From 22ae58b7d063f2a1c7fe90facb7ab68dcfa8e823 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Tue, 8 Mar 2005 17:03:16 +0000
Subject: [PATCH] Fixed bug that was causing a small number of HUGO xrefs to
have null labels (hence xref displayed was numeric HGNC instead).
---
.../xref_mapping/XrefParser/HUGOParser.pm | 44 ++++++++-----------
1 file changed, 19 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm b/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
index 8ffe6a7abe..45881f7e84 100644
--- a/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
@@ -1,37 +1,33 @@
package XrefParser::HUGOParser;
-
+
use strict;
-use POSIX qw(strftime);
use File::Basename;
-
+
use XrefParser::BaseParser;
-
+
use vars qw(@ISA);
@ISA = qw(XrefParser::BaseParser);
-
my $xref_sth ;
my $dep_sth;
-
-
-
+
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
-
+
if (!defined(caller())) {
-
+
if (scalar(@ARGV) != 1) {
print "\nUsage: HUGOParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
-
+
run(@ARGV);
}
-
sub run {
+
my $self = shift if (defined(caller(1)));
my $file = shift;
-
+
my $source_id = shift;
my $species_id = shift;
@@ -44,9 +40,9 @@ sub run {
}
my $dir = dirname($file);
-
+
my %hugo;
-
+
open (ENS4, $dir."/ens4.txt") || die "Can't open hugo ens4 $dir/ens4.txt\n";
#HGNC Symbol Literature Aliases Withdrawn Symbols
#5 A1BG
@@ -57,15 +53,14 @@ sub run {
my @array = split(/\t/,$_);
my $hgnc = $array[0];
my $label = $array[1];
-
- $hugo{$hgnc} = $label
+
+ $hugo{$hgnc} = $label;
+
}
close ENS4;
-
my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
-
my $count = 0;
my $mismatch = 0;
@@ -78,7 +73,7 @@ sub run {
chomp;
my @array = split(/\t/,$_);
my $hgnc = $array[0];
-
+
if ($array[1]) { #swissprot
my $master = $swiss{$array[1]};
my $dep = $hugo{$hgnc};
@@ -91,7 +86,7 @@ sub run {
}
# print "$array[1]\tSPTR\t$hgnc\tHUGO\t$hugo_id{$hgnc}\t$hugo_syn{$hgnc}\tXREF\n";
}
-
+
if ($array[2]) {
my $master = $refseq{$array[2]};
my $dep = $hugo{$hgnc};
@@ -99,7 +94,7 @@ sub run {
$mismatch++;
}
else{
- XrefParser::BaseParser->add_to_xrefs($master,$hgnc,'',$hugo{hgnc},"","",$source_id,$species_id);
+ XrefParser::BaseParser->add_to_xrefs($master,$hgnc,'',$hugo{$hgnc},"","",$source_id,$species_id);
$count++;
}
}
@@ -108,8 +103,7 @@ sub run {
print "\t$count xrefs succesfully loaded\n";
print "\t$mismatch xrefs ignored\n";
}
-
-
+
sub new {
my $self = {};
@@ -117,7 +111,7 @@ sub new {
return $self;
}
-
+
1;
--
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