Raw content of XrefParser::MGDParser
<![CDATA[package XrefParser::MGDParser;
use strict;
use POSIX qw(strftime);
use File::Basename;
use base qw( XrefParser::BaseParser );
my $xref_sth ;
my $dep_sth;
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print "\nUsage: MGDParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run($ARGV[0]);
}
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files = shift;
my $release_file = shift;
$verbose = shift;
my $file = @{$files}[0];
die "No longer used. MGI is taken form the uniprot file\n";
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 (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
my $count = 0;
my $mismatch = 0;
my %mgi_good;
my $file_io = $self->get_filehandle($file);
if ( !defined $file_io ) {
print "ERROR: Could not open file $file";
return 1; # 1 is an error
}
while ( my $line = $file_io->getline() ) {
chomp $line;
my ($key,$label,$desc,$sps) = (split("\t",$line))[0,1,3,6];
my @sp = split(/\s/,$sps);
foreach my $value (@sp){
if(defined($value) and $value and defined($swiss{$value})){
XrefParser::BaseParser->add_to_xrefs($swiss{$value},$key,'',$label,$desc,"",$source_id,$species_id);
$mgi_good{$key} = 1;
$count++;
}
elsif(defined($value) and $value and defined($refseq{$value})){
$mismatch++;
}
}
}
$file_io->close();
my $dir = dirname($file);
my $syn_file = $dir."/MRK_Synonym.sql.rpt";
$file_io = $self->get_filehandle($syn_file);
if ( !defined $file_io ) {
print "ERROR: Could not open file $syn_file";
return 1;
}
my $synonyms=0;
while ( $_ = $file_io->getline() ) {
if(/MGI:/){
chomp ;
my ($key,$syn) = (split)[0,4];
if(defined($mgi_good{$key})){
$self->add_to_syn($key, $source_id, $syn, $species_id);
$synonyms++;
}
}
}
$file_io->close();
print "\t$count xrefs succesfully loaded\n";
print "\t$synonyms synonyms successfully loaded\n";
print "\t$mismatch xrefs failed to load\n";
return 0;
}
1;
]]>