SYNOPSIS
use Bio::DB::SeqFeature::Store;
# Open the sequence database
my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
-dsn => 'dbi:mysql:test');
my ($feature) = $db->get_features_by_name('ZK909');
my @subfeatures = $feature->get_SeqFeatures();
my @exons_only = $feature->get_SeqFeatures('exon');
# create a new object
$db->seqfeature_class('Bio::DB::SeqFeature::NormalizedFeature');
my $new = $db->new_feature(-primary_tag=>'gene',
-seq_id => 'chr3',
-start => 10000,
-end => 11000);
# add a new exon
$feature->add_SeqFeature($db->new_feature(-primary_tag=>'exon',
-seq_id => 'chr3',
-start => 5000,
-end => 5551));
DESCRIPTION
The Bio::DB::SeqFeature::NormalizedFeature object is an alternative representation of SeqFeatures for use with Bio::DB::SeqFeature::Store database system. It is identical to Bio::DB::SeqFeature, except that instead of storing feature/subfeature relationships in a database table, the information is stored in the object itself. This actually makes the objects somewhat inconvenient to work with from SQL, but does speed up access somewhat.To use this class, pass the name of the class to the Bio::DB::SeqFeature::Store object's seqfeature_class() method. After this, $db->new_feature() will create objects of type Bio::DB::SeqFeature::NormalizedFeature. If you are using the GFF3 loader, pass Bio::DB::SeqFeature::Store::GFF3Loader->new() the -seqfeature_class argument:
use Bio::DB::SeqFeature::Store::GFF3Loader;
my $store = connect_to_db_somehow();
my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(
-store=>$db,
-seqfeature_class => 'Bio::DB::SeqFeature::NormalizedFeature'
);
new
Title : new Usage : $feature = Bio::DB::SeqFeature::NormalizedFeature->new(@args) Function: create a new feature Returns : the new seqfeature Args : see below Status : public
This method creates and, if possible stores into a database, a new Bio::DB::SeqFeature::NormalizedFeature object using the specialized Bio::DB::SeqFeature class.
The arguments are the same to Bio::SeqFeature::Generic->new() and Bio::Graphics::Feature->new(). The most important difference is the -store option, which if present creates the object in a Bio::DB::SeqFeature::Store database, and he -index option, which controls whether the feature will be indexed for retrieval (default is true). Ordinarily, you would only want to turn indexing on when creating top level features, and off only when storing subfeatures. The default is on.
Arguments are as follows:
-seq_id the reference sequence
-start the start position of the feature
-end the stop position of the feature
-display_name the feature name (returned by seqname)
-primary_tag the feature type (returned by primary_tag)
-source the source tag
-score the feature score (for GFF compatibility)
-desc a description of the feature
-segments a list of subfeatures (see Bio::Graphics::Feature)
-subtype the type to use when creating subfeatures
-strand the strand of the feature (one of -1, 0 or +1)
-phase the phase of the feature (0..2)
-url a URL to link to when rendered with Bio::Graphics
-attributes a hashref of tag value attributes, in which the key is the tag
and the value is an array reference of values
-store a previously-opened Bio::DB::SeqFeature::Store object
-index index this feature if true
Aliases:
-id an alias for -display_name -seqname an alias for -display_name -display_id an alias for -display_name -name an alias for -display_name -stop an alias for end -type an alias for primary_tag
Bio::SeqFeatureI methods
The following Bio::SeqFeatureI methods are supported:
seq_id(), start(), end(), strand(), get_SeqFeatures(), display_name(), primary_tag(), source_tag(), seq(), location(), primary_id(), overlaps(), contains(), equals(), intersection(), union(), has_tag(), remove_tag(), add_tag_value(), get_tag_values(), get_all_tags()
Some methods that do not make sense in the context of a genome annotation database system, such as attach_seq(), are not supported.
Please see Bio::SeqFeatureI for more details.
add_SeqFeature
Title : add_SeqFeature Usage : $flag = $feature->add_SeqFeature(@features) Function: Add subfeatures to the feature Returns : true if successful Args : list of Bio::SeqFeatureI objects Status : public
Add one or more subfeatures to the feature. For best results, subfeatures should be of the same class as the parent feature (i.e. don't try mixing Bio::DB::SeqFeature::NormalizedFeature with other feature types).
An alias for this method is add_segment().
update
Title : update Usage : $flag = $feature->update() Function: Update feature in the database Returns : true if successful Args : none Status : public
After changing any fields in the feature, call update() to write it to the database. This is not needed for add_SeqFeature() as update() is invoked automatically.
get_SeqFeatures
Title : get_SeqFeature Usage : @subfeatures = $feature->get_SeqFeatures([@types]) Function: return subfeatures of this feature Returns : list of subfeatures Args : list of subfeature primary_tags (optional) Status : public
This method extends the Bio::SeqFeatureI get_SeqFeatures() slightly by allowing you to pass a list of primary_tags, in which case only subfeatures whose primary_tag is contained on the list will be returned. Without any types passed all subfeatures are returned.
object_store
Title : object_store Usage : $store = $feature->object_store([$new_store]) Function: get or set the database handle Returns : current database handle Args : new database handle (optional) Status : public
This method will get or set the Bio::DB::SeqFeature::Store object that is associated with the feature. After changing the store, you should probably unset the feature's primary_id() and call update() to ensure that the object is written into the database as a new feature.
overloaded_names
Title : overloaded_names Usage : $overload = $feature->overloaded_names([$new_overload]) Function: get or set overloading of object strings Returns : current flag Args : new flag (optional) Status : public
For convenience, when objects of this class are stringified, they are represented in the form ``primary_tag(display_name)''. To turn this feature off, call overloaded_names() with a false value. You can invoke this on an individual feature object or on the class:
Bio::DB::SeqFeature::NormalizedFeature->overloaded_names(0);
segment
Title : segment Usage : $segment = $feature->segment Function: return a Segment object corresponding to feature Returns : a Bio::DB::SeqFeature::Segment Args : none Status : public
This turns the feature into a Bio::DB::SeqFeature::Segment object, which you can then use to query for overlapping features. See Bio::DB::SeqFeature::Segment.
AUTOLOADED methods
@subfeatures = $feature->Exon;
If you use an unknown method that begins with a capital letter, then the feature autogenerates a call to get_SeqFeatures() using the lower-cased method name as the primary_tag. In other words $feature->Exon is equivalent to:
@subfeature s= $feature->get_SeqFeatures('exon')
If you use an unknown method that begins with Tag_(tagname), Att_(tagname) Is_(tagname), then it will be the same as calling the each_tag_value() method with the tagname. In a list context, these autogenerated procedures return the list of results. In scalar context, they return the first item in the list!!
load_id
Title : load_id Usage : $id = $feature->load_id Function: get the GFF3 load ID Returns : the GFF3 load ID (string) Args : none Status : public
For features that were originally loaded by the GFF3 loader, this method returns the GFF3 load ID. This method may not be supported in future versions of the module.
notes
Title : notes Usage : @notes = $feature->notes Function: get contents of the GFF3 Note tag Returns : List of GFF3 Note tags Args : none Status : public
For features that were originally loaded by the GFF3 loader, this method returns the contents of the Note tag as a list. This is a convenience for Bio::Graphics, which looks for notes() when it constructs a default description line.
primary_id
Title : primary_id Usage : $id = $feature->primary_id([$new_id]) Function: get/set the feature's database ID Returns : the current primary ID Args : none Status : public
This method gets or sets the primary ID of the feature in the underlying Bio::DB::SeqFeature::Store database. If you change this field and then call update(), it will have the effect of making a copy of the feature in the database under a new ID.
target
Title : target Usage : $segment = $feature->target Function: return the segment correspondent to the "Target" attribute Returns : a Bio::DB::SeqFeature::Segment object Args : none Status : public
For features that are aligned with others via the GFF3 Target attribute, this returns a segment corresponding to the aligned region. The CIGAR gap string is not yet supported.
Internal methods
- $feature->as_string()
- Internal method used to implement overloaded stringification.
- $boolean = $feature->type_match(@list_of_types)
- Internal method that will return true if the feature's primary_tag and source_tag match any of the list of types (in primary_tag:source_tag format) provided.
BUGS
This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs.AUTHOR
Lincoln Stein <[email protected]>.Copyright (c) 2006 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.