Raw content of XrefParser::ZFINParser
<![CDATA[package XrefParser::ZFINParser;
use strict;
use POSIX qw(strftime);
use File::Basename;
use File::Spec::Functions;
use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print STDERR "\nUsage: ZFINParser.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 $dir = dirname($file);
my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
my $swissprot_io =
$self->get_filehandle( catfile( $dir, 'uniprot.txt' ) );
if ( !defined $swissprot_io ) {
print STDERR "ERROR: Could not open " . catfile( $dir, 'uniprot.txt' ). "\n" ;
return 1; # 1 error
}
#e.g.
#ZDB-GENE-000112-30 couptf2 O42532
#ZDB-GENE-000112-32 couptf3 O42533
#ZDB-GENE-000112-34 couptf4 O42534
my $spcount =0;
my $rscount =0;
my $mismatch=0;
while ( $_ = $swissprot_io->getline() ) {
chomp;
my ($zfin, $label, $acc) = split (/\s+/,$_);
if(defined($swiss{$acc})){
XrefParser::BaseParser->add_to_xrefs($swiss{$acc},$zfin,'',$label,'','',$source_id,$species_id);
$spcount++;
}
else{
$mismatch++;
}
}
$swissprot_io->close();
my $refseq_io = $self->get_filehandle( catfile( $dir, 'refseq.txt' ) );
if ( !defined $refseq_io ) {
print STDERR "ERROR: Could not open " . catfile( $dir, 'refseq.txt' ),"\n" ;
return 1;
}
#ZDB-GENE-000125-12 igfbp2 NM_131458
#ZDB-GENE-000125-12 igfbp2 NP_571533
#ZDB-GENE-000125-4 dlc NP_571019
while ( $_ = $refseq_io->getline() ) {
chomp;
my ($zfin, $label, $acc) = split (/\s+/,$_);
if(defined($refseq{$acc})){
XrefParser::BaseParser->add_to_xrefs($refseq{$acc},$zfin,'',$label,'','',$source_id,$species_id);
$rscount++;
}
else{
$mismatch++;
}
}
$refseq_io->close();
my (%zfin) = %{XrefParser::BaseParser->get_valid_codes("zfin",$species_id)};
my $zfin_io = $self->get_filehandle( catfile( $dir, 'aliases.txt' ) );
if ( !defined $zfin_io ) {
print STDERR "ERROR: Could not open " . catfile( $dir, 'aliases.txt' ), "\n" ;
return 1;
}
#ZDB-GENE-000125-4 deltaC dlc bea
#ZDB-GENE-000125-4 deltaC dlc beamter
my $syncount = 0;
while ( $_ = $zfin_io->getline() ) {
chomp;
my ($acc, undef, undef, $syn) = split (/\t/,$_);
if(defined($zfin{$acc})){
XrefParser::BaseParser->add_to_syn($acc, $source_id, $syn, $species_id);
$syncount++;
}
}
$zfin_io->close();
if($verbose){
print "\t$spcount xrefs from UniProt and\n";
print "\t$rscount xrefs from RefSeq succesfully loaded\n";
print "\t$syncount synonyms loaded\n";
print "\t$mismatch xrefs ignored\n";
}
return 0;
}
1;
]]>