plucky (3) Bio::DB::SeqFeature::Store::memory.3pm.gz

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.