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Bio::DB::GFF::Adaptor::biofetch.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::DB::GFF::Adaptor::biofetch -- Cache BioFetch objects in a Bio::DB::GFF databaseSYNOPSIS
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.
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