Raw content of XrefParser::EntrezGeneParser
<![CDATA[package XrefParser::EntrezGeneParser;
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: EntrezGeneParser.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 $wiki_source_id = $self->get_source_id_for_source_name("WikiGene");
my %species_tax_id = %{$self->get_taxonomy_from_species_id($species_id)};
my $eg_io = $self->get_filehandle($file);
if ( !defined $eg_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 is an error
}
my %seen;
my $head = $eg_io->getline(); # first record are the headers
chomp $head;
my (@arr) = split(/\s+/,$head);
# process this to the correct indexes to use. (incase they change);
my $gene_id_index = -2;
my $gene_symbol_index = -2;
my $gene_desc_index = -2;
my $gene_tax_id_index = -2;
my $gene_synonyms_index = -2;
foreach (my $i=0; $i<= $#arr; $i++){
#-1 as first one is "#Format:"q
if($arr[$i] eq "tax_id"){
$gene_tax_id_index = $i-1;
}
elsif($arr[$i] eq "GeneID"){
$gene_id_index = $i-1;
}
elsif($arr[$i] eq "Symbol"){
$gene_symbol_index = $i-1;
}
elsif($arr[$i] eq "description"){
$gene_desc_index = $i-1;
}
elsif($arr[$i] eq "Synonyms"){
$gene_synonyms_index = $i-1;
}
}
if( $gene_id_index == -2 ||
$gene_symbol_index == -2 ||
$gene_desc_index == -2 ||
$gene_synonyms_index == -2 ||
$gene_tax_id_index == -2){
print "HEADER\n$head\n\n";
print "Unable to get all the indexes needed\n";
print "gene_id = $gene_id_index\n";
print "tax_id = $gene_tax_id_index\n";
print "symbol = $gene_symbol_index\n";
print "desc = $gene_desc_index\n";
print "synonyms = $gene_synonyms_index\n";
return 0; # this is an error
}
my $xref_count = 0;
my $syn_count = 0;
while ( $_ = $eg_io->getline() ) {
chomp;
my (@arr) = split(/\t/,$_);
if(!defined($species_tax_id{$arr[$gene_tax_id_index]})){
next;
}
my $acc = $arr[$gene_id_index];
if($seen{$acc}){
next;
}
else{
$seen{$acc} = 1;
}
my $symbol = $arr[$gene_symbol_index];
my $desc = $arr[$gene_desc_index];
$self->add_xref($acc,"",$symbol,$desc,$source_id,$species_id, "DEPENDENT");
$self->add_xref($acc,"",$symbol,$desc,$wiki_source_id,$species_id, "DEPENDENT","From EntrezGene $acc");
$xref_count++;
my (@syn) = split(/\|/ ,$arr[$gene_synonyms_index]);
foreach my $synonym (@syn){
if($synonym ne "-"){
$self->add_to_syn($acc, $source_id, $synonym, $species_id);
$syn_count++;
}
}
}
$eg_io->close();
print $xref_count." EntrezGene Xrefs added with $syn_count synonyms\n" if($verbose);
return 0; #successful
}
1;
]]>