my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $files = $ref_arg->{files};
my $verbose = $ref_arg->{verbose};
if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
croak "Need to pass source_id, species_id and files as pairs";
}
$verbose |=0;
my $file = @{$files}[0];
# need to uncompress the zip file, whihc is not supported by the xrefs framework
# print STDERR "uncompressing the zip file\n";
$file =~ /(.+)\/.+\.zip$/;
my $dir = $1;
#print STDERR "dir, $dir\n";
system ("unzip -o $file -d $dir");
$file =~ s/\.zip$
# print STDERR "file after decompression, $file\n";
my $gene_source_id = $self->get_source_id_for_source_name("PGSC_GENE");
my $pgsc_io = $self->get_filehandle($file);
if ( !defined $pgsc_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 is an error
}
my $xref_count =0;
my $syn_count =0;
while ( $_ = $pgsc_io->getline() ) {
chomp;
if ($_ =~ /^([^\t]+)\t([^\t]+)$/) {
my ($pgsc_id, $desc) = ($1,$2);
if ($verbose) {
#print STDERR "pgsc_id, $pgsc_id\n";
#print STDERR "desc: $desc\n";
}
my $locus_name = $pgsc_id;
my $gene_xref_id = $self->add_xref({ acc => $pgsc_id,
label => $locus_name,
desc => $desc,
source_id => $gene_source_id,
species_id => $species_id,
info_type => "DIRECT"} );
$self->add_direct_xref($gene_xref_id, $pgsc_id, "Gene", "DIRECT");
$xref_count++;
}
else {
if ($verbose) {
print STDERR "failed to parse line, $_\n\n";
}
}
}
$pgsc_io->close();
print $xref_count." PGSC Xrefs added\n" if($verbose);
return 0; #successful
}
Code:
