Provided by: libbio-perl-perl_1.7.2-3_all
Bio::DB::GFF::Adaptor::memory -- Bio::DB::GFF database adaptor for in-memory databases
use Bio::DB::GFF; my $db = Bio::DB::GFF->new(-adaptor=> 'memory', -gff => 'my_features.gff', -fasta => 'my_dna.fa' ); or my $db = Bio::DB::GFF->new(-adaptor=>'memory'); $db->load_gff_file('my_features.gff'); $db->load_fasta_file('my_dna.fa'); See Bio::DB::GFF for other methods.
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.
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 -dir 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. Alternatively you may create an empty in-memory object using just the -adaptor=>'memory' argument and then call the load_gff_file() and load_fasta_file() methods to load GFF and/or sequence information. This is recommended in CGI/mod_perl/fastCGI environments because these methods do not modify STDIN, unlike the constructor.
See Bio::DB::GFF for inherited methods.
Shuly Avraham <email@example.com>. 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().