 Nov 2011 10:50:40 +0000
Subject: [PATCH] added option -show_links to show the genes linked to for the
xrefs if a name is given
---
misc-scripts/xref_mapping/xref_data_analysis.pl | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/xref_data_analysis.pl b/misc-scripts/xref_mapping/xref_data_analysis.pl
index 18b11847b2..8174311993 100644
--- a/misc-scripts/xref_mapping/xref_data_analysis.pl
+++ b/misc-scripts/xref_mapping/xref_data_analysis.pl
@@ -10,6 +10,7 @@ my $user;
my $dbname;
my $display_name;
my $source;
+my $show_links;
my $ret = Getopt::Long::GetOptions ('dbname=s' => \$dbname,
'species=s' => \$species,
@@ -18,6 +19,7 @@ my $ret = Getopt::Long::GetOptions ('dbname=s' => \$dbname,
'version=s' => \$version,
'name=s' => \$display_name,
'source=s' => \$source,
+ 'show_links' => \$show_links,
'help' => sub {usage(); exit(0); } );
@@ -120,6 +122,7 @@ sub specific_example {
my ($search_name, $source_name) = @_;
my $db_adap = Bio::EnsEMBL::Registry->get_adaptor($species,"core","dbentry");
+ my $gene_adap = Bio::EnsEMBL::Registry->get_adaptor($species,"core","gene");
my $dbentrys = $db_adap->fetch_all_by_name($search_name, $source_name);
@@ -139,6 +142,13 @@ sub specific_example {
if(defined $dbentry->info_text){
print "info text: ".$dbentry->info_text."\n";
}
+ if($show_links && !($dbentry->info_type =~ /UNMAPPED/ms)){
+ print "Linked to the following genes: ";
+ foreach my $gene (@{$gene_adap->fetch_all_by_external_name($dbentry->primary_id, $dbentry->dbname)}){
+ print $gene->stable_id." ";
+ }
+ print "\n";
+ }
print "##############################\n";
}
if(!$found){
@@ -174,6 +184,8 @@ sub usage {
-source the source name for the accession (i.e. HGNC, MGI, RefSeq_mRNA)
+ -show_links If name used then show which ensembl objects is is linked to.
+
A typical run would be to see what xrefs are there for human :-
perl xref_data_analysis.pl -species human
@@ -196,9 +208,9 @@ sub usage {
To find how a partcular xref was mapped use -name to specify this and -source if more than
one xref may have the same accession
- e.g. how was accession BRCA2 in HGNC mapped to ensembl
+ e.g. how was accession BRCA2 in HGNC mapped to ensembl and to which genes
- perl xref_data_analysis.pl -species human -name BRCA2 -source HGNC
+ perl xref_data_analysis.pl -species human -name BRCA2 -source HGNC -show_links
EOF
--
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