Raw content of XrefMapper::CoreInfo
<![CDATA[package XrefMapper::CoreInfo;
use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
use strict;
use warnings;
use XrefMapper::BasicMapper;
use Cwd;
use DBI;
use File::Basename;
use IPC::Open3;
# Get info from the core database.
# Need to load tables:-
#
# gene_transcript_translation
# gene_stable_id
# transcript_stable_id
# translation_stable_id
# Also for Direct xref process these and add to object_xref
# also add dependents while we are at it.
sub new {
my($class, $mapper) = @_;
my $self ={};
bless $self,$class;
$self->core($mapper->core);
$self->xref($mapper->xref);
$self->verbose($mapper->verbose);
return $self;
}
sub get_core_data {
my $self = shift;
# gene_transcript_translation
# gene_stable_id
# transcript_stable_id
# translation_stable_id
my $object_xref_id;
my $ox_sth = $self->xref->dbc->prepare("select max(object_xref_id) from object_xref");
$ox_sth->execute();
$ox_sth->bind_columns(\$object_xref_id);
$ox_sth->fetch();
$ox_sth->finish;
# load table gene_transcript_translation
my $ins_sth = $self->xref->dbc->prepare("insert into gene_transcript_translation (gene_id, transcript_id, translation_id) values (?, ?, ?)");
my $sql = "select tn.gene_id, tn.transcript_id, tl.translation_id from transcript tn left join translation tl on tl.transcript_id = tn.transcript_id";
my $sth = $self->core->dbc->prepare($sql);
$sth->execute();
my ($gene_id, $transcript_id, $translation_id);
$sth->bind_columns(\$gene_id, \$transcript_id, \$translation_id);
while($sth->fetch()){
$ins_sth->execute($gene_id, $transcript_id, $translation_id);
}
$ins_sth->finish;
$sth->finish;
# load table xxx_stable_id
my ($id, $stable_id);
foreach my $table (qw(gene transcript translation)){
my $sth = $self->core->dbc->prepare("select ".$table."_id, stable_id from ".$table."_stable_id");
my $ins_sth = $self->xref->dbc->prepare("insert into ".$table."_stable_id (internal_id, stable_id) values(?, ?)");
$sth->execute();
$sth->bind_columns(\$id, \$stable_id);
while($sth->fetch){
$ins_sth->execute($id, $stable_id);
}
$ins_sth->finish;
$sth->finish;
}
$sth = $self->xref->dbc->prepare("insert into process_status (status, date) values('core_data_loaded',now())");
$sth->execute();
$sth->finish;
# Now process the direct xrefs and add data to the object xrefs remember dependent xrefs.
my $ins_ox_sth = $self->xref->dbc->prepare("insert into object_xref (object_xref_id, ensembl_id, xref_id, ensembl_object_type, linkage_type) values(?, ?, ?, ?, ?)");
# Direct xrefs can be considered to be 100% matching
my $ins_ix_sth = $self->xref->dbc->prepare("insert into identity_xref (object_xref_id, query_identity, target_identity) values(?, 100, 100)");
local $ins_ox_sth->{RaiseError}; # want to see duplicates and not add de
local $ins_ox_sth->{PrintError};
my $ins_go_sth = $self->xref->dbc->prepare("insert into go_xref (object_xref_id, linkage_type, source_xref_id) values(?,?,?)");
my $dep_sth = $self->xref->dbc->prepare("select dependent_xref_id, linkage_annotation from dependent_xref where master_xref_id = ?");
my $stable_sql=(<<SQL);
SELECT dx.general_xref_id, s.internal_id, dx.ensembl_stable_id
FROM TYPE_direct_xref dx left join TYPE_stable_id s on s.stable_id = dx.ensembl_stable_id
SQL
my $err_count = 0;
foreach my $table (qw(gene transcript translation)){
my ($xref_id, $internal_id, $stable_id);
my $sql = $stable_sql;
$sql =~ s/TYPE/$table/g;
my $sth = $self->xref->dbc->prepare($sql);
# print "sql = $sql\n";
$sth->execute();
$sth->bind_columns(\$xref_id, \$internal_id, \$stable_id);
my $count =0;
my $duplicate_direct_count = 0;
my $duplicate_dependent_count = 0;
while($sth->fetch){
if(!defined($internal_id)){ # not found either it is an internal id already or stable_id no longer exists
if($stable_id =~ /^\d+$/){
$internal_id = $stable_id;
}
else{
print "Could not find stable id $stable_id in table to get the internal id hence ignoring!!!\n" if($self->verbose);
$err_count++;
next;
}
}
$object_xref_id++;
$count++;
my @master_xref_ids;
$ins_ox_sth->execute($object_xref_id, $internal_id, $xref_id, $table, 'DIRECT');
if($ins_ox_sth->err){
$duplicate_direct_count++;
next; #duplicate
}
else{
$ins_ix_sth->execute($object_xref_id);
push @master_xref_ids, $xref_id;
}
while(my $master_xref_id = pop(@master_xref_ids)){
my ($dep_xref_id, $link);
$dep_sth->execute($master_xref_id);
$dep_sth->bind_columns(\$dep_xref_id, \$link);
while($dep_sth->fetch){
$object_xref_id++;
$ins_ox_sth->execute($object_xref_id, $internal_id, $dep_xref_id, $table, 'DEPENDENT');
if($ins_ox_sth->err){
my $err = $ins_ox_sth->errstr;
if($err =~ /Duplicate/){
$duplicate_dependent_count++;
next;
}
else{
die "Problem loading error is $err\n";
}
}
$ins_ix_sth->execute($object_xref_id);
push @master_xref_ids, $dep_xref_id; # get the dependent, dependents just in case
if(defined($link) and $link ne ""){ # we have a go term linkage type
$ins_go_sth->execute($object_xref_id, $link, $master_xref_id);
}
}
}
}
$sth->finish;
if($duplicate_direct_count or $duplicate_dependent_count){
print "duplicate entrys ignored for $duplicate_direct_count direct xrefs and $duplicate_dependent_count dependent xrefs\n" if($self->verbose);
}
if($err_count or $self->verbose){
print STDERR $count." direct_xrefs added to ensembl ".$table."s BUT $err_count stable ids could not be found\n";
}
}
$ins_go_sth->finish;
$ins_ox_sth->finish;
$dep_sth->finish;
$sth = $self->xref->dbc->prepare("insert into process_status (status, date) values('direct_xrefs_parsed',now())");
$sth->execute();
$sth->finish;
}
1;
]]>