Bio::DB::Universal man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::DB::Universal(3) User Contributed Perl DocumentationBio::DB::Universal(3)

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:

	 http://bugzilla.open-bio.org/

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	:

perl v5.14.1			  2011-07-22		 Bio::DB::Universal(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net