Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::DB::SeqFeature::Store::DBI::mysql -- Mysql implementation of


         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
         $f->update($f) or die "Couldn't update!";

         # searching...
         # id
         my @features = $db->fetch_many(@list_of_ids);

         # name
         @features = $db->get_features_by_name('ZK909');

         # alias
         @features = $db->get_features_by_alias('sma-3');

         # type
         @features = $db->get_features_by_name('gene');

         # location
         @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);

         # attribute
         @features = $db->get_features_by_attribute({description => 'protein kinase'})

         # the GFF "Note" field
         @result_list = $db->search_notes('kinase');

         # 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
         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);


       Bio::DB::SeqFeature::Store::mysql is the Mysql 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 Mysql adaptor
       Before you can use the adaptor, you must use the mysqladmin tool to create a database and
       establish a user account with write permission. In order to use "fast" loading, the user
       account must have "file" privileges.

       To establish a connection to the database, call
       Bio::DB::SeqFeature::Store->new(-adaptor=>'DBI::mysql',@more_args). The additional
       arguments are as follows:

         Argument name       Description
         -------------       -----------

        -dsn              The database name. You can abbreviate
                          "dbi:mysql:foo" as "foo" if you wish.

        -user             Username for authentication.

        -pass             Password for authentication.

        -namespace        A prefix to attach to each table. This allows you
                          to have several virtual databases in the same
                          physical database.

        -temp             Boolean flag. If true, a temporary database
                          will be created and destroyed as soon as
                          the Store object goes out of scope. (synonym -temporary)

        -autoindex        Boolean flag. If true, features in the database will be
                          reindexed every time they change. This is the default.

        -tmpdir           Directory in which to place temporary files during "fast" loading.
                          Defaults to File::Spec->tmpdir(). (synonyms -dump_dir, -dumpdir, -tmp)

        -dbi_options      A hashref to pass to DBI->connect's 4th argument, the "attributes."
                          (synonyms -options, -dbi_attr)

        -write            Pass true to open database for writing or updating.

       If successful, a new instance of Bio::DB::SeqFeature::Store::DBI::mysql will be returned.

       In addition to the standard methods supported by all well-behaved
       Bio::DB::SeqFeature::Store databases, several following adaptor-specific methods are
       provided. These are described in the next sections.

        Title   : types
        Usage   : @type_list = $db->types
        Function: Get all the types in the database
        Returns : array of Bio::DB::GFF::Typename objects
        Args    : none
        Status  : public

        Title   : toplevel_types
        Usage   : @type_list = $db->toplevel_types
        Function: Get the toplevel types in the database
        Returns : array of Bio::DB::GFF::Typename objects
        Args    : none
        Status  : public

       This is similar to types() but only returns the types of INDEXED (toplevel) features.