my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
my $db = $ref_arg->{dba};
my $dbi = $ref_arg->{dbi};
$dbi = $self->dbi unless defined $dbi;
if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and file as pairs";
}
$verbose |=0;
my $user = "ensro";
my $host;
my $port = 3306;
my $dbname;
my $pass;
if($file =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($file =~ /port[=][>](\S+?)[,]/){
$port = $1;
}
if($file =~ /dbname[=][>](\S+?)[,]/){
$dbname = $1;
}
if($file =~ /pass[=][>](\S+?)[,]/){
$pass = $1;
}
my ($ccds_db, $dbi2);
if (defined $host) {
port => $port,
user => $user,
dbname => $dbname,
pass => $pass});
$dbi2 = $ccds_db->dbi();
} elsif (defined $db) {
$dbi2 = $db->dbc();
}
if(!defined($dbi2)){
return 1;
}
my $sql =(<<'SCD');
SELECT t.stable_id, x.dbprimary_acc
FROM xref x, object_xref ox,
transcript t, external_db e
WHERE x.xref_id=ox.xref_id AND
ox.ensembl_object_type = "Transcript" AND
ox.ensembl_id = t.transcript_id AND
e.external_db_id = x.external_db_id AND
e.db_name like "Ens\_%\_transcript"
SCD
my %seen;
my $sth = $dbi2->prepare($sql) or die "Could not prepare sql $sql\n";
$sth->execute() or die "Could not execute $sql\n";
my $xref_count = 0;
my $direct_count=0;
my ($stable_id, $display_label);
$sth->bind_columns( \$display_label,\$stable_id);
while ( $sth->fetch ) {
my ($acc, $version) = split (/\./,$display_label);
my $xref_id;
if (!defined($seen{$display_label})) {
$xref_id = $self->add_xref({ acc => $acc,
version => $version,
label => $display_label,
source_id => $source_id,
species_id => $species_id,
dbi => $dbi,
info_type => "DIRECT"} );
$xref_count++;
$seen{$display_label} = $xref_id;
}
else{
$xref_id = $seen{$display_label};
}
$self->add_direct_xref($xref_id, $stable_id, "Transcript", "", $dbi);
$direct_count++;
}
print "Parsed CCDS identifiers from $file, added $xref_count xrefs and $direct_count direct_xrefs\n" if($verbose);
return 0;
}
Code:
