Bio::DB::GFF::Adaptor:UseroContributed Perl DoBio::DB::GFF::Adaptor::memory(3)NAMEBio::DB::GFF::Adaptor::memory-- Bio::DB::GFF database adaptor for
in-memory databases
SYNOPSIS
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.
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 -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.
METHODS
See Bio::DB::GFF for inherited methods.
BUGS
none ;-)
SEE ALSO
Bio::DB::GFF, bioperl
AUTHOR
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().
perl v5.14.1 2011-07-22 Bio::DB::GFF::Adaptor::memory(3)
