oracular (3) Bio::DB::SeqFeature::Store::Alias.3pm.gz
NAME
Bio::DB::SeqFeature::Store::Alias -- override feature type, method, source and attribute fields
SYNOPSIS
# override feature type, method, source and attribute fields
# with the contents of a simple text index file
use Bio::DB::SeqFeature::Store::Alias;
use Bio::DB::SeqFeature::Store;
my $db = Bio::DB::SeqFeature::Store->new(-adaptor=>'DBI::mysql',
-dsn =>'testdb');
my $meta = Bio::DB::SeqFeature::Store::Alias->new(-store => $db,
-index => '/usr/local/testdb/meta.index',
-default_type => 'example_feature',
);
my @features = $meta->get_seq_stream(-seq_id => 'I',
-attributes => {foo => 'bar'});
meta.index has the following structure
[feature_name_1]
:dbid = f101
:selected = 1
display_name = My First Feature
type = some_type1
method = my_method1
source = my_source1
some_attribute = value1
another_attribute = value2
[feature_name_2]
:dbid = f102
:selected = 1
display_name = My Second Feature
type = some_type2
method = my_method2
source = my_source2
some_attribute = value3
another_attribute = value4
[feature_name_3]
:dbid = f103
type = some_type2
method = my_method2
source = my_source2
some_attribute = value5
another_attribute = value6
DESCRIPTION
This module can be used as a wrapper around any BioPerl database that supports the get_feature_by_name()
method. It allows you to dynamically override the type, source, method and display name of each feature,
as well as to assign new metadata attributes to each one.
It is used by GBrowse to create subtracks for tracks that have a small number of named features,
primarily wiggle tracks.
Metadata Format
The wrapper is associated with a text file that contains metadata about each feature. You can use any
name for the text file, but it must follow this format:
[feature_name_1]
:dbid = f101
:selected = 1
type = some_type1
method = my_method1
source = my_source1
some_attribute = value1
another_attribute = value2
[feature_name_2]
:dbid = f102
:selected = 1
type = some_type2
method = my_method2
source = my_source2
some_attribute = value3
another_attribute = value4
[feature_name_3]
:dbid = f103
type = some_type2
method = my_method2
source = my_source2
some_attribute = value5
another_attribute = value6
Each [stanza] begins with the name of a feature as it is represented in the underlying database. A call
to the database's get_feature_by_name() method with the [stanza] heading contents (e.g. "feature_name_2")
and a genomic position should return one and only one feature.
Below each [stanza] heading are a series of tag=value pairs. The following tag names have special
meaning:
:dbid Unique identifier for the feature, used by GBrowse to process
clicks on the feature.
:selected If true, this subtrack is selected by default when the
containing track is turned on.
display_name Display name for the feature. If not present, will
default to the feature's native display name
(i.e. the one in the [stanza]).
type What is returned by calling the feature's type()
method.
method What is returned by calling the feature's method()
method.
source What is returned by calling the feature's source()
method.
score What is returned by calling the feature's score() method.
Any other tags become sortable attributes which are displayed by the GBrowse subtrack selection dialog
box. For this to work properly, each tag must be present in each stanza. Tags that are present in some
stanzas and not others are ignored.
METHODS
$aliasdb = Bio::DB::SeqFeature::Store::Alias->new(-metadata=>$path,-store=>$db,-type=>$type)
new() creates the Alias database. The arguments are:
-metadata Full path to the metadata file.
-store Previously opened handle to the feature database
(e.g. Bio::SeqFeature::Store, Bio::DB::GFF,
Bio::DB::Chado)
-type Default type to use for features in this database.
$type = $aliasdb->default_type([$type])
Gets or sets the default type.
$store = $aliasdb->store
Gets the underlying feature database specified during new() (immutable).
$index = $aliasdb->index
Returns the path to the metadata description file.
$meta = $aliasdb->metadata
Return a hashref in which the keys are the feature IDs (or an arbitrary numeric value if :dbid was not
specified), and the values are a hashref of attribute/value pairs.
$f = $aliasdb->get_feature($name)
Calls the underlying database's get_feature_by_name() method and returns a list of response.
@f = $aliasdb->features(@args)
Same as calling the underlying database's features() method, except that the values you specified in the
metadata file for display_name, type, method, source, score and other attributes will override the
original values.
$segment = $aliasdb->segment(@args)
Creates a segment object (see Bio::DB::SeqFeature::Store->segment()), which records a genomic range for
use in further query refinement:
$chr1 = $aliasdb->segment(-seqid=>'chr1');
@f = $chr1->features;
$iterator = $aliasdb->get_seq_stream(@args)
This method is similar to the underlying database's get_seq_stream() method, except that it wraps each
feature. Example:
$iterator = $aliasdb->get_seq_stream(-type=>'some_type2');
while (my $seq = $iterator->next_seq) {
# do something with the seq object.
}
@f = $aliasdb->get_features_by_location(@args)
This method is similar to the underlying database's get_features_by_location() method.
$iterator = $aliasdb->get_seq_stream(-type=>'some_type2');
while (my $seq = $iterator->next_seq) {
# do something with the seq object.
}
@f = $aliasdb->get_features_by_name(@args)
This method is similar to the underlying database's get_features_by_location() method.
@f = $aliasdb->get_features_by_name(@args)
This method is similar to the underlying database's get_features_by_location() method.
@f = $aliasdb->get_features_by_alias(@args);
This method is similar to the underlying database's get_features_by_alias() method.
@f = $aliasdb->get_features_by_attribute(@args);
This method is similar to the underlying database's get_features_by_attribute() method.
BUGS
Please report them.
SEE ALSO
Bio::SeqFeature::Store, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, Bio::Graphics::Browser2
AUTHOR
Copyright (c) 2012 Ontario Institute for Cancer Research
This library is free software; you can redistribute it and/or modify it under the same terms as Perl
itself. See DISCLAIMER.txt for disclaimers of warranty.