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Bio::DB::GFF::Adaptor::biofetch(3pm) User Contributed Perl Documentation Bio::DB::GFF::Adaptor::biofetch(3pm)


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


Proof of principle. Not for production use.


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.


Lincoln Stein <>.

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.


 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.

2020-01-13 perl v5.30.0