XrefParser::RFAMParser Class Reference
Public Member Functions | |
| public | run_script () |
Detailed Description
Definition at line 5 of file RFAMParser.pm.
Member Function Documentation
◆ run_script()
| public XrefParser::RFAMParser::run_script | ( | ) |
Undocumented method
Code:
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sub run_script {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $species_name = $ref_arg->{species};
my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
my $core_db = $ref_arg->{dba};
my $dbi = $ref_arg->{dbi};
$dbi = $self->dbi unless defined $dbi;
if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and file as pairs";
}
$verbose |=0;
my $wget;
my $user = "ensro";
my $host;
my $port = 3306;
my $dbname;
my $pass;
if($file =~ /wget[=][>](\S+?)[,]/){
$wget = $1;
}
if($file =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($file =~ /port[=][>](\S+?)[,]/){
$port = $1;
}
if($file =~ /dbname[=][>](\S+?)[,]/){
$dbname = $1;
}
if($file =~ /pass[=][>](\S+?)[,]/){
$pass = $1;
}
if($file =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
#get direct RFAM xrefs from core
my $registry = "Bio::EnsEMBL::Registry";
my $dba;
#get the species name
my %id2name = $self->species_id2name($dbi);
if (defined $species_name) { push @{$id2name{$species_id}}, $species_name; }
if (!defined $id2name{$species_id}) { next; }
$species_name = $id2name{$species_id}[0];
if ($host) {
$dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
'-host' => $host,
'-user' => $user,
'-pass' => $pass,
'-dbname' => $dbname,
'-port' => $port,
'-species' => $species_name,
'-group' => 'core',
);
} elsif (defined $core_db) {
$dba = $core_db;
} else {
$registry->load_registry_from_multiple_dbs(
{
'-host' => 'mysql-ens-sta-1',
'-port' => 4519,
'-user' => 'ensro',
},
);
$dba = $registry->get_DBAdaptor($species_name, 'core');
}
my $rfam_sql = "select distinct t.stable_id, hit_name from analysis a join transcript t on (a.analysis_id = t.analysis_id and a.logic_name like 'ncrna%' and t.biotype != 'miRNA') join exon_transcript et on (t.transcript_id = et.transcript_id) join supporting_feature sf on (et.exon_id = sf.exon_id and sf.feature_type = 'dna_align_feature' ) join dna_align_feature df on (sf.feature_id = df.dna_align_feature_id) order by hit_name";
$sth->execute();
#hash keyed on RFAM accessions, value is an array of ensembl transcript stable_ids
my %rfam_transcript_stable_ids;
while (my ($stable_id, $hit_name) = $sth->fetchrow_array ) {
my $rfam_id;
if ($hit_name =~ /^(RF\d+)/) {
$rfam_id = $1;
}
if ($rfam_id) {
push @{$rfam_transcript_stable_ids{$rfam_id}}, $stable_id;
}
}
$sth->finish;
my @lines;
if (defined $wget) {
my $ua = LWP::UserAgent->new();
$ua->timeout(10);
$ua->env_proxy();
my $request = HTTP::Request->new(GET => $wget);
my $response = $ua->request($request);
if ( !$response->is_success() ) {
warn($response->status_line);
return 1;
}
@lines = split(/\n\n\n/, $response->decoded_content);
} else {
my $file_io = $self->get_filehandle($file);
if ( !defined $file_io ) {
print "ERROR: Can't open RFAM file $file\n";
return 1;
}
my $temp_line;
while (my $line = $file_io->getline()) {
if ($line =~ /\/\//) {
push @lines, $temp_line;
$temp_line = '';
} else {
$temp_line .= $line . "\n";
}
}
}
my @xrefs;
my $xref_count = 0;
my $direct_count = 0;
while (my $entry = shift @lines) {
my $xref;
chomp $entry;
next if (!$entry);
my ($accession) = $entry =~ /#=GF\sAC\s+(\w+)/ ;
my ($label) = $entry =~ /#=GF\sID\s+([^\n]+)/;
my ($description) = $entry =~ /#=GF\sDE\s+([^\n]+)/;
if ($accession) {
if (exists($rfam_transcript_stable_ids{$accession})){
#add xref
my $xref_id = $self->add_xref({ acc => $accession,
version => 0,
label => $label || $accession ,
desc => $description,
source_id => $source_id,
species_id => $species_id,
dbi => $dbi,
info_type => "DIRECT"} );
my @transcript_stable_ids = @{$rfam_transcript_stable_ids{$accession}};
foreach my $stable_id (@transcript_stable_ids){
$self->add_direct_xref($xref_id, $stable_id, "Transcript", "", $dbi);
$direct_count++;
}
$xref_count++;
}
}
}
print "Added $xref_count RFAM xrefs and $direct_count direct xrefs\n" if($verbose);
return 0; # successfull
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
