my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $file = $ref_arg->{file};
my $db = $ref_arg->{dba};
my $verbose = $ref_arg->{verbose}
my $dbi = $ref_arg->{dbi}
if ((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
confess "Need to pass source_id, species_id, file as pairs";
}
# parse the file string and set default user
my $file_params = $self->parse_file_string($file);
$file_params->{user}
# Prepare lookup lists
my (%swissprot) = %{$self->get_valid_codes('Uniprot/SWISSPROT',$species_id, $dbi)};
my (%refseq) = %{$self->get_valid_codes('refseq',$species_id, $dbi)};
my @list = ('refseq_peptide', 'refseq_mRNA');
my (%entrezgene) = %{$self->get_valid_xrefs_for_dependencies('EntrezGene', $dbi, @list)};
# Prepare sources
my $self_source_name = $self->get_source_name_for_source_id($source_id, $dbi);
# get RefSeq source ids
foreach my $source_name (@SOURCES) {
$self->{source_ids}->{$source_name} = $self->get_source_id_for_source_name( $self_source_name, $source_name , $dbi );
}
$self->{source_ids}->{'lrg'} = $self->get_source_id_for_source_name( 'LRG_HGNC_notransfer', undef, $dbi );
$self->{source_ids}->{'genecards'} = $self->get_source_id_for_source_name('GeneCards', undef, $dbi);
# statistics counts
my %name_count;
my $mismatch = 0;
# Get CCDS data from core db
my $core_db;
if (defined $db) {
$core_db = $db->dbc();
} elsif (defined $file_params->{host}) {
host => $file_params->{host},
port => $file_params->{port},
user => $file_params->{user},
dbname => $file_params->{dbname},
pass => $file_params->{pass}
})->dbi;
} else {
confess "No ensembl core database provided\n";
}
if (!defined $core_db) {
confess "No ensembl core database!\n";
}
my $sql =(<<'CCDS');
SELECT ta.value, t.stable_id
INNER JOIN transcript_attrib ta ON t.transcript_id = ta.transcript_id
INNER JOIN attrib_type a ON ta.attrib_type_id = a.attrib_type_id
WHERE a.code = 'ccds_transcript';
CCDS
my %ccds_to_ens;
my $sth = $core_db->prepare($sql);
$sth->execute() or croak( $core_db->errstr() );
while ( my ($ccds_id, $ens_id) = $sth->fetchrow_array() ) {
# Remove version
$ccds_id =~ s/\.\d+
$ccds_to_ens{$ccds_id} = $ens_id;
}
$sth->finish;
# in memory HGNC file
my $mem_file;
# use wget link to get file
if (defined $file_params->{wget}) {
my $ua = LWP::UserAgent->new();
$ua->timeout(10);
$ua->env_proxy();
my $request = HTTP::Request->new(
GET => $file_params->{wget}
);
my $response = $ua->request($request);
if ( !$response->is_success() ) {
confess $response->status_line;
}
$mem_file = $response->decoded_content;
# else get file from disk
} else {
my $disk_fh = $self->get_filehandle($file);
if ( !defined $disk_fh ) {
confess "Can't open HGNC file '$file'\n";
}
$mem_file = do { local $/; <$disk_fh> };
}
my $input_file = Text::CSV->new({
sep_char => "\t",
empty_is_undef => 1,
binary => 1,
auto_diag => 1
}) or croak "Cannot use file $file: ".Text::CSV->error_diag ();
# make sure it's utf8
$mem_file = Encode::encode("UTF-8", $mem_file);
# get rid of non-conventional " used in the Locus specific databases field
$mem_file =~ s/"//xg;
open my $fh, '<', \$mem_file or confess "Can't open HGNC in-memory file: $!\n";
$input_file->column_names( @{ $input_file->getline( $fh ) } );
# loop through each row
while ( my $data = $input_file->getline_hr( $fh ) ) {
my $acc = $data->{'HGNC ID'};
my $symbol = $data->{'Approved symbol'};
my $name = $data->{'Approved name'};
my $previous_symbols = $data->{'Previous symbols'};
my $synonyms = $data->{'Alias symbols'};
my $seen = 0;
# Direct CCDS to ENST mappings
my $ccds = $data->{'CCDS IDs'};
my @ccds_list;
if ( defined $ccds ) {
@ccds_list = split( /,\s/x, $ccds );
}
CCDS:
foreach my $ccds (@ccds_list) {
my $enst_id = $ccds_to_ens{$ccds};
if (!defined $enst_id) {
next CCDS;
}
$self->add_to_direct_xrefs({
stable_id => $enst_id,
type => 'gene',
acc => $acc,
label => $symbol,
desc => $name,
source_id => $self->{source_ids}->{'ccds'},
dbi => $dbi,
species_id => $species_id
});
$self->add_synonyms_for_hgnc({
source_id => $self->{source_ids}->{'ccds'},
name => $acc,
species_id => $species_id,
dbi => $dbi,
dead => $previous_symbols,
alias => $synonyms
});
$name_count{'ccds'}++;
}
# Direct LRG to ENST mappings
my $lrg_id = $data->{'Locus specific databases'};
if ( defined $lrg_id && $lrg_id =~ m/(LRG_\d+)\|/x){
$lrg_id = $1;
$self->add_to_direct_xrefs({
stable_id => $lrg_id,
type => 'gene',
acc => $acc,
label => $symbol,
desc => $name,
source_id => $self->{source_ids}->{'lrg'},
dbi => $dbi,
species_id => $species_id
});
$self->add_synonyms_for_hgnc({
source_id => $self->{source_ids}->{'lrg'},
name => $acc,
species_id => $species_id,
dbi => $dbi,
dead => $previous_symbols,
alias => $synonyms
});
$name_count{'lrg'}++;
}
# Direct Ensembl mappings
my $ensg_id = $data->{'Ensembl gene ID'};
if ( defined $ensg_id ){
$seen = 1;
$self->add_to_direct_xrefs({
stable_id => $ensg_id,
type => 'gene',
acc => $acc,
label => $symbol,
desc => $name,
dbi => $dbi,
source_id => $self->{source_ids}->{'ensembl_manual'},
species_id => $species_id
});
$self->add_synonyms_for_hgnc({
source_id => $self->{source_ids}->{'ensembl_manual'},
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
dbi => $dbi,
alias => $synonyms
});
$name_count{'ensembl_manual'}++;
# GeneCards
my $direct_id = $self->get_xref($acc, $self->{source_ids}->{'ensembl_manual'}, $species_id, $dbi);
my ($hgnc_id) = $acc =~ /HGNC:(\d+)/;
$self->add_dependent_xref({
master_xref_id => $direct_id,
acc => $hgnc_id,
label => $symbol,
desc => $name,
source_id => $self->{source_ids}->{'genecards'},
dbi => $dbi,
species_id => $species_id
});
$self->add_synonyms_for_hgnc({
source_id => $self->{source_ids}->{'genecards'},
name => $hgnc_id,
species_id => $species_id,
dbi => $dbi,
dead => $previous_symbols,
alias => $synonyms
});
$name_count{'genecards'}++;
}
# RefSeq
my $refseq_id = $data->{'RefSeq IDs'};
if ($refseq_id) {
if ( defined $refseq{$refseq_id} ){
$seen = 1;
foreach my $xref_id ( @{$refseq{$refseq_id}} ){
$self->add_dependent_xref({
master_xref_id => $xref_id,
acc => $acc,
label => $symbol,
desc => $name,
source_id => $self->{source_ids}->{'refseq_manual'},
dbi => $dbi,
species_id => $species_id
});
$name_count{'refseq_manual'}++;
}
$self->add_synonyms_for_hgnc({
source_id => $self->{source_ids}->{'refseq_manual'},
name => $acc,
species_id => $species_id,
dbi => $dbi,
dead => $previous_symbols,
alias => $synonyms
});
}
}
# EntrezGene
my $entrez_id = $data->{'NCBI Gene ID'};
if ( defined $entrez_id ){
if ( defined $entrezgene{$entrez_id} ){
$seen = 1;
$self->add_dependent_xref({
master_xref_id => $entrezgene{$entrez_id},
acc => $acc,
label => $symbol,
desc => $name,
source_id => $self->{source_ids}->{'entrezgene_manual'},
dbi => $dbi,
species_id => $species_id
});
$self->add_synonyms_for_hgnc({
source_id => $self->{source_ids}->{'entrezgene_manual'},
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
dbi => $dbi,
alias => $synonyms
});
$name_count{'entrezgene_manual'}++;
}
}
# Store to keep descriptions if stored yet
if ( !$seen ){
$self->add_xref({
acc => $acc,
label => $symbol,
desc => $name,
source_id => $self->{source_ids}->{'desc_only'},
species_id => $species_id,
dbi => $dbi,
info_type => "MISC"
});
$self->add_synonyms_for_hgnc({
source_id => $self->{source_ids}->{'desc_only'},
name => $acc,
species_id => $species_id,
dbi => $dbi,
dead => $previous_symbols,
alias => $synonyms
});
$mismatch++;
}
}
close $fh;
if ( $verbose ){
print "HGNC xrefs loaded:\n";
foreach my $type (sort keys %name_count){
print "\t$type\t$name_count{$type}\n";
}
print "$mismatch HGNC ids could not be associated in xrefs\n";
}
return 0; # successful
}
Code:
