| Bio::DB::SeqFeature::Store::DBI::Pg(3pm) | User Contributed Perl Documentation | Bio::DB::SeqFeature::Store::DBI::Pg(3pm) |
Bio::DB::SeqFeature::Store::DBI::Pg -- PostgreSQL implementation of Bio::DB::SeqFeature::Store
use Bio::DB::SeqFeature::Store;
# Open the sequence database
my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::Pg',
-dsn => 'dbi:Pg: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);
# 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::Pg is the Pg 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.
Before you can use the adaptor, you must use the Pgadmin 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::Pg',@more_args). The additional arguments are as follows:
Argument name Description
------------- -----------
-dsn The database name. You can abbreviate
"dbi:Pg:foo" as "foo" if you wish.
-user Username for authentication.
-pass Password for authentication.
-namespace Creates a SCHEMA for the tables. 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::Pg 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
| 2020-01-13 | perl v5.30.0 |