Raw content of XrefParser::GOParser
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package XrefParser::GOParser;
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: GoParser.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];
my $file_desc = @{$files}[1];
#
# Get the descriptions from the desc file.
#
my $go_io = $self->get_filehandle($file_desc);
if ( !defined $go_io ) {
print STDERR "ERROR: Could not open $file_desc\n";
return 1; # 1 error
}
my %go_to_desc;
print "description file for GO\n" if($verbose);
my $term = undef;
my $desc = undef;
while ( $_ = $go_io->getline() ) {
if(/\<id\>(GO:\d+)\<\/id\>/){
$term = $1;
}
elsif(/\<name\>(.*)\<\/name\>/){
if(defined($term)){
$go_to_desc{$term} = $1;
}
$term = undef;
}
}
$go_io->close();
my %wrongtype;
#get the "main" GO source id.
$source_id = $self->get_source_id_for_source_name("GO","main");
#get the mapping that are already there so that we don't get lots of duplicates.
# stored in the global hash xref_dependent_mapped.
$self->get_dependent_mappings($source_id);
if(!defined($species_id)){
$species_id = $self->get_species_id_for_filename($file);
}
my $swiss_miss=0;
my (%swiss) = %{$self->get_valid_codes("uniprot",$species_id)};
my $refseq_miss=0;
my (%refseq) = %{$self->get_valid_codes("refseq",$species_id)};
# complication with GO xrefs from JAX - linked to MGI symbols, which are themselves
# dependent, so we need to get the MGI->Uniprot mapping and store the *Uniprot*
# as the master xref
my %mgi_to_uniprot = %{
$self->get_existing_mappings( "MGI", "Uniprot/Swissprot",
$species_id ) };
my %worm;
my %worm_label;
my $wormset;
my %fish;
my $fishset;
my $count = 0;
my %sp2tax = $self->species_id2taxonomy(); #some species have multiple
#tax_id i.e. strains
my @tax_ids = @{$sp2tax{$species_id}};
foreach my $tax_id ( @tax_ids){
my $go_io = $self->get_filehandle($file);
if ( !defined $go_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 error
}
print "processing for taxon: $tax_id\n" if($verbose);
my $taxon_line = "taxon:".$tax_id;
my $miss =0;
while ( $_ = $go_io->getline() ) {
if(/$taxon_line/){
chomp;
my @array = split (/\t/,$_);
# Skip "NOT" terms entirely
next if ($array[3] eq "NOT");
$array[9] =~ s/\'/\\\'/g;
my $master=0;
if($array[0] =~ /ENSEMBL/){
#these might be good for a check
# match GO to Uniprot
# match Uniprot to ENSEMBL
# check ENSEMBL's are the same.
}
elsif($array[0] =~ /RefSeq/){
if($refseq{$array[1]}) {
$self->add_to_xrefs($refseq{$array[1]},$array[4],'',$array[4],$go_to_desc{$array[4]} || '',$array[6],$source_id,$species_id);
$count++;
#print join (" ", "RefSeq" ,$refseq{$array[1]}, $array[4], "\n");
}
else{
$refseq_miss++;
}
}
elsif($array[0] =~ /UniProt/){
if($swiss{$array[1]}){
$self->add_to_xrefs($swiss{$array[1]},$array[4],'',$array[4],$go_to_desc{$array[4]} || '',$array[6],$source_id,$species_id);
$count++;
#print join (" ", "UniProt" ,$swiss{$array[1]}, $array[4], "\n");
}
else{
$swiss_miss++;
}
}
elsif($array[0] =~ /^WB/){
#WB CE20707 ZYG-9 GO:0008017 WB:WBPaper00003099|PMID:9606208 ISS F protein taxon:6239 20030829 WB
if(!defined($wormset)){
$wormset = 1;
%worm = %{$self->get_valid_xrefs_for_direct_xrefs('worm')};
}
my $worm_acc=$array[1];
if(!defined($worm{$worm_acc})){
if(defined($worm{$array[10]})){
$worm_acc = $array[10];
}
elsif(defined($worm{$array[2]})){
$worm_acc = $array[2];
}
}
if(defined($worm{$worm_acc})){
my ($xref_id, $stable_id, $type, $link) = split(/::/,$worm{$worm_acc});
my $new_xref_id=$self->get_xref($array[4],$source_id, $species_id);
if(!defined($new_xref_id)){
$new_xref_id = $self->add_xref($array[4],undef,$array[4],"", $source_id, $species_id, "DIRECT");
$count++;
}
if(!defined($self->get_direct_xref($stable_id,$type, $array[6]))){
$self->add_direct_xref($new_xref_id, $stable_id, $type, $array[6]);
}
}
else{
$miss++;
}
}
elsif($array[0] =~ /^ZFIN/){
#ZFIN ZDB-GENE-030131-5418 rfng GO:0030902 ZFIN:ZDB-PUB-050125-4|PMID:15659486 IMP ZFIN:ZDB-MRPHLNO-050308-5 radical fringe homolog (Drosophila) gene taxon:7955 20050310 ZFIN
if(!defined($fishset)){
$fishset = 1;
%fish = %{$self->get_valid_xrefs_for_dependencies
('ZFIN_ID','Uniprot/SPTREMBL','RefSeq_peptide',
'Uniprot/SWISSPROT')};
}
if(defined($fish{$array[1]})){
$self->add_to_xrefs($fish{$array[1]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
$count++;
}
}
elsif($array[0] =~ /MGI/){
# MGI MGI:1923501 0610007P08Rik GO:0004386 MGI:MGI:1354194 IEA F RIKEN cDNA 0610007P08 gene gene taxon:10090 20060213 UniProt
# 0 1 2 3 4 5 6 7 8
if($mgi_to_uniprot{$array[1]}){
$self->add_to_xrefs($mgi_to_uniprot{$array[1]}, $array[4], '', $array[4], $go_to_desc{$array[4]} || '', $array[6], $source_id, $species_id);
$count++;
#print join (" ", "MGI" ,$mgi_to_uniprot{$array[1]}, $array[4], "\n");
}
}
elsif(!defined($wrongtype{$array[0]})){
print STDERR "WARNING: unknown type ".$array[0]."\n" if($verbose);
$wrongtype{$array[0]} = 1;
}
}
}
$go_io->close();
print "\t$count GO dependent xrefs added $refseq_miss refseq not found and $swiss_miss Swissprot not found \n" if($verbose);
}
if ( defined $release_file ) {
# Parse and set release information from $release_file.
my $release_io = $self->get_filehandle($release_file);
# Slurp mode.
local $/;
my $release = <$release_io>;
$release_io->close();
$release =~ tr /\n/ /;
$release =~
s#.*The following table describes.*?of (GOA.*?)<ul>.*#$1#;
$release =~ s#<[^>]+>##g;
print "GO release: '$release'\n" if($verbose);
$self->set_release( $source_id, $release );
}
return 0;
}
1;
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