From d66b8d395c4cb036a2bb0b8064ce588e01eb8de8 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 22 Sep 2011 09:50:03 +0000
Subject: [PATCH] add_xref now takes a hash instead of a list for easy
maintainance.
---
.../xref_mapping/XrefParser/AnoXcelParser.pm | 7 +-
.../xref_mapping/XrefParser/CCDSParser.pm | 7 +-
.../xref_mapping/XrefParser/DBASSParser.pm | 8 ++-
.../xref_mapping/XrefParser/DirectParser.pm | 12 ++--
.../xref_mapping/XrefParser/EG_DBParser.pm | 7 +-
.../XrefParser/EntrezGeneParser.pm | 16 ++++-
.../xref_mapping/XrefParser/FlybaseParser.pm | 44 +++++++++----
.../xref_mapping/XrefParser/GOParser.pm | 66 +++++++++++--------
.../xref_mapping/XrefParser/GOSlimParser.pm | 7 +-
.../xref_mapping/XrefParser/HGNCParser.pm | 23 +++++--
.../XrefParser/HGNC_CCDSParser.pm | 11 +++-
.../xref_mapping/XrefParser/HPAParser.pm | 8 ++-
.../xref_mapping/XrefParser/IKMCParser.pm | 7 +-
.../xref_mapping/XrefParser/ImmunoDBParser.pm | 7 +-
.../xref_mapping/XrefParser/MGIParser.pm | 9 ++-
.../XrefParser/MGI_Desc_Parser.pm | 7 +-
.../xref_mapping/XrefParser/MIMParser.pm | 29 ++++++--
.../xref_mapping/XrefParser/OTTTParser.pm | 6 +-
.../xref_mapping/XrefParser/PomBaseParser.pm | 26 ++++++--
.../xref_mapping/XrefParser/RGDParser.pm | 16 +++--
.../XrefParser/RefSeq_CCDSParser.pm | 9 ++-
.../xref_mapping/XrefParser/SGDParser.pm | 16 ++++-
.../xref_mapping/XrefParser/SegmentParser.pm | 8 ++-
.../XrefParser/UniProtDirectParser.pm | 10 ++-
.../XrefParser/VBCommunitySymbolParser.pm | 7 +-
.../XrefParser/VBExternalDescriptionParser.pm | 7 +-
.../xref_mapping/XrefParser/VBPubMedParser.pm | 7 +-
.../XrefParser/VBRNADescriptionParser.pm | 7 +-
.../XrefParser/VBribosomalParser.pm | 7 +-
.../xref_mapping/XrefParser/VbDirectParser.pm | 8 ++-
.../XrefParser/VegaOfficialNameParser.pm | 9 ++-
.../XrefParser/WilsonAffyParser.pm | 7 +-
.../xref_mapping/XrefParser/WormPepParser.pm | 12 +++-
.../WormbaseDatabaseStableIDParser.pm | 12 ++--
.../xref_mapping/XrefParser/ZFINDescParser.pm | 7 +-
.../XrefParser/curated_transcriptParser.pm | 24 ++++++-
.../xref_mapping/XrefParser/ncRNAParser.pm | 7 +-
.../xref_mapping/XrefParser/ncRNA_DBParser.pm | 7 +-
38 files changed, 381 insertions(+), 113 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm b/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm
index 8fbae67a98..5c1714b7a8 100644
--- a/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm
@@ -48,7 +48,12 @@ sub run {
my $xref_id = $self->get_xref($gene_id,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($gene_id,"", $gene_id, $gene_id, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $gene_id,
+ label => $gene_id,
+ desc =>$gene_id,
+ source_id => $source_id,
+ species_id =>$species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(defined($gene_id) and $gene_id ne "-"){
diff --git a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
index 50ae7cc20c..fef1ae2979 100644
--- a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
@@ -83,7 +83,12 @@ SCD
my $xref_id;
if (!defined($seen{$display_label})) {
- $xref_id = $self->add_xref($acc, $version, $display_label, "", $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $acc,
+ version => $version,
+ label => $display_label,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$xref_count++;
$seen{$display_label} = $xref_id;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
index 323ff5d77d..2a200bf567 100644
--- a/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
@@ -84,7 +84,13 @@ sub run {
my $xref_id = $self->get_xref( $dbass_gene_id, $source_id, $species_id );
if ( !defined($xref_id) || $xref_id eq '' ) {
- $xref_id = $self->add_xref($dbass_gene_id, $version, $label, $description, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $dbass_gene_id,
+ version => $version,
+ label => $label,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
}
$self->add_direct_xref( $xref_id, $ensembl_id, $type, '');
diff --git a/misc-scripts/xref_mapping/XrefParser/DirectParser.pm b/misc-scripts/xref_mapping/XrefParser/DirectParser.pm
index b8f3c833a6..5d36e5607d 100644
--- a/misc-scripts/xref_mapping/XrefParser/DirectParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/DirectParser.pm
@@ -66,11 +66,13 @@ sub run {
if ( !defined($xref_id) || $xref_id eq '' ) {
$xref_id =
- $self->add_xref(
- $accession, $version, $label,
- $description, $source_id, $species_id,
- "DIRECT"
- );
+ $self->add_xref({ acc => $accession,
+ version => $version,
+ label => $label,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
}
$self->add_direct_xref( $xref_id, $ensembl_id,
$type, $accession );
diff --git a/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm b/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm
index c481a6b5af..473519ba04 100644
--- a/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm
@@ -91,7 +91,12 @@ SQL
}
my $xref_id = $self->get_xref($acc,$source{$source_name}, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($acc,"",$label,$description,$source{$source_name}, $species_id,"DIRECT");
+ $xref_id = $self->add_xref({ acc => $acc,
+ label => $label,
+ desc => $description,
+ source_id => $source{$source_name},
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$added++;
}
my $transcript_id = $transcript_dbid;
diff --git a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
index f368304807..9c28c07cb6 100644
--- a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
@@ -94,8 +94,20 @@ sub run {
}
my $symbol = $arr[$gene_symbol_index];
my $desc = $arr[$gene_desc_index];
- $self->add_xref($acc,"",$symbol,$desc,$source_id,$species_id, "DEPENDENT");
- $self->add_xref($acc,"",$symbol,$desc,$wiki_source_id,$species_id, "DEPENDENT","From EntrezGene $acc");
+
+ $self->add_xref({ acc => $acc,
+ label => $symbol,
+ desc => $desc,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type =>"DEPENDENT"} );
+
+ $self->add_xref({ acc => $acc,
+ label => $symbol,
+ desc => $desc,
+ source_id => $wiki_source_id,
+ species_id => $species_id,
+ info_type => "DEPENDENT" } ); #,"From EntrezGene $acc");
$xref_count++;
my (@syn) = split(/\|/ ,$arr[$gene_synonyms_index]);
diff --git a/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm b/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
index 1579774a74..500ba4768c 100644
--- a/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm
@@ -287,12 +287,18 @@ sub run {
# for this source.
if ( $dbxref_name eq 'bdgpinsituexpr' ) {
$xref_id =
- $self->add_xref( $id, undef, $accession, '',
- $source_id, $species_id, 'DIRECT' );
+ $self->add_xref({ acc => $id,
+ label => $accession,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type =>'DIRECT'} );
} else {
$xref_id =
- $self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id, 'DIRECT' );
+ $self->add_xref({ acc => $accession,
+ label => $accession,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => 'DIRECT'} );
}
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -318,8 +324,11 @@ sub run {
$xref_id = $xref_ids{$source_name}{$accession};
} else {
$xref_id =
- $self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id ,'DIRECT');
+ $self->add_xref({ acc => $accession,
+ label => $accession,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => 'DIRECT'} );
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -343,8 +352,11 @@ sub run {
$xref_id = $xref_ids{$source_name}{$accession};
} else {
$xref_id =
- $self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id, 'DIRECT' );
+ $self->add_xref({ acc => $accession,
+ label => $accession,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => 'DIRECT'} );
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -371,8 +383,13 @@ sub run {
$xref_id = $xref_ids{$source_name}{$accession};
} else {
$xref_id =
- $self->add_xref( $id, undef, $accession, $description, $source_id,
- $species_id, 'DIRECT' );
+ $self->add_xref({ acc => $id,
+ label => $accession,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => 'DIRECT'} );
+
$xref_ids{$source_name}{$accession} = $xref_id;
}
@@ -394,8 +411,11 @@ sub run {
$xref_id = $xref_ids{$source_name}{$accession};
} else {
$xref_id =
- $self->add_xref( $accession, undef, $accession, '',
- $source_id, $species_id, 'DIRECT' );
+ $self->add_xref({ acc => $accession,
+ label => $accession,
+ source_id => $source_id,
+ species_id => $species_id,
+ onfo_type => 'DIRECT'} );
$xref_ids{$source_name}{$accession} = $xref_id;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/GOParser.pm b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
index a2e6f9a73a..a82cfd978a 100644
--- a/misc-scripts/xref_mapping/XrefParser/GOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
@@ -29,36 +29,38 @@ sub run {
# Get the descriptions from the desc file.
#
- my $go_desc_io = $self->get_filehandle($file_desc);
-
- if ( !defined $go_desc_io ) {
- print STDERR "ERROR: Could not open description file, $file_desc\n";
- return 1; # 1 error
- }
-
my %go_to_desc;
- print "description file for GO\n" if($verbose);
- my $term = undef;
- my $desc = undef;
- while ( $_ = $go_desc_io->getline() ) {
- if(/\<id\> # start of id tag
- (GO:\d+) # GO: followed by the id
- \<\/id\> # end of id tag
- /x){
- $term = $1;
+ if($file_desc){
+ my $go_desc_io = $self->get_filehandle($file_desc);
+
+ if ( !defined $go_desc_io ) {
+ print STDERR "ERROR: Could not open description file, $file_desc\n";
+ return 1; # 1 error
}
- elsif(/\<name\> # start of name tag
- (.*) # the name we want
- \<\/name\> # end of name tag
- /x){
- if(defined($term)){
- $go_to_desc{$term} = $1;
- }
- $term = undef;
+
+
+ print "description file for GO\n" if($verbose);
+ my $term = undef;
+ my $desc = undef;
+ while ( $_ = $go_desc_io->getline() ) {
+ if(/\<id\> # start of id tag
+ (GO:\d+) # GO: followed by the id
+ \<\/id\> # end of id tag
+ /x){
+ $term = $1;
+ }
+ elsif(/\<name\> # start of name tag
+ (.*) # the name we want
+ \<\/name\> # end of name tag
+ /x){
+ if(defined($term)){
+ $go_to_desc{$term} = $1;
+ }
+ $term = undef;
+ }
}
+ $go_desc_io->close();
}
- $go_desc_io->close();
-
my %wrongtype;
@@ -81,6 +83,7 @@ sub run {
my %worm;
my $wormset;
+ my $worm_separator;
my %fish;
my $fishset;
@@ -163,7 +166,8 @@ sub run {
#WB CE20707 ZYG-9 GO:0008017 WB:WBPaper00003099|PMID:9606208 ISS F protein taxon:6239 20030829 WB
if(!defined($wormset)){
$wormset = 1;
- %worm = %{$self->get_valid_xrefs_for_direct_xrefs('worm')};
+ $worm_separator = qw{::};
+ %worm = %{$self->get_valid_xrefs_for_direct_xrefs('worm', $worm_separator)};
}
my $worm_acc=$array[1];
if(!defined($worm{$worm_acc})){
@@ -176,13 +180,17 @@ sub run {
}
if(defined($worm{$worm_acc})){
- my ($xref_id, $stable_id, $type, $link) = split(/::/x,$worm{$worm_acc});
+ my ($xref_id, $stable_id, $type, $link) = split(/$worm_separator/x,$worm{$worm_acc});
my $new_xref_id = $self->get_xref($array[4],$source_id, $species_id);
if(!defined($new_xref_id)){
$new_xref_id =
- $self->add_xref($array[4],undef,$array[4],"", $source_id, $species_id, "DIRECT");
+ $self->add_xref({ acc => $array[4],
+ label => $array[4],
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(!defined($self->get_direct_xref($stable_id,$type, $array[6]))){
diff --git a/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm b/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm
index 9d707f7793..1b65d880ec 100644
--- a/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm
@@ -83,7 +83,12 @@ sub run_script {
if(defined($go{$term_acc})){
foreach my $go_xref_id (@{$go{$term_acc}}) {
- my $xref_id = $self->add_xref($subterm_acc, undef, $subterm_acc, $desc, $source_id, $species_id, "DEPENDENT");
+ my $xref_id = $self->add_xref({ acc => $subterm_acc,
+ label => $subterm_acc,
+ desc => $desc,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DEPENDENT"} );
$add_dependent_xref_sth->execute($go_xref_id, $xref_id);
$count++;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
index a5deeee434..809eec03fa 100644
--- a/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
@@ -68,13 +68,13 @@ sub run {
label => $symbol,
desc => $name,
source_id => $source_id,
- species_id => $species_id});
+ species_id => $species_id} );
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
- alias => $synonyms});
+ alias => $synonyms} );
$name_count{$type}++;
}
@@ -88,9 +88,14 @@ sub run {
if ($id){ # Ensembl direct xref
$seen = 1;
$name_count{$type}++;
- $self->add_to_direct_xrefs($id,'gene', $acc, $empty,
- $symbol, $name, $empty,
- $source_id, $species_id);
+ $self->add_to_direct_xrefs({ stable_id => $id,
+ type => 'gene',
+ acc => $acc,
+ label => $symbol,
+ desc => $name,,
+ source_id => $source_id,
+ species_id => $species_id} );
+
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
@@ -182,7 +187,13 @@ sub run {
if(!$seen){ # Store to keep descriptions etc
$type = 'desc_only';
$source_id = $name_to_source_id->{$type};
- $self->add_xref($acc, $empty, $symbol, $name, $source_id, $species_id, "MISC");
+ $self->add_xref({ acc => $acc,
+ label => $symbol,
+ desc => $name,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "MISC"} );
+
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
diff --git a/misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm
index 1a0eb76194..71f4c34eb2 100644
--- a/misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm
@@ -162,7 +162,7 @@ SQL
}
}
$sth->finish;
-
+
my $xref_count = 0;
my $no_ccds_to_hgnc = 0;
my $direct_count = 0;
@@ -170,8 +170,13 @@ SQL
if(defined($ccds_to_hgnc{$ccds})){
my $hgnc = $ccds_to_hgnc{$ccds};
$hgnc =~ s/HGNC://;
- my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc ,
- $description{$hgnc}, $source_id, $species_id, "DIRECT");
+ my $xref_id = $self->add_xref({ acc => $hgnc,
+ version => $version{$hgnc} ,
+ label => $label{$hgnc}||$hgnc ,
+ desc => $description{$hgnc},
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
foreach my $stable_id (@{$ccds_to_stable_id{$ccds}}){
$self->add_direct_xref($xref_id, $stable_id, "Transcript", "");
diff --git a/misc-scripts/xref_mapping/XrefParser/HPAParser.pm b/misc-scripts/xref_mapping/XrefParser/HPAParser.pm
index 468a261c78..1035f966ff 100644
--- a/misc-scripts/xref_mapping/XrefParser/HPAParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HPAParser.pm
@@ -62,7 +62,13 @@ sub run {
my $xref_id = $self->get_xref( $antibody_id, $source_id, $species_id );
if ( !defined($xref_id) || $xref_id eq '' ) {
- $xref_id = $self->add_xref($antibody_id, $version, $label, $description, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $antibody_id,
+ version => $version,
+ label => $label,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
}
diff --git a/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm b/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm
index 57854529f8..e400183bda 100644
--- a/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IKMCParser.pm
@@ -176,8 +176,11 @@ XXML
if ( !defined($xref_id) || $xref_id eq '' ) {
$xref_id =
- $self->add_xref( $acc, undef, $label,
- '', $source_id, $species_id, "DIRECT");
+ $self->add_xref({ acc => $acc,
+ label => $label,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
}
next if(!defined($ensembl_ids{$acc}));
$direct_count++;
diff --git a/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm b/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm
index 395e4bfafc..8cdbfbd276 100644
--- a/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm
@@ -45,7 +45,12 @@ sub run {
my $xref_id = $self->get_xref($acc,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($acc,"", $acc, $full_description, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $acc,
+ label => $acc,
+ desc => $full_description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(defined($gene_id) and $gene_id ne "-"){
diff --git a/misc-scripts/xref_mapping/XrefParser/MGIParser.pm b/misc-scripts/xref_mapping/XrefParser/MGIParser.pm
index 16e2b9b433..799ec49f72 100644
--- a/misc-scripts/xref_mapping/XrefParser/MGIParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MGIParser.pm
@@ -77,7 +77,14 @@ sub run {
if($line =~ /(MGI:\d+).*(ENSMUSG\d+)/){
my $acc = $1;
my $ensid = $2;
- my $xref_id = $self->add_xref($acc, $version{$acc}, $label{$acc}, $description{$acc}, $source_id, $species_id, "DIRECT");
+ my $xref_id = $self->add_xref({ acc => $acc,
+ version => $version{$acc},
+ label => $label{$acc},
+ desc => $description{$acc},
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
+
$self->add_direct_xref( $xref_id, $ensid, "Gene", '');
if(defined($syn_hash->{$acc})){
foreach my $syn (@{$syn_hash->{$acc}}){
diff --git a/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm b/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
index d6cc51473a..6bbe61b38b 100644
--- a/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm
@@ -48,7 +48,12 @@ sub run {
my $type = pop @part_desc; # last array element is the type.
my $desc= join(" ",@part_desc);
- $acc_to_xref{$acc} = $self->add_xref($acc,"",$label,$desc,$source_id,$species_id,"MISC");
+ $acc_to_xref{$acc} = $self->add_xref({ acc => $acc,
+ label => $label,
+ desc => $desc,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "MISC"} );
if($verbose and $desc eq ""){
print "$acc has no description\n";
}
diff --git a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
index bb81216479..4abdf23d80 100644
--- a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
@@ -72,17 +72,38 @@ sub run {
$label = substr($label,0,35)." [".$type."]";
if($type eq "*"){ # gene only
$gene++;
- $self->add_xref($number,"",$label,$long_desc,$gene_source_id,$species_id,"DEPENDENT");
+ $self->add_xref({ acc => $number,
+ label => $label,
+ desc => $long_desc,
+ source_id => $gene_source_id,
+ species_id => $species_id,
+ info_type => "DEPENDENT"} );
}
elsif((!defined $type) or ($type eq "") or ($type eq "#") or ($type eq "%")){ #phenotype only
$phenotype++;
- $self->add_xref($number,"",$label,$long_desc,$morbid_source_id,$species_id,"DEPENDENT");
+ $self->add_xref({ acc => $number,
+ label => $label,
+ desc => $long_desc,
+ source_id => $morbid_source_id,
+ species_id => $species_id,
+ info_type => "DEPENDENT"} );
}
elsif($type eq "+"){ # both
$gene++;
$phenotype++;
- $self->add_xref($number,"",$label,$long_desc,$gene_source_id,$species_id,"DEPENDENT");
- $self->add_xref($number,"",$label,$long_desc,$morbid_source_id,$species_id,"DEPENDENT");
+ $self->add_xref({ acc => $number,
+ label => $label,
+ desc => $long_desc,
+ source_id => $gene_source_id,
+ species_id => $species_id,
+ info_type => "DEPENDENT"} );
+
+ $self->add_xref({ acc => $number,
+ label => $label,
+ desc => $long_desc,
+ source_id => $morbid_source_id,
+ species_id => $species_id,
+ info_type => "DEPENDENT"} );
}
elsif($type eq "^"){
if(/\*FIELD\*\sTI\n[\^]\d+ MOVED TO (\d+)/){
diff --git a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
index 68754cab95..923f22e8ff 100644
--- a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
@@ -82,7 +82,11 @@ SQL
my $xref_count = 0;
foreach my $ott (keys %ott_to_enst){
- my $xref_id = $self->add_xref($ott, "" , $ott , "", $source_id, $species_id, "DIRECT");
+ my $xref_id = $self->add_xref({ acc => $ott,
+ label => $ott,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$xref_count++;
$self->add_direct_xref($xref_id, $ott_to_enst{$ott}, "transcript", "");
}
diff --git a/misc-scripts/xref_mapping/XrefParser/PomBaseParser.pm b/misc-scripts/xref_mapping/XrefParser/PomBaseParser.pm
index f4952b45a6..5b5c232ca6 100644
--- a/misc-scripts/xref_mapping/XrefParser/PomBaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/PomBaseParser.pm
@@ -44,10 +44,10 @@ sub run {
chomp;
if ($_ =~ /^([^\t]+)\t([^\t]+)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)$/) {
-
+
my @line = split(m/\t/ms, $_);
my ($pombase_id, $name, $info_type, $biotype, $external_db_source, $desc, $ensembl_object_type, $synonyms) = undef;
-
+
$pombase_id = $line[0];
$name = $line[1];
$info_type = $line[2];
@@ -55,22 +55,34 @@ sub run {
$external_db_source = $line[4];
$desc = $line[5];
$ensembl_object_type = $line[6];
-
+
if (scalar @line == 8) {
$synonyms = $line[7];
}
# parse the lines corresponding to the gene entries
# and filter out lines corresponding to the CDS for example
-
+
#print "$ensembl_object_type\n";
if ($ensembl_object_type eq 'Gene') {
- my $ensembl_xref_id = $self->add_xref($pombase_id,"",$name,$desc,$gene_source_id,$species_id,$info_type);
+ my $ensembl_xref_id = $self->add_xref({ acc => $pombase_id,
+ label => $name,
+ desc => $desc,
+ source_id => $gene_source_id,
+ species_id => $species_id,
+ info_type => $info_type} );
+
$self->add_direct_xref($ensembl_xref_id, $pombase_id, $ensembl_object_type, $info_type);
} elsif ($ensembl_object_type eq 'Transcript') {
- my $ensembl_xref_id = $self->add_xref($pombase_id,"",$name,$desc,$transcript_source_id,$species_id,$info_type);
+ my $ensembl_xref_id = $self->add_xref({ acc => $pombase_id,
+ label => $name,
+ desc => $desc,
+ source_id => $transcript_source_id,
+ species_id => $species_id,
+ info_type => $info_type} );
+
$self->add_direct_xref($ensembl_xref_id, $pombase_id, $ensembl_object_type, $info_type);
}
-
+
$xref_count++;
if ($synonyms) {
my (@syn) = split(/,/,$synonyms);
diff --git a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
index c156d872a9..05a3ffd5b4 100644
--- a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
@@ -103,8 +103,12 @@ sub run {
}
if(!$done){
-# print STDERR "$rgd FAILED for $failed_list\n";
- $self->add_xref($rgd,"",$symbol,$name,$source_id,$species_id,"MISC");
+ $self->add_xref({ acc => $rgd,
+ label => $symbol,
+ desc => $name,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "MISC"} );
$mismatch++;
}
@@ -112,9 +116,11 @@ sub run {
$rgd_io->close();
- print "\t$count xrefs succesfully loaded and dependent on refseq\n" if($verbose);
- print "\t$mismatch xrefs added but with NO dependencies\n" if($verbose);
- print "added $syn_count synonyms\n" if($verbose);
+ if($verbose){
+ print "\t$count xrefs succesfully loaded and dependent on refseq\n";
+ print "\t$mismatch xrefs added but with NO dependencies\n";
+ print "added $syn_count synonyms\n";
+ }
return 0;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
index 504029d8ee..6b527baf95 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
@@ -190,8 +190,13 @@ CCDS
# if($refseq =~ /^XM/){
# $new_source_id = $dna_pred;
# }
- my $xref_id = $self->add_xref($refseq, $version{$refseq} , $label{$refseq}||$refseq ,
- $description{$refseq}, $new_source_id, $species_id, "DIRECT");
+ my $xref_id = $self->add_xref({ acc => $refseq,
+ version => $version{$refseq} ,
+ label => $label{$refseq}||$refseq ,
+ desc => $description{$refseq},
+ source_id => $new_source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
foreach my $stable_id (@{$internal_to_stable_id{$internal_id}}){
diff --git a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
index ab9381f247..bdf2498a87 100644
--- a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
@@ -72,10 +72,22 @@ sub run {
my (@syn) = split(/\|/,$alias_name);
- my $gene_xref_id = $self->add_xref($sgd_id,"",$locus_name,$desc,$gene_source_id,$species_id,"DIRECT");
+ my $gene_xref_id = $self->add_xref({ acc => $sgd_id,
+ label => $locus_name,
+ desc => $desc,
+ source_id => $gene_source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
+
$self->add_direct_xref($gene_xref_id, $orf_name, "Gene", "DIRECT");
- my $transcript_xref_id = $self->add_xref($sgd_id,"",$locus_name,$desc,$transcript_source_id,$species_id,"DIRECT");
+ my $transcript_xref_id = $self->add_xref({ acc => $sgd_id,
+ label => $locus_name,
+ desc => $desc,
+ source_id => $transcript_source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
+
$self->add_direct_xref($transcript_xref_id, $orf_name, "Transcript", "DIRECT");
$xref_count++;
diff --git a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
index 5626c68843..bfd34822f2 100644
--- a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
@@ -37,10 +37,14 @@ sub run {
my $xref_id = $self->get_xref($acc,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($acc,"",$acc,$description,$source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $acc,
+ label => $acc,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$added++;
}
-# print "$acc, $xref_id, $gene_id\n";
$self->add_direct_xref($xref_id, $gene_id, "Gene", "");
}
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
index 830f923aee..a5892c6fd3 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm
@@ -85,7 +85,7 @@ sub run {
$get_desc_sth->bind_columns(\$old_xref_id, \$version, \$label, \$description);
$get_desc_sth->fetch;
if(!defined($old_xref_id)){
- print STDERR "Could not find $key in the database\n" if ($err_count <10);
+ print "Could not find $key in the database\n" if ($err_count <10);
$err_count++;
next;
}
@@ -109,7 +109,13 @@ sub run {
# Add the new xref
#
- my $xref_id = $self->add_xref($key, $version, $label, $description, $source_id, $species_id, "DIRECT");
+ my $xref_id = $self->add_xref({ acc => $key,
+ version => $version,
+ label => $label,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
#
diff --git a/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm b/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm
index bef422f699..a161e6cf82 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm
@@ -43,7 +43,12 @@ sub run {
my $xref_id = $self->get_xref($acc,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($acc,"", $acc, $full_description, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $acc,
+ label => $acc,
+ desc => $full_description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(defined($gene_id) and $gene_id ne "-"){
diff --git a/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm b/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm
index f58add18eb..d4d6db1672 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBExternalDescriptionParser.pm
@@ -47,7 +47,12 @@ sub run {
my $xref_id = $self->get_xref($gene_id,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($gene_id,"", $gene_id, $description, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $gene_id,
+ label => $gene_id,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(defined($gene_id) and $gene_id ne "-"){
diff --git a/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm b/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm
index 00c6243423..892cddd392 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm
@@ -50,7 +50,12 @@ sub run {
my $xref_id = $self->get_xref($gene_id,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($gene_id,"", $gene_id, $descr_full, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $gene_id,
+ label => $gene_id,
+ desc => $descr_full,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(defined($gene_id) and $gene_id ne "-"){
diff --git a/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm b/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm
index c2d8c4320b..a7f4969584 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBRNADescriptionParser.pm
@@ -47,7 +47,12 @@ sub run {
my $xref_id = $self->get_xref($gene_id,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($gene_id,"", $gene_id, $description, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $gene_id,
+ label => $gene_id,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(defined($gene_id) and $gene_id ne "-"){
diff --git a/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm b/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
index c632177deb..324955c14f 100644
--- a/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VBribosomalParser.pm
@@ -49,7 +49,12 @@ sub run {
my $xref_id = $self->get_xref($gene_id,$source_id, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($gene_id,"", $gene_id, $descr_full, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $gene_id,
+ label => $gene_id,
+ desc => $descr_full,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$count++;
}
if(defined($gene_id) and $gene_id ne "-"){
diff --git a/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm b/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm
index 35e9daba31..0859e50820 100644
--- a/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm
@@ -41,7 +41,13 @@ sub run {
my $xref_id = $self->get_xref($probe, $source_id, $species_id);
if (!defined($xref_id) || $xref_id eq "") {
- $xref_id = $self->add_xref($probe, 1, $probe, $description, $source_id, $species_id, "DIRECT");
+ $xref_id = $self->add_xref({ acc => $probe,
+ version => 1,
+ label => $probe,
+ desc => $description,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type =>"DIRECT"} );
}
$self->add_direct_xref($xref_id, $ensembl_id, $type, $probe);
}
diff --git a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
index 6817d31796..00d771f1d7 100644
--- a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
@@ -289,7 +289,14 @@ EXT
my $version ="";
$line_count++;
if(!defined($acc{$ext})){
- my $xref_id = $self->add_xref($ext, $version{$ext} , $label{$ext}||$ext , $description{$ext}, $source_id, $species_id, "DIRECT");
+ my $xref_id = $self->add_xref({ acc => $ext,
+ version => $version{$ext} ,
+ label => $label{$ext}||$ext ,
+ desc => $description{$ext},
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
+
$acc{$ext} = $xref_id;
$xref_count++;
if ((defined($xref_id)) and ($at_least_1_xref_loaded == 0)){
diff --git a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
index c070987278..bb3634efef 100644
--- a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
@@ -74,7 +74,12 @@ sub create_xrefs {
# add xref - not we're assuming it doesn't already exist;
# may need to check like in CCDS parser
- my $xref_id = $self->add_xref($acc, 0, $acc, "$target direct mapping", $source_id, $species_id);
+ my $xref_id = $self->add_xref({ acc => $acc,
+ version => 0,
+ label => $acc,
+ desc => "$target direct mapping",
+ source_id => $source_id,
+ species_id => $species_id} );
$self->add_direct_xref($xref_id, $target, "transcript", "");
$direct++;
diff --git a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
index 2195efc853..0e04dfc0bd 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
@@ -54,7 +54,11 @@ sub run {
$xref_sth->execute($wb);
my $xref_id = ($xref_sth->fetchrow_array())[0];
if (!$xref_id) {
- $xref_id = $self->add_xref($wb, undef, $wb, "", $worm_source_id, $species_id);
+ $xref_id = $self->add_xref({ acc => $wb,
+ label => $wb,
+ source_id => $worm_source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$x_count++;
}
# and direct xref
@@ -65,7 +69,11 @@ sub run {
$xref_sth2->execute($display);
my $xref_id2 = ($xref_sth2->fetchrow_array())[0];
if (!$xref_id2) {
- $xref_id2 = $self->add_xref($display, undef, $display, "", $worm_locus_id, $species_id);
+ $xref_id2 = $self->add_xref({ acc => $display,
+ label => $display,
+ source_id => $worm_locus_id,
+ species_id => $species_id,
+ info_type => "DIRECT" });
$x_count++;
}
# and direct xref
diff --git a/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm b/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
index ea36878a96..125cec3fe3 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
@@ -12,7 +12,8 @@ use base qw( XrefParser::DatabaseParser );
sub run {
my ($self, $ref_arg) = @_;
- my $source_id = $ref_arg->{source_id};
+
+ my $source_id = $ref_arg->{source_id} || confess "Need a source_id";
my $species_id = $ref_arg->{species_id};
my $dsn = $ref_arg->{dsn};
my $verbose = $ref_arg->{verbose};
@@ -26,12 +27,15 @@ sub run {
my $xref_db = $self->dbi();
my $xref_sth = $xref_db->prepare( "INSERT INTO xref (accession,label,source_id,species_id) VALUES (?,?,?,?)" );
- my $direct_xref_sth = $xref_db->prepare( "INSERT INTO direct_xref (general_xref_id,ensembl_stable_id,type,linkage_xref) VALUES (?,?,?,?)" );
+
# read stable IDs
foreach my $type ('gene', 'transcript') {
- print "Building xrefs from $type stable IDs\n" if($verbose);
+ my $direct_xref_sth = $xref_db->prepare( "INSERT INTO ${type}_direct_xref (general_xref_id,ensembl_stable_id,linkage_xref) VALUES (?,?,?)" );
+ if($verbose) {
+ print "Building xrefs from $type stable IDs\n";
+ }
my $wb_source_id = $self->get_source_id_for_source_name("wormbase_$type");
@@ -44,7 +48,7 @@ sub run {
# add an xref & a direct xref
$xref_sth->execute($id, $id, $wb_source_id, $species_id);
my $xref_id = $xref_sth->{'mysql_insertid'};
- $direct_xref_sth->execute($xref_id, $id, $type, "Stable ID direct xref");
+ $direct_xref_sth->execute($xref_id, $id, 'Stable ID direct xref');
} # while fetch stable ID
diff --git a/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm b/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm
index 8f57043f68..da6847815a 100644
--- a/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm
@@ -42,7 +42,12 @@ sub run {
$withdrawn++;
}
else{
- $self->add_xref($zfin,"",$label,$desc,$source_id,$species_id,"MISC");
+ $self->add_xref({ acc => $zfin,
+ label => $label,
+ desc => $desc,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "MISC"} );
$count++;
}
}
diff --git a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
index c363eedfca..68dd9ad2ae 100644
--- a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
@@ -7,6 +7,7 @@ use File::Basename;
use base qw( XrefParser::BaseParser );
+use XrefParser::Database;
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
@@ -101,12 +102,25 @@ sub run_script {
my $core_dbc;
if(defined($vdbname)){
print "Using $host $vdbname for Vega and cdbname for Core\n";
- $vega_dbc = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
+
+ my $vega_db = XrefParser::Database->new({ host => $vhost,
+ port => $vport,
+ user => $vuser,
+ dbname => $vdbname,
+ pass => $vpass});
+
+ $vega_dbc = $vega_db->dbi;
if(!defined($vega_dbc)){
print "Problem could not open connectipn to $vhost, $vport, $vuser, $vdbname, $vpass\n";
return 1;
}
- $core_dbc = $self->dbi2($chost, $cport, $cuser, $cdbname, $cpass);
+
+ my $core_db = XrefParser::Database->new({ host => $chost,
+ port => $cport,
+ user => $cuser,
+ dbname => $cdbname,
+ pass => $cpass});
+ $core_dbc = $core_db->dbi;
if(!defined($core_dbc)){
print "Problem could not open connectipn to $chost, $cport, $cuser, $cdbname, $cpass\n";
return 1;
@@ -189,7 +203,11 @@ sub run_script {
# number is no longer the clone version but the gene number so we need to keep it now.
# $name =~ s/[.]\d+//; #remove .number #
}
- my $xref_id = $self->add_xref($name, "" , $name , "", $id, $species_id, "DIRECT");
+ my $xref_id = $self->add_xref({ acc => $name,
+ label => $name,
+ source_id => $id,
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$xref_count++;
$self->add_direct_xref($xref_id, $ott_to_enst{$ott}, "transcript", "");
diff --git a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
index 21b1a7f94b..d49c932d1a 100644
--- a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
@@ -60,7 +60,12 @@ sub run {
}
my $xref_id = $self->get_xref($acc,$name_2_source_id{$source_name}, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($acc,"",$display_label,$description,$name_2_source_id{$source_name}, $species_id,"DIRECT");
+ $xref_id = $self->add_xref({ acc => $acc,
+ label => $display_label,
+ desc => $description,
+ source_id => $name_2_source_id{$source_name},
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$added++;
}
$self->add_direct_xref($xref_id, $transcript_id, "Transcript", "") if (defined($transcript_id));
diff --git a/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm b/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
index c722ecaaac..cd892319ff 100644
--- a/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
@@ -87,7 +87,12 @@ SQL
}
my $xref_id = $self->get_xref($acc,$source{$source_name}, $species_id);
if(!defined($xref_id)){
- $xref_id = $self->add_xref($acc,"",$label,$description,$source{$source_name}, $species_id,"DIRECT");
+ $xref_id = $self->add_xref({ acc => $acc,
+ label => $label,
+ desc => $description,
+ source_id => $source{$source_name},
+ species_id => $species_id,
+ info_type => "DIRECT"} );
$added++;
}
my $transcript_id = $dbid;
--
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