From 32cf1ef26b6e14fd7b6d0fc123a2180ebe53357c Mon Sep 17 00:00:00 2001
From: Rhoda Kinsella <rhoda@ebi.ac.uk>
Date: Thu, 31 Jul 2008 13:36:01 +0000
Subject: [PATCH] Update to add synonyms and remove data from the linkage_xref
column
---
.../xref_mapping/XrefParser/DBASSParser.pm | 40 ++++++++++++++++++-
1 file changed, 38 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
index 14d0929d67..6086efb561 100644
--- a/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
@@ -3,6 +3,8 @@ package XrefParser::DBASSParser;
use strict;
use base qw( XrefParser::BaseParser);
+use DBI;
+use Carp;
# This parser will read direct xrefs from a simple comma-delimited file downloaded from the DBASS database.
# The columns of the file should be the following:
@@ -12,6 +14,10 @@ use base qw( XrefParser::BaseParser);
# 3) Ensembl Gene ID
+my $dbi;
+my $xref_id;
+my $source_id;
+
sub new {
my $proto = shift;
@@ -21,6 +27,7 @@ sub new {
return $self;
}
+
sub run {
my $self = shift;
@@ -52,10 +59,28 @@ sub run {
return 1;
}
- my $label = $dbass_gene_name;
+
+ my $first_gene_name;
+ my $second_gene_name;
+
+
+ if ($dbass_gene_name =~ /.\/./){
+ ($first_gene_name, $second_gene_name) = split( /\//, $dbass_gene_name );
+ }
+
+ if ($dbass_gene_name =~ /(.*)\((.*)\)/){
+ $first_gene_name = $1;
+ $second_gene_name = $2;
+ print $first_gene_name, "\n", $second_gene_name, "\n";
+ }
+
+
+
+ my $label = $first_gene_name;
my $type = 'gene';
my $description = '';
my $version = '1';
+ my $synonym = $second_gene_name;
++$parsed_count;
@@ -65,8 +90,18 @@ sub run {
$xref_id = XrefParser::BaseParser->add_xref($dbass_gene_id, $version, $label, $description, $source_id, $species_id);
}
+ XrefParser::BaseParser->add_direct_xref( $xref_id, $ensembl_id, $type, '');
+
+ if (defined ($synonym)) {
+ XrefParser::DBASSParser->add_synonym($xref_id, $synonym);
+ }
+ elsif ($synonym =~ /^\s/){
+ print "There is white space! \n";
+ }
+ else {
+ next;
+ }
- XrefParser::BaseParser->add_direct_xref( $xref_id, $ensembl_id, $type, $dbass_gene_id);
} ## end while ( defined( my $line...
@@ -79,4 +114,5 @@ sub run {
return 0;
} ## end sub run
+
1;
--
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