Bio::DB::SeqFeature::Store Bio::DB::SeqFeature::Store is a Perl module for storage and retrieval of sequence annotation data.
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Bio::DB::SeqFeature::Store Tags

storage Perl module sequence annotation annotation data storage retrieve annotation data

Bio::DB::SeqFeature::Store Description

Bio::DB::SeqFeature::Store is a Perl module for storage and retrieval of sequence annotation data. Bio::DB::SeqFeature::Store is a Perl module for storage and retrieval of sequence annotation data.SYNOPSIS use Bio::DB::SeqFeature::Store; # Open the feature database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test', -write => 1 ); # get a feature from somewhere my $feature = Bio::SeqFeature::Generic->new(...); # store it $db->store($feature) or die "Couldn't store!"; # primary ID of the feature is changed to indicate its primary ID # in the database... my $id = $feature->primary_id; # get the feature back out my $f = $db->fetch($id); # change the feature and update it $f->start(100); $db->update($f) or die "Couldn't update!"; # searching... # ...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=>); # 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); # load an entire GFF3 file, using the GFF3 loader... my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $db, -verbose => 1, -fast => 1); $loader->load('./my_genome.gff3'); Requirements: · Perl

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