XrefParser VbDirectParser
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Package variables
No package variables defined.
Included modules
Bio::SeqIO
File::Basename
XrefParser::BaseParser
Inherit
XrefParser::BaseParser
Synopsis
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Description
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Methods
new
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Code
run
No description
Code
Methods description
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Methods code
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sub new {
  my $self = {};
  bless $self, "XrefParser::VbDirectParser";
  return $self;

}

1;
}
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sub run {
	my ($self, $file, $source_id, $species_id) = @_;

	open (INFILE, "<$file");
	my $i=0;
	print STDERR "source: ".$source_id."\tspecies: ".$species_id."\n";
	

	my $type = "transcript";

	while (my $ln = <INFILE>) {
		chomp($ln);
		my ($probe,$id, $version, $description, $ensembl_id) = split("\t",$ln);      
		$i++;

		my $xref_id = XrefParser::BaseParser->get_xref($probe, $source_id, $species_id);
		if (!defined($xref_id) || $xref_id eq "") {
			$xref_id = XrefParser::BaseParser->add_xref($probe, 1, $probe, $description, $source_id, $species_id, "DIRECT");
			}
		XrefParser::BaseParser->add_direct_xref($xref_id, $ensembl_id, $type, $probe);
		}

	print $i." VB direct xrefs succesfully parsed\n" if($verbose);

	close(INFILE);

	return 0;
}
General documentation
No general documentation available.