Raw content of XrefParser::DBASSParser
<![CDATA[package XrefParser::DBASSParser;
use strict;
use base qw( XrefParser::BaseParser);
use DBI;
use Carp;
# This parser will read direct xrefs from a simple comma-delimited file downloaded from the DBASS database.
# The columns of the file should be the following:
#
# 1) DBASS Gene ID
# 2) DBASS Gene Name
# 3) Ensembl Gene ID
my $dbi;
my $xref_id;
my $source_id;
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files = shift;
my $rel_url = shift;
my $verbose = shift;
my $filename = @{$files}[0];
# my ( $source_id, $species_id, $filename, $rel_url,$verbose ) = @_;
my $file_io = $self->get_filehandle($filename);
if ( !defined($file_io) ) {
return 1;
}
my $parsed_count = 0;
$file_io->getline();
while ( defined( my $line = $file_io->getline() ) ) {
$line =~ s/\s*$//;
my ( $dbass_gene_id, $dbass_gene_name, $ensembl_id) = split( /,/, $line );
if ( !defined($dbass_gene_id) || !defined($ensembl_id) ) {
printf STDERR ( "Line %d contains has less than two columns.\n",
1 + $parsed_count );
print STDERR ("The parsing failed\n");
return 1;
}
my $first_gene_name = $dbass_gene_name;
my $second_gene_name;
if ($dbass_gene_name =~ /.\/./){
($first_gene_name, $second_gene_name) = split( /\//, $dbass_gene_name );
}
if ($dbass_gene_name =~ /(.*)\((.*)\)/){
$first_gene_name = $1;
$second_gene_name = $2;
# print $first_gene_name, "\n", $second_gene_name, "\n" if($verbose);
}
my $label = $first_gene_name;
my $type = 'gene';
my $description = '';
my $version = '1';
my $synonym = $second_gene_name;
++$parsed_count;
my $xref_id = XrefParser::BaseParser->get_xref( $dbass_gene_id, $source_id, $species_id );
if ( !defined($xref_id) || $xref_id eq '' ) {
$xref_id = XrefParser::BaseParser->add_xref($dbass_gene_id, $version, $label, $description, $source_id, $species_id, "DIRECT");
}
XrefParser::BaseParser->add_direct_xref( $xref_id, $ensembl_id, $type, '');
if (defined ($synonym)) {
XrefParser::DBASSParser->add_synonym($xref_id, $synonym);
}
elsif ($synonym =~ /^\s/){
print "There is white space! \n" if($verbose);
}
else {
next;
}
} ## end while ( defined( my $line...
printf( "%d direct xrefs succesfully parsed\n", $parsed_count ) if($verbose);
$file_io->close();
return 0;
} ## end sub run
1;
]]>