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lib/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm  view on Meta::CPAN

sub lookup_current {
  my $self    = shift;
  my $arch_id = shift;

  my $type = lc( $arch_id->type );

  unless ($type) {
    warning("Can't lookup current version without a type.");
    return 0;
  }

  my $sql = qq(
    SELECT version FROM ${type}
    WHERE stable_id = ?
  );
  my $sth = $self->prepare($sql);
  $sth->execute( $arch_id->stable_id );
  my ($version) = $sth->fetchrow_array;
  $sth->finish;

  if ($version) {
    $arch_id->current_version($version);
    return 1;
  }

  # didn't find a current version
  return 0;
} ## end sub lookup_current


# infer type from stable ID format
sub _resolve_type {
  my $self = shift;
  my $arch_id = shift;
  
  my $stable_id = $arch_id->stable_id();
  my $id_type;

  # first, try to infer type from stable ID format
  #
  # Anopheles IDs
  if ($stable_id =~ /^AGAP.*/) {
    if ($stable_id =~ /.*-RA/) {
      $id_type = "Transcript";
    } elsif ($stable_id =~ /.*-PA/) {
      $id_type = "Translation";
    } else {
      $id_type = "Gene";
    }

  # standard Ensembl IDs
  } elsif ($stable_id =~ /.*G\d+(\.\d+)?$/) {
    $id_type = "Gene";
  } elsif ($stable_id =~ /.*T\d+(\.\d+)?$/) { 
    $id_type = "Transcript";
  } elsif ($stable_id =~ /.*P\d+(\.\d+)?$/) { 
    $id_type = "Translation";
  } elsif ($stable_id =~ /.*E\d+(\.\d+)?$/) { 
    $id_type = "Exon";

  # if guessing fails, look in db
  } else {
    my $sql = qq(
      SELECT type from stable_id_event
      WHERE old_stable_id = ?
      OR new_stable_id = ?
    );
    my $sth = $self->prepare($sql);
    $sth->execute($stable_id, $stable_id);
    ($id_type) = $sth->fetchrow_array;
    $sth->finish;
  }

  warning("Couldn't resolve stable ID type.") unless ($id_type);
  
  $arch_id->type($id_type);
}


1;