my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $filename = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
if((!defined $source_id) or (!defined $species_id) or (!defined $filename) ){
croak "Need to pass source_id, species_id and file as pairs";
}
$verbose |=0;
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) ) {
print {*STDERR} "Line $parsed_count contains has less than two columns.\n";
print {*STDERR} ("The parsing failed\n");
return 1;
}
$type ||= 'gene';
$label ||= $accession;
$description ||= '';
$version ||= '1';
++$parsed_count;
my $xref_id =
$self->get_xref( $accession, $source_id, $species_id );
if ( !defined($xref_id) || $xref_id eq '' ) {
$xref_id =
$self->add_xref({ acc => $accession,
version => $version,
label => $label,
desc => $description,
source_id => $source_id,
species_id => $species_id,
info_type => "DIRECT"} );
}
$self->add_direct_xref( $xref_id, $ensembl_id,
$type, $accession );
} ## end while ( defined( my $line...
printf( "%d direct xrefs succesfully parsed\n", $parsed_count ) if($verbose);
$file_io->close();
print "Done\n" if($verbose);;
return 0;
Code:
