Raw content of XrefParser::RGDParser
<![CDATA[package XrefParser::RGDParser;
use strict;
use POSIX qw(strftime);
use File::Basename;
use base qw( XrefParser::BaseParser );
my $xref_sth ;
my $dep_sth;
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print "\nUsage: RGDParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run($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;
my $verbose = shift;
my $file = @{$files}[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 (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
my $rgd_io = $self->get_filehandle($file);
if ( !defined $rgd_io ) {
print "ERROR: Could not open $file\n";
return 1;
}
my $line = $rgd_io->getline();
chomp $line;
my @linearr = split(/\t/,$line);
#
#warn if sanity check fails
#
if($linearr[0] =~ /GENE_RDB_ID/){
die ($linearr[0]."!= GENE_RDB_ID is not the first element in the header\n");
}
if($linearr[1] ne "SYMBOL"){
die ("SYMBOL is not the second element in the header\n");
}
if($linearr[2] ne "NAME"){
die ("NAME is not the third element in the header\n");
}
if($linearr[25] ne "GENBANK_NUCLEOTIDE"){
die ("GENBANK_NUCLEOTIDE is not the twentysixth element in the header but ".$linearr[25]." is.\\n");
}
my $count= 0;
my $mismatch = 0;
while ( $line = $rgd_io->getline() ) {
chomp $line;
my ($rgd, $symbol, $name, $refseq) = (split (/\t/,$line))[0,1,2,25];
my @nucs = split(/\,/,$refseq);
my $done = 0;
my $failed_list ="";
foreach my $nuc (reverse @nucs){
if(!$done){
my $xref=undef;
$xref=$refseq{$nuc} if defined($refseq{$nuc});
if(defined($xref)){
$done = 1;
XrefParser::BaseParser->add_to_xrefs($xref,$rgd,"",$symbol,$name,"",$source_id,$species_id);
$count++;
}
else{
$failed_list .= " $nuc";
}
}
}
if(!$done){
# print STDERR "$rgd FAILED for $failed_list\n";
$self->add_xref($rgd,"",$symbol,$name,$source_id,$species_id,"MISC");
$mismatch++;
}
}
$rgd_io->close();
print "\t$count xrefs succesfully loaded and dependent on refseq\n" if($verbose);
print "\t$mismatch xrefs added but with NO dependencies\n" if($verbose);
return 0;
}
1;
]]>