Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::DB::SeqFeature::Store::memory -- In-memory implementation of
       Bio::DB::SeqFeature::Store

SYNOPSIS

         use Bio::DB::SeqFeature::Store;

         # Open the sequence database
         my $db      = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory',
                                                        -dsn     => '/var/databases/test');
         # search... by id
         my @features = $db->fetch_many(@list_of_ids);

         # ...by name
         @features = $db->get_features_by_name('ZK909');

         # ...by alias
         @features = $db->get_features_by_alias('sma-3');

         # ...by type
         @features = $db->get_features_by_type('gene');

         # ...by location
         @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);

         # ...by attribute
         @features = $db->get_features_by_attribute({description => 'protein kinase'})

         # ...by the GFF "Note" field
         @result_list = $db->search_notes('kinase');

         # ...by arbitrary combinations of selectors
         @features = $db->features(-name => $name,
                                   -type => $types,
                                   -seq_id => $seqid,
                                   -start  => $start,
                                   -end    => $end,
                                   -attributes => $attributes);

         # ...using an iterator
         my $iterator = $db->get_seq_stream(-name => $name,
                                            -type => $types,
                                            -seq_id => $seqid,
                                            -start  => $start,
                                            -end    => $end,
                                            -attributes => $attributes);

         while (my $feature = $iterator->next_seq) {
           # do something with the feature
         }

         # ...limiting the search to a particular region
         my $segment  = $db->segment('Chr1',5000=>6000);
         my @features = $segment->features(-type=>['mRNA','match']);

         # getting & storing sequence information
         # Warning: this returns a string, and not a PrimarySeq object
         $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...');
         my $sequence = $db->fetch_sequence('Chr1',5000=>6000);

         # what feature types are defined in the database?
         my @types    = $db->types;

         # create a new feature in the database
         my $feature = $db->new_feature(-primary_tag => 'mRNA',
                                        -seq_id      => 'chr3',
                                        -start      => 10000,
                                        -end        => 11000);

DESCRIPTION

       Bio::DB::SeqFeature::Store::memory is the in-memory adaptor for
       Bio::DB::SeqFeature::Store. You will not create it directly, but instead use
       Bio::DB::SeqFeature::Store->new() to do so.

       See Bio::DB::SeqFeature::Store for complete usage instructions.

   Using the memory adaptor
       Before using the memory adaptor, populate a readable-directory on the file system with
       annotation and/or sequence files. The annotation files must be in GFF3 format, and sholud
       end in the extension .gff or .gff3. They may be compressed with "compress", "gzip" or
       "bzip2" (in which case the appropriate compression extension must be present as well.)

       You may include sequence data inline in the GFF3 files, or put the sequence data in one or
       more separate FASTA-format files. These files must end with .fa or .fasta and may be
       compressed. Because of the way the adaptor works, you will get much better performance if
       you keep the sequence data in separate FASTA files.

       Initialize the database using the -dsn option. This should point to the directory creating
       the annotation and sequence files, or to a single GFF3 file. Examples:

         # load all GFF3 and FASTA files located in /var/databases/test directory
         $db  = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory',
                                                 -dsn     => '/var/databases/test');

         # load the data in a single compressed GFF3 file located at
         # /usr/annotations/worm.gf33.gz
         $db  = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory',
                                                 -dsn     => '/usr/annotations/worm.gff3.gz');

       For compatibility with the Bio::DB::GFF memory adaptor, -gff is recognized as an alias for
       -dsn.

       See Bio::DB::SeqFeature::Store for all the access methods supported by this adaptor. The
       various methods for storing and updating features and sequences into the database are
       supported, including GFF3 loading support, but since this is an in-memory adaptor all
       changes you make will be lost when the script exits.

   types
        Title   : types
        Usage   : @type_list = $db->types
        Function: Get all the types in the database
        Returns : array of Bio::DB::GFF::Typename objects (arrayref in scalar context)
        Args    : none
        Status  : public

BUGS

       This is an early version, so there are certainly some bugs. Please use the BioPerl bug
       tracking system to report bugs.

SEE ALSO

       bioperl, Bio::DB::SeqFeature, Bio::DB::SeqFeature::Store, Bio::DB::SeqFeature::GFF3Loader,
       Bio::DB::SeqFeature::Segment, Bio::DB::SeqFeature::Store::berkeleydb,
       Bio::DB::SeqFeature::Store::DBI::mysql

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2006 Cold Spring Harbor Laboratory.

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.