Raw content of XrefParser::SGDParser
<![CDATA[package XrefParser::SGDParser;
use strict;
use POSIX qw(strftime);
use File::Basename;
use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print "\nUsage: SGDParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run($ARGV[0]);
}
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files_ref = shift;
my $rel_file = shift;
my $verbose = shift;
my $file = @{$files_ref}[0];
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
}
if(!defined($species_id)){
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
my $sgd_io = $self->get_filehandle($file);
if ( !defined $sgd_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 is an error
}
my $xref_count =0;
my $syn_count =0;
while ( $_ = $sgd_io->getline() ) {
chomp;
my ($locus_name, $alias_name, $desc, $gene_prod, $phenotype, $orf_name, $sgd_id) = split(/\t/,$_);
my (@syn) = split(/\|/,$alias_name);
$self->add_xref($sgd_id,"",$locus_name,$desc,$source_id,$species_id,"MISC");
$xref_count++;
foreach my $synonym (@syn){
$self->add_to_syn($sgd_id, $source_id, $synonym, $species_id);
$syn_count++;
}
}
$sgd_io->close();
print $xref_count." SGD Xrefs added with $syn_count synonyms\n" if($verbose);
return 0; #successful
}
1;
]]>