NAME¶

Bio::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.

 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