Bio::DB::SeqFeature::SUser:Contributed PeBio::DB::SeqFeature::Store::memory(3)NAMEBio::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);
# 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);
DESCRIPTIONBio::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');
For compatibility with the Bio::DB::GFF memory adapter, -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.
perl v5.14.12011-07Bio::DB::SeqFeature::Store::memory(3)