- AUTHOR - Ewan Birney
Bio::DB::Universal - Artificial database that delegates to specific databases
$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');
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_Seq_by_id Usage : Function: Example : Returns : Args :
Title : get_Seq_by_acc Usage : Function: Example : Returns : Args :
Title : guess_id Usage : Function: Example : Returns : Args :
Title : use_database Usage : Function: Example : Returns : Args :