Bio::DB::SeqFeature::Store::memory Bio::DB::SeqFeature::Store::memory is a in-memory implementation of Bio::DB::SeqFeature::Store.
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Perl module implementation in-memory implementation in-memory

Bio::DB::SeqFeature::Store::memory Description

Bio::DB::SeqFeature::Store::memory is a in-memory implementation of Bio::DB::SeqFeature::Store. Bio::DB::SeqFeature::Store::memory is a 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=>); # 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); Requirements: · Perl

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