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.