From f7658f8fe92d3e8871380995d20c6f0ca4ea4f4d Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 22 Dec 2017 08:00:48 +0000
Subject: [PATCH] can read db from db_url option
---
misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm | 3 +++
misc-scripts/xref_mapping/XrefParser/RFAMParser.pm | 5 ++++-
.../xref_mapping/XrefParser/RefSeqCoordinateParser.pm | 4 ++++
3 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm b/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm
index 532ecc944d..aee71d17a6 100644
--- a/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm
@@ -40,6 +40,7 @@ sub run_script {
my $species_id = $ref_arg->{species_id};
my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
+ my $db = $ref_arg->{dba};
if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and file as pairs";
@@ -123,6 +124,8 @@ sub run_script {
},
);
$gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene');
+ } elsif (defined $db) {
+ $gene_adaptor = $db->get_GeneAdaptor();
} else {
die("Missing or unsupported project value. Supported values: ensembl, ensemblgenomes");
}
diff --git a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
index 4110558200..def94e241e 100644
--- a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
@@ -33,8 +33,9 @@ sub run_script {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
- my $file = $ref_arg->{file};
+ my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
+ my $core_db = $ref_arg->{db};
if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and file as pairs";
@@ -86,6 +87,8 @@ sub run_script {
'-species' => $species_name,
'-group' => 'core',
);
+ } elsif (defined $core_db) {
+ $dba = $core_db;
} else {
$registry->load_registry_from_multiple_dbs(
{
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
index b855ec950a..b650d3e20d 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
@@ -34,6 +34,7 @@ sub run_script {
my $species_id = $ref_arg->{species_id};
my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
+ my $db = $ref_arg->{dba};
if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and file as pairs";
@@ -189,6 +190,9 @@ sub run_script {
$core_dba = $registry->get_DBAdaptor($species_name,'core');
$otherf_dba = $registry->get_DBAdaptor($species_name, 'otherfeatures');
+ } elsif (defined $db) {
+ $otherf_dba = $db;
+ $core_dba = $db->dnadb();
} else {
die("Missing or unsupported project value. Supported values: ensembl, ensemblgenomes");
}
--
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