Raw content of XrefParser::Vega_TranParser
<![CDATA[package XrefParser::Vega_TranParser;
use strict;
use DBI;
use base qw( XrefParser::BaseParser );
# Parse file of Vega transcript name records and assign direct xrefs
# All assumed to be linked to transcripts
sub run {
my ($self, $source_id, $species_id, $file) = @_;
die "No longer used try HGNC_curated_transcript\n";
my $vega_io = $self->get_filehandle($file);
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');
if ( !defined $vega_io ) {
print STDERR "Could not open $file\n";
return 1;
}
my $xref_count = 0;
my $line_count = 0;
my %vega_name;
my %vega_priority;
while ( $_ = $vega_io->getline() ) {
my $line_count++;
my ($stable_id, $name, $priority) = split;
if(!defined($vega_name{$stable_id}) or $vega_priority{$stable_id} < $priority){
$vega_name{$stable_id} = $name;
$vega_priority{$stable_id} = $priority;
}
}
foreach my $stable_id (keys %vega_name){
my $name = $vega_name{$stable_id};
my $id = $curated_source_id;
if($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, $stable_id, "transcript", "");
}
print "Parsed $line_count lines from $file, added $xref_count xrefs and $xref_count direct_xrefs\n" if($verbose);
$vega_io->close();
return 0;
}
1;
]]>