From 5453e5d323b3b216bb3ab6ada51025b3b577e73a Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 2 Jun 2016 11:49:05 +0100
Subject: [PATCH] ENSCORESW-1741: add VGNC source for vertebrate naming
---
.../xref_mapping/XrefParser/HGNCParser.pm | 9 +-
misc-scripts/xref_mapping/xref_config.ini | 89 +++++++++++++++++++
2 files changed, 95 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
index fe7ca4c2ed..ae2296296d 100644
--- a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
@@ -59,7 +59,9 @@ sub run {
return 1;
}
- my $name_to_source_id = $self->get_hgnc_sources();
+ my $source_name = $self->get_source_name_for_source_id($source_id);
+
+ my $name_to_source_id = $self->get_sources($source_name);
# Skip header
$hugo_io->getline();
@@ -259,15 +261,16 @@ sub run {
-sub get_hgnc_sources {
+sub get_sources {
my $self = shift;
+ my $source_name = shift;
my %name_to_source_id;
my @sources = ('entrezgene_manual', 'refseq_manual', 'entrezgene_mapped', 'refseq_mapped', 'ensembl_manual', 'swissprot_manual', 'desc_only');
foreach my $key (@sources) {
- my $source_id = $self->get_source_id_for_source_name('HGNC', $key);
+ my $source_id = $self->get_source_id_for_source_name($source_name, $key);
if(!(defined $source_id)){
die 'Could not get source id for HGNC and '. $key ."\n";
}
diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini
index 899e49917f..30b020b481 100644
--- a/misc-scripts/xref_mapping/xref_config.ini
+++ b/misc-scripts/xref_mapping/xref_config.ini
@@ -1102,6 +1102,85 @@ parser = CGNCParser
release_uri =
data_uri = http://birdgenenames.org/cgnc/downloads.jsp?file=standard
+[source VGNC::MULTI]
+# Used by pan_troglodytes
+name = VGNC
+download = Y
+order = 29
+priority = 1
+parser = HGNCParser
+release_uri =
+data_uri = file:VGNC_to_Ensembl_mapping.txt.gz
+
+[source VGNC::MULTI#01]
+name = VGNC
+download = N
+order = 30
+priority = 5
+prio_descr = refseq_manual
+parser = HGNCParser
+release_uri =
+data_uri =
+
+[source VGNC::MULTI#02]
+name = VGNC
+download = N
+order = 30
+priority = 5
+prio_descr = swissprot_manual
+parser = HGNCParser
+release_uri =
+data_uri =
+
+[source VGNC::MULTI#03]
+name = VGNC
+download = N
+order = 30
+priority = 5
+prio_descr = ensembl_manual
+parser = HGNCParser
+release_uri =
+data_uri =
+
+[source VGNC::MULTI#04]
+name = VGNC
+download = N
+order = 30
+priority = 6
+prio_descr = entrezgene_mapped
+parser = HGNCParser
+release_uri =
+data_uri =
+
+[source VGNC::MULTI#05]
+name = VGNC
+download = N
+order = 30
+priority = 7
+prio_descr = refseq_mapped
+parser = HGNCParser
+release_uri =
+data_uri =
+
+[source VGNC::MULTI#06]
+name = VGNC
+download = N
+order = 30
+priority = 7
+prio_descr = desc_only
+parser = HGNCParser
+release_uri =
+data_uri =
+
+[source VGNC::MULTI#07]
+name = VGNC
+download = N
+order = 30
+priority = 6
+prio_descr = entrezgene_manual
+parser = HGNCParser
+release_uri =
+data_uri =
[source HGNC::homo_sapiens#01]
# Used by homo_sapiens
@@ -3979,6 +4058,15 @@ prio_descr =
parser = done_in_official_naming
release_uri =
+[source VGNC_trans_name]
+name = VGNC_trans_name
+download = N
+order = 49
+priority = 1
+prio_descr =
+parser = done_in_official_naming
+release_uri =
+
[source HGNC_gene_name]
name = HGNC_gene_name
download = N
@@ -6570,6 +6658,7 @@ source = ArrayExpress::MULTI
[species pan_troglodytes]
taxonomy_id = 9598
aliases = pantroglodytes, ptroglodytes, chimpanzee, chimp
+source = VGNC::MULTI
source = EntrezGene::MULTI
source = GO::MULTI
source = Reactome::MULTI
--
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