Raw content of XrefParser::DirectParser
<![CDATA[package XrefParser::DirectParser;
use strict;
use base qw( XrefParser::BaseParser );
# This parser will read Direct Xrefs from a simple tab-delimited file.
# The columns of the file should be the following:
#
# 1) Accession ID
# 2) Ensembl ID
# 3) Type (one of 'transcript', 'gene', or 'translation',
# will default to 'gene')
# 4) Display label (will default to the Accession ID in column 1)
# 5) Description (will default to the empty string)
# 6) Version (will default to '1')
#
# Columns 1 and 2 are obligatory.
sub new {
my $proto = shift;
my $class = ref $proto || $proto;
my $self = bless {}, $class;
return $self;
}
sub run {
my $self = shift;
my ( $source_id, $species_id, $filename ) = @_;
my $file_io = $self->get_filehandle($filename);
if ( !defined($file_io) ) {
return 1;
}
my $parsed_count = 0;
printf( STDERR "source = %d\t species = %d\n",
$source_id, $species_id );
while ( defined( my $line = $file_io->getline() ) ) {
chomp $line;
my ( $accession, $ensembl_id, $type, $label, $description,
$version )
= split( /\t/, $line );
if ( !defined($accession) || !defined($ensembl_id) ) {
printf( "Line %d contains has less than two columns.\n",
1 + $parsed_count );
print("The parsing failed\n");
return 1;
}
$type ||= 'gene';
$label ||= $accession;
$description ||= '';
$version ||= '1';
++$parsed_count;
my $xref_id =
XrefParser::BaseParser->get_xref( $accession, $source_id, $species_id );
if ( !defined($xref_id) || $xref_id eq '' ) {
$xref_id =
XrefParser::BaseParser->add_xref(
$accession, $version, $label,
$description, $source_id, $species_id, "DIRECT"
);
}
XrefParser::BaseParser->add_direct_xref( $xref_id, $ensembl_id,
$type, $accession );
} ## end while ( defined( my $line...
printf( "%d direct xrefs succesfully parsed\n", $parsed_count );
$file_io->close();
print "Done\n";
return 0;
} ## end sub run
1;
]]>