Bio::DB::SeqFeature::Segment(3pm) | User Contributed Perl Documentation | Bio::DB::SeqFeature::Segment(3pm) |
Bio::DB::SeqFeature::Segment -- Location-based access to genome annotation data
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');
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.
The following are public methods intended for external use.
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.
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');
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.
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
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.
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.
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.
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.
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:
This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs.
bioperl, Bio::DB::SeqFeature::Store, Bio::DB::SeqFeature::GFF3Loader, Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::bdb
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.
2023-01-27 | perl v5.36.0 |