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Bio::DB::SeqFeature::Store::DBI::mysql.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::DB::SeqFeature::Store::DBI::mysql -- Mysql implementation of Bio::DB::SeqFeature::StoreSYNOPSIS
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);
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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre