Bio::DB::GFF::Adaptor::biofetch.3pm

Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::DB::GFF::Adaptor::biofetch -- Cache BioFetch objects in a Bio::DB::GFF database

SYNOPSIS

Proof of principle. Not for production use.

DESCRIPTION

This adaptor is a proof-of-principle. It is used to fetch BioFetch sequences into a Bio::DB::GFF database (currently uses a hard-coded EMBL database) as needed. This allows the Generic Genome Browser to be used as a Genbank/EMBL browser.

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright 2002 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

new

  Title   : new
  Usage   : $db = Bio::DB::GFF->new(-adaptor=>'biofetch',@args)
  Function: create a new adaptor
  Returns : a Bio::DB::GFF object
  Args    :   -adaptor : required.  Which adaptor to use; biofetch for mysql, biofetch_oracle for Oracle
              -preferred_tags : optional.  A hash of {classname => weight,...}
                                used to determine the class and name of the feature
                                when a choice of possible feature classes is available
                                (e.g. a feature has both a 'gene' and a 'locus' tag).
                                Common defaults are provided that work well for eukaryotic
                                features (but not well for viral/prokaryotic)
               see below for additional arguments.
  Status  : Public
 
 

This is the constructor for the adaptor. It is called automatically by Bio::DB::GFF->new. In addition to arguments that are common among all adaptors, the following class-specific arguments are recgonized:

   Argument       Description
   --------       -----------
 
   -dsn           the DBI data source, e.g. 'dbi:mysql:ens0040'
 
   -user          username for authentication
 
   -pass          the password for authentication
 
   -proxy         [['http','ftp'],'http://proxy:8080']
 
   -source        source to use for loaded features ('EMBL')
 
 

-dsn,-user and -pass indicate the local database to cache results in, and as are per Bio::DB::GFF::Adaptor::dbi. The -proxy argument allows you to set the biofetch web proxy, and uses the same syntax described for the proxy() method of Bio::DB::WebDBSeqI, except that the argument must be passed as an array reference.