Bio::DB Universal
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Summary
Bio::DB::Universal - Artificial database that delegates to specific databases
Package variables
No package variables defined.
Included modules
Bio::DB::EMBL
Bio::DB::GenBank
Bio::DB::SwissProt
Inherit
Bio::DB::RandomAccessI Bio::Root::Root
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 = $uni->get_Seq_by_id('ROA1_HUMAN');
Description
Artificial database that delegates to specific databases, with a
"smart" (well, smartish) guessing routine for what the ids. No doubt
the smart routine can be made smarter.
The hope is that you can make this database and just throw ids at it -
for most easy cases it will sort you out. Personally, I would be
making sure I knew where each id came from and putting it into its own
database first - but this is a quick and dirty solution.
By default this connects to web orientated databases, with all the
reliability and network bandwidth costs this implies. However you can
subsistute your own local databases - they could be Bio::Index
databases (DBM file and flat file) or bioperl-db based (MySQL based)
or biocorba-based (whatever you like behind the corba interface).
Internally the tags for the databases are
   genbank - ncbi dna database
embl - ebi's dna database (these two share accession number space)
swiss - swissprot + sptrembl (EBI's protein database)
We should extend this for RefSeq and other sequence databases which
are out there... ;)
Inspired by Lincoln Stein, written by Ewan Birney.
Methods
new
No description
Code
get_Seq_by_idDescriptionCode
get_Seq_by_accDescriptionCode
guess_idDescriptionCode
use_databaseDescriptionCode
Methods description
get_Seq_by_idcode    nextTop
 Title   : get_Seq_by_id
Usage :
Function:
Example :
Returns :
Args :
get_Seq_by_acccodeprevnextTop
 Title   : get_Seq_by_acc
Usage :
Function:
Example :
Returns :
Args :
guess_idcodeprevnextTop
 Title   : guess_id
Usage :
Function:
Example :
Returns :
Args :
use_databasecodeprevnextTop
 Title   : use_database
Usage :
Function:
Example :
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my ($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 $self;
}
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
   my ($self,$str) = @_;

   my ($tag,$id) = $self->guess_id($str);

   return $self->{'db_hash'}->{$tag}->get_Seq_by_id($id);
}
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
   my ($self,$str) = @_;

   my ($tag,$id) = $self->guess_id($str);

   return $self->{'db_hash'}->{$tag}->get_Seq_by_acc($id);
}
guess_iddescriptionprevnextTop
sub guess_id {
   my ($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,$str); }
}
use_databasedescriptionprevnextTop
sub use_database {
   my ($self,$name,$database) = @_;

   $self->{'db_hash'}->{$name} = $database;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _