bionic (3) Bio::DB::Universal.3pm.gz

NAME

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

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.

FEEDBACK

   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

   Support
       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 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 the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

       Email birney@ebi.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded
       with a _

   get_Seq_by_id
        Title   : get_Seq_by_id
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   get_Seq_by_acc
        Title   : get_Seq_by_acc
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

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

   use_database
        Title   : use_database
        Usage   :
        Function:
        Example :
        Returns :
        Args    :