Raw content of Bio::DB::Universal # # BioPerl module for Bio::DB::Universal # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =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'); =head1 DESCRIPTION Artificial database that delegates to specific databases, with a "smart" (well, smartish) guessing routine for what the ids. No doubt the smart routine can be made smarter. The hope is that you can make this database and just throw ids at it - for most easy cases it will sort you out. Personally, I would be making sure I knew where each id came from and putting it into its own database first - but this is a quick and dirty solution. By default this connects to web orientated databases, with all the reliability and network bandwidth costs this implies. However you can subsistute your own local databases - they could be Bio::Index databases (DBM file and flat file) or bioperl-db based (MySQL based) or biocorba-based (whatever you like behind the corba interface). Internally the tags for the databases are genbank - ncbi dna database embl - ebi's dna database (these two share accession number space) swiss - swissprot + sptrembl (EBI's protein database) We should extend this for RefSeq and other sequence databases which are out there... ;) Inspired by Lincoln Stein, written by Ewan Birney. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bio.perl.org =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::DB::Universal; use vars qw(@ISA); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use Bio::DB::RandomAccessI; use Bio::DB::GenBank; use Bio::DB::SwissProt; use Bio::DB::EMBL; @ISA = qw(Bio::DB::RandomAccessI Bio::Root::Root); # new() can be inherited from Bio::Root::Root sub new { my ($class) = @_; my $self = {}; bless $self,$class; $self->{'db_hash'} = {}; # default databases $self->use_database('embl',Bio::DB::EMBL->new); $self->use_database('genbank',Bio::DB::GenBank->new); $self->use_database('swiss',Bio::DB::GenBank->new); return $self; } =head2 get_Seq_by_id Title : get_Seq_by_id Usage : Function: Example : Returns : Args : =cut sub get_Seq_by_id{ my ($self,$str) = @_; my ($tag,$id) = $self->guess_id($str); return $self->{'db_hash'}->{$tag}->get_Seq_by_id($id); } =head2 get_Seq_by_acc Title : get_Seq_by_acc Usage : Function: Example : Returns : Args : =cut sub get_Seq_by_acc { my ($self,$str) = @_; my ($tag,$id) = $self->guess_id($str); return $self->{'db_hash'}->{$tag}->get_Seq_by_acc($id); } =head2 guess_id Title : guess_id Usage : Function: Example : Returns : Args : =cut sub guess_id{ my ($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,$str); } } =head2 use_database Title : use_database Usage : Function: Example : Returns : Args : =cut sub use_database{ my ($self,$name,$database) = @_; $self->{'db_hash'}->{$name} = $database; }