From 0323765dc066962d8a247b727761aae514f2bac6 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 4 Nov 2009 10:06:52 +0000
Subject: [PATCH] get the refseq data from the normal ccds database rather than
the tracker ccds database
---
.../XrefParser/RefSeq_CCDSParser.pm | 74 ++++++++++++++-----
1 file changed, 54 insertions(+), 20 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
index 0aa1d45bea..8a704ee89a 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
@@ -57,6 +57,9 @@ sub run_script {
}
$sth->finish;
+
+
+
$sql = 'select x.accession, x.xref_id, d.ensembl_stable_id, "Transcript"
from xref x, transcript_direct_xref d, source s
where s.source_id = x.source_id and
@@ -87,34 +90,65 @@ sub run_script {
if(!defined($dbi2)){
return 1;
}
-
- my $sql = "select cu.ccds_uid, a.nuc_acc from Accessions a, Accessions_GroupVersions agv, GroupVersions gv, CcdsUids cu where a.accession_uid = agv.accession_uid and a.organization_uid=1 and agv.group_version_uid=gv.group_version_uid and gv.ccds_status_val_uid in (3) and cu.group_uid=gv.group_uid order by gv.ccds_status_val_uid, cu.ccds_uid";
-
-
+
+
+##############################NEW#########################################
+
+ # get ccds -> xref transcript_id ensembl_stable_id{CCDS1} = ENST00001
+ # get ccds -> internal transcript_id ccds_to_internal_id(CCDS1} = 12345
+
+ $sql = 'select x.dbprimary_acc, ox.ensembl_id from xref x, object_xref ox, external_db e where x.xref_id = ox.xref_id and x.external_db_id = e.external_db_id and e.db_name like ?';
+
+
+
+ # calculate internal_id -> xref transcript_id
+ my %internal_to_stable_id;
+ my ($acc, $internal_id);
+
my $sth = $dbi2->prepare($sql);
- $sth->execute() or croak( $dbi2->errstr() );
+ $sth->execute("CCDS") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
- my $ccds = $row[0];
- my $refseq = $row[1];
-
+ my $acc = $row[0];
+ my $internal_id = $row[1];
+ if(defined($ensembl_stable_id{$acc})){
+ $internal_to_stable_id{$internal_id} = $ensembl_stable_id{$acc};
+ }
+ else{
+ print "$acc not found in ccds database????\n";
+ }
+ }
+
+ # for each object_xref for refseq_dna change internal_id to xref transcript_id
+ $sth->execute("Refseq_dna") or croak( $dbi2->errstr() );
+ while ( my @row = $sth->fetchrow_array() ) {
+ my $refseq = $row[0];
+ my $internal_id = $row[1];
+
+ if(defined($internal_to_stable_id{$internal_id})){
+ }
+ else{
+ print "Problem no internal_to_stable_id for $internal_id\n";
+ next;
+ }
+
$line_count++;
if(!defined($seen{$refseq})){
$seen{$refseq} = 1;
- my $key = "CCDS".$ccds;
- if(defined($ensembl_stable_id{$key})){
- my $new_source_id = $source_id;
- if($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");
- $self->add_direct_xref($xref_id, $ensembl_stable_id{$key}, $ensembl_type{$key}, "");
- $old_to_new{$old_xref{$refseq}} = $xref_id;
- $xref_count++;
+ my $new_source_id = $source_id;
+ if($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");
+
+ $self->add_direct_xref($xref_id, $internal_to_stable_id{$internal_id}, "Transcript", "");
+
+ $old_to_new{$old_xref{$refseq}} = $xref_id;
+ $xref_count++;
}
}
-
+############################END NEW######################################
+
#for each one seen get all its dependent xrefs and load them fro the new one too;
my $add_dependent_xref_sth = $dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)");
--
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