Bio::DB::SeqFeature::Store::DBI::mysql 1.5.2_102

Bio::DB::SeqFeature::Store::DBI::mysql is a Mysql implementation of Bio::DB::SeqFeature::Store.

SYNOPSIS

use Bio::DB::SeqFeature::Store;

# Open the sequence database
my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
-dsn => 'dbi:mysql:test');

# 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=>['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);

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Requirements:

· Perl