my $db = Bio::DB::GFF->new(-adaptor=> 'memory',
-gff => 'my_features.gff',
-fasta => 'my_dna.fa'
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.
DESCRIPTIONThis 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.
CONSTRUCTORUse 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.
METHODSSee Bio::DB::GFF for inherited methods.
AUTHORShuly Avraham <[email protected]>.
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.
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().