From 5bf17195244a100233a94707065945067c500964 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 17 Nov 2004 15:54:25 +0000
Subject: [PATCH] check for correct species
---
.../xref_mapping/XrefParser/UniProtParser.pm | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index 1aca898d0a..7dd725462d 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -22,7 +22,7 @@ use vars qw(@ISA);
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
- print "\nUsage: UniProtParser.pm file.SPC\n\n";
+ print "\nUsage: UniProtParser.pm file.SPC <soure_id> <species_id>\n\n";
exit(1);
}
@@ -37,11 +37,14 @@ sub run {
my $self = shift if (defined(caller(1)));
my $file = shift;
my $source_id = shift;
+ my $species_id = shift;
+ my $species_name;
my ($sp_source_id, $sptr_source_id);
- my ($species_id, $species_name) = get_species($file);
-
+ if(!defined($species_id)){
+ ($species_id, $species_name) = get_species($file);
+ }
$sp_source_id = XrefParser::BaseParser->get_source_id_for_source_name('Uniprot/SWISSPROT');
$sptr_source_id = XrefParser::BaseParser->get_source_id_for_source_name('Uniprot/SPTREMBL');
print "SwissProt source id for $file: $sp_source_id\n";
@@ -101,7 +104,8 @@ sub create_xrefs {
my ($sp_source_id, $sptr_source_id, $species_id, $file) = @_;
- my ($num_sp, $num_sptr) = 0;
+ my $num_sp = 0;
+ my $num_sptr = 0;
my %dependent_sources = XrefParser::BaseParser->get_dependent_xref_sources(); # name-id hash
@@ -119,8 +123,9 @@ sub create_xrefs {
if (defined $ox) {
my $taxon = $1;
my %taxonomy2species_id = XrefParser::BaseParser->taxonomy2species_id();
- if (!exists $taxonomy2species_id{$taxon}) {
- print "Skipping xref for species with taxonomy ID $taxon\n";
+ if (!exists $taxonomy2species_id{$taxon}
+ or $taxonomy2species_id{$taxon} ne $species_id) {
+# print "Skipping xref for species with taxonomy ID $taxon\n";
next;
}
}
--
GitLab