Raw content of XrefParser::HGNC_curated_transcriptParser
<![CDATA[package XrefParser::HGNC_curated_transcriptParser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
#my $dbi2;
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print STDERR "\nUsage: HGNC_curated_transcriptParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run(@ARGV);
}
sub run_script {
my $self = shift if (defined(caller(1)));
my $file = shift;
my $source_id = shift;
my $species_id = shift;
my $verbose = shift;
my ($type, $my_args) = split(/:/,$file);
my $user ="ensro";
my $host;
my $port;
my $dbname;
my $pass;
if($my_args =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($my_args =~ /port[=][>](\S+?)[,]/){
$port = $1;
}
if($my_args =~ /dbname[=][>](\S+?)[,]/){
$dbname = $1;
}
if($my_args =~ /pass[=][>](\S+?)[,]/){
$pass = $1;
}
if($my_args =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
print "Using $host $dbname for Vega\n" if($verbose);
my $clone_source_id =
$self->get_source_id_for_source_name('Clone_based_vega_transcript');
my $curated_source_id =
$self->get_source_id_for_source_name('HGNC_curated_transcript');
my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
my %ott_to_vega_name;
my %ott_to_enst;
my $dbi2 = $self->dbi2($host, $port, $user, $dbname, $pass);
if(!defined($dbi2)){
return 1;
}
my $sth = $dbi2->prepare($sql); # funny number instead of stable id ?????
$sth->execute("Vega_transcript") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_vega_name{$row[0]} = $row[1];
}
$sth->finish;
$sth = $dbi2->prepare($sql); # funny number instead of stable id ?????
$sth->execute("ENST_CDS") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[0]} = $row[1];
}
$sth->finish;
$sth = $dbi2->prepare($sql);
$sth->execute("ENST_ident") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[0]} = $row[1];
}
$sth->finish;
my $xref_count = 0;
foreach my $ott (keys %ott_to_enst){
if(defined($ott_to_vega_name{$ott})){
my $id = $curated_source_id;
my $name = $ott_to_vega_name{$ott};
my $primary_acc = $name;
if($name =~ /[.]/){
$id = $clone_source_id;
}
my $xref_id = $self->add_xref($name, "" , $name , "", $id, $species_id, "DIRECT");
$xref_count++;
$self->add_direct_xref($xref_id, $ott_to_enst{$ott}, "transcript", "");
}
}
print "$xref_count direct xrefs succesfully parsed\n" if($verbose);
return 0;
}
1;
]]>