NAME

Bio::DB::SeqFeature::Store::DBI::mysql -- 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);
$f->update($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);

# 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);

DESCRIPTION

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.

types

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

toplevel_types

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.