[Bioperl-l] Forgot to post to the list; DB::Universal

[Ewan Birney]

I forgot to post this to the list but last week on one of my daily
london<->hinxton train rides I implemented Lincoln's universal DB idea.

Here is its synopsis

=head1 NAME

Bio::DB::Universal - Artificial database that delegates to specific
databases

=head1 SYNOPSIS

    $uni = Bio::DB::Universal->new();

    # by default connects to web databases. We can also
    # substitute local databases

    $embl = Bio::Index::EMBL->new( -filename => '/some/index/filename/locally/stored');
    $uni->use_database('embl',$embl);

    # treat it like a normal database. Recognises strings
    # like gb|XXXXXX and embl:YYYYYY

    $seq1 = $uni->get_Seq_by_id("embl:HSHNRNPA");
    $seq2 = $uni->get_Seq_by_acc("gb|A000012");

    # with no separator, tries to guess database. In this case the
    # _ is considered to be indicative of swissprot
    $seq3 = $uni->get_Seq_by_id('ROA1_HUMAN');


The magic happens here:

(if anyone can think of better regex's - shout. If there is another
datase we could add *sensibly* that would also be great)




=head2 guess_id

 Title   : guess_id
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :


=cut

sub guess_id{
   my ($self,$str) = @_;
   
   if( $str =~ /(\S+)[:|\/;](\w+)/ ) {
       my $tag;
       my $db = $1;
       my $id = $2;
       if( $db =~ /gb/i || $db =~ /genbank/i || $db =~ /ncbi/i ) {
	   $tag = 'genbank';
       } elsif ( $db =~ /embl/i || $db =~ /emblbank/ || $db =~ /^em/i ) {
	   $tag = 'embl';
       } elsif ( $db =~ /swiss/i || $db =~ /^sw/i || $db =~ /sptr/ ) {
	   $tag = 'swiss';
       } else {
	   # throw for the moment
	   $self->throw("Could not guess database type $db from $str");
       }
       return ($tag,$id);

   } else {
       my $tag;
       # auto-guess from just the id
       if( $str =~ /_/ ) {
	   $tag = 'swiss';
       } elsif ( $str =~ /^[QPR]\w+\d$/ ) {
	   $tag = 'swiss';
       } elsif ( $str =~ /[A-Z]\d+/ ) {
	   $tag = 'genbank';
       } else {
	   # default genbank...
	   $tag = 'genbank';
       }
       return ($tag,$str);
   }

   
}


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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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