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Bio::DB::SeqFeature::Store::memory.3pm

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_name('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);
 
   # 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 shold 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');
 
 

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.

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.