Rechercher une page de manuel
Bio::DB::GFF::Adaptor::memory.3pm
Langue: en
Version: 2008-06-24 (ubuntu - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::DB::GFF::Adaptor::memory -- Bio::DB::GFF database adaptor for in-memory databasesSYNOPSIS
use Bio::DB::GFF; my $db = Bio::DB::GFF->new(-adaptor=> 'memory', -gff => 'my_features.gff', -fasta => 'my_dna.fa' );
See Bio::DB::GFF for other methods.
DESCRIPTION
This adaptor implements an in-memory version of Bio::DB::GFF. It can be used to store and retrieve SHORT GFF files. It inherits from Bio::DB::GFF.CONSTRUCTOR
Use Bio::DB::GFF->new() to construct new instances of this class. Three named arguments are recommended:Argument Description -adaptor Set to "memory" to create an instance of this class. -gff Read the indicated file or directory of .gff file. -fasta Read the indicated file or directory of fasta files. -dir Indicates a directory containing .gff and .fa files
If you use the -dsn option and the indicated directory is writable by the current process, then this library will create a FASTA file index that greatly diminishes the memory usage of this module.
METHODS
See Bio::DB::GFF for inherited methods.BUGS
none ;-)SEE ALSO
Bio::DB::GFF, bioperlAUTHOR
Shuly Avraham <avraham@cshl.org>.Copyright (c) 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.
_feature_by_name
Title : _feature_by_name Usage : $db->get_features_by_name($name,$class,$callback) Function: get a list of features by name and class Returns : count of number of features retrieved Args : name of feature, class of feature, and a callback Status : protected
This method is used internally. The callback arguments are those used by make_feature().
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre