Provided by: libbio-db-seqfeature-perl_1.7.4-1_all 
NAME
Bio::DB::SeqFeature::Segment -- Location-based access to genome annotation data
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 $segment = $db->segment('Chr1',5000=>6000);
my @features = $segment->features('mRNA','match');
DESCRIPTION
The segment object simplifies access to Bio::DB::SeqFeature store by acting as a
placeholder for a region of the genome. You can replace this statement:
@features = $db->features(-seq_id=>'Chr1',
-start=>5000,
-end=>6000,
-types=>['mRNA','match','repeat_region']);
with these statements:
$segment = $db->segment('Chr1',5000=>6000);
@features = $segment->features('mRNA','match','repeat_region');
You can also initialize a segment from an existing SeqFeature object. The range will be
picked up from the SeqFeature boundaries:
$segment = Bio::DB::SeqFeature::Segment->new($feature); # for Bio::DB::SeqFeature
$segment = Bio::DB::SeqFeature::Segment->new($feature,$store); # for other Bio::SeqFeatureI objects
The segment object implements the full Bio::SeqFeature::CollectionI interface, thereby
allowing you to iterate over all features in the range.
PUBLIC METHODS
The following are public methods intended for external use.
new
Title : new
Usage : $segment = Bio::DB::SeqFeature::Segment->new(@options)
Function: create a new Segment object
Returns : A Bio::DB::SeqFeature::Segment object
Args : several - see below
Status : public
This class method creates a Bio::DB::SeqFeature::Segment object. You must provide a
Bio::DB::SeqFeature::Store as well as the coordinates of the segment. These arguments can
be provided explicitly or indirectly.
First form:
$segment = Bio::DB::SeqFeature::Segment->new($store,$seqid,$start,$end,$strand)
In this form a segment is defined by a Bio::DB::SeqFeature::Store, the sequence ID, the
start, end and strand. This is the form that is invoked internally by
Bio::DB::SeqFeature::Store when you call its segment() method.
Second form:
$segment = Bio::DB::SeqFeature::Segment->new($seqfeature [,$store]);
In this form, you pass new() a Bio::SeqFeatureI object. The segment is constructed from
the seq_id and coordinates are taken from the object. If you pass a store-aware seqfeature
object (e.g. Bio::DB::SeqFeature) then the store database is also derived from the
feature. Otherwise you will have to pass the store as a second argument.
features
Title : features
Usage : @features = $segment->features(@args)
Function: fetch seqfeatures that overlap the segment
Returns : list of features
Args : see below
Status : Public
This is the workhorse for feature query and retrieval. It takes a series of -name=>$value
arguments filter arguments. Features that match all the filters are returned.
Argument Value
-------- -----
Location filters:
-strand Strand
-range_type Type of range match ('overlaps','contains','contained_in')
Name filters:
-name Name of feature (may be a glob expression)
-aliases If true, match aliases as well as display names
-class Archaic argument for backward compatibility.
(-class=>'Clone',-name=>'ABC123') is equivalent
to (-name=>'Clone:ABC123')
Type filters:
-types List of feature types (array reference) or one type (scalar)
-type Synonym for the above
-primary_tag Synonym for the above
-attributes Hashref of attribute=>value pairs as per
get_features_by_attribute(). Multiple alternative values
can be matched by providing an array reference.
-attribute synonym for -attributes
This is identical to the Bio::DB::SeqFeature::Store->features() method, except that the
-seq_id, -start, and -end arguments are provided by the segment object. If a simple list
of arguments is provided, then the list is taken to be the set of feature types (primary
tags) to filter on.
Examples:
All features that overlap the current segment:
@features = $segment->features;
All features of type mRNA that overlap the current segment:
@features = $segment->features('mRNA');
All features that are completely contained within the current segment:
@features = $segment->features(-range_type=>'contains');
All "confirmed" mRNAs that overlap the current segment:
@features = $segment->features(-attributes=>{confirmed=>1},-type=>'mRNA');
get_seq_stream
Title : get_seq_stream
Usage : $iterator = $segment->get_seq_stream(@args)
Function: return an iterator across all features in the database
Returns : a Bio::DB::SeqFeature::Store::Iterator object
Args : (optional) the feature() method
Status : public
This is identical to Bio::DB::SeqFeature::Store->get_seq_stream() except that the location
filter is always automatically applied so that the iterator you receive returns features
that overlap the segment's region.
When called without any arguments this method will return an iterator object that will
traverse all indexed features in the database that overlap the segment's region. Call the
iterator's next_seq() method to step through them (in no particular order):
my $iterator = $db->get_seq_stream;
while (my $feature = $iterator->next_seq) {
print $feature->primary_tag,' ',$feature->display_name,"\n";
}
You can select a subset of features by passing a series of filter arguments. The arguments
are identical to those accepted by $segment->features().
get_feature_stream() ican be used as a synonym for this method.
store
Title : store
Usage : $store = $segment->store
Function: return the Bio::DB::SeqFeature::Store object associated with the segment
Returns : a Bio::DB::SeqFeature::Store: object
Args : none
Status : public
primary_tag, type,
Title : primary_tag,type
Usage : $primary_tag = $segment->primary_tag
Function: returns the string "region"
Returns : "region"
Args : none
Status : public
The primary_tag method returns the constant tag "region". type() is a synonym for this
method.
as_string
Title : as_string
Usage : $name = $segment->as_string
Function: expands the object into a human-readable string
Returns : "seq_id:start..end"
Args : none
Status : public
The as_string() method is overloaded into the "" operator so that the object is
represented as a human readable string in the form "seq_id:start..end" when used in a
string context.
rel2abs
Title : rel2abs
Usage : @coords = $s->rel2abs(@coords)
Function: convert relative coordinates into absolute coordinates
Returns : a list of absolute coordinates
Args : a list of relative coordinates
Status : Public
This function takes a list of positions in relative coordinates to the segment, and
converts them into absolute coordinates.
abs2rel
Title : abs2rel
Usage : @rel_coords = $s->abs2rel(@abs_coords)
Function: convert absolute coordinates into relative coordinates
Returns : a list of relative coordinates
Args : a list of absolute coordinates
Status : Public
This function takes a list of positions in absolute coordinates and returns a list
expressed in relative coordinates.
Bio::SeqFeatureI compatibility methods
For convenience, segments are interchangeable with Bio::SeqFeature objects in many cases.
This means that segments can be passed to BioPerl modules that expect Bio::SeqFeature
objects and they should work as expected. The primary tag of segment objects is "region"
(SO:0000001 "Continous sequence >=1 base pair").
All these methods are read-only except for the primary_id, which can be get or set.
The following Bio::SeqFeatureI methods are supported:
start
end
seq_id
strand
length
display_name
primary_id
primary_tag (always returns "region")
source_tag (always returns "Bio::DB::SeqFeature::Segment")
get_SeqFeatures (always returns an empty list)
seq
entire_seq
location
All Bio::RangeI methods
BUGS
This is an early version, so there are certainly some bugs. Please use the BioPerl bug
tracking system to report bugs.
SEE ALSO
bioperl, Bio::DB::SeqFeature::Store, Bio::DB::SeqFeature::GFF3Loader,
Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::bdb
AUTHOR
Lincoln Stein <lstein@cshl.org>.
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.