Bio::SeqFeature::Lite(3pm) User Contributed Perl Documentation Bio::SeqFeature::Lite(3pm)
NAME
Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class
SYNOPSIS
# create a simple feature with no internal structure
$f = Bio::SeqFeature::Lite->new(-start => 1000,
-stop => 2000,
-type => 'transcript',
-name => 'alpha-1 antitrypsin',
-desc => 'an enzyme inhibitor',
);
# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::SeqFeature::Lite->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => 'ABC-3',
-type => 'gapped_alignment',
-subtype => 'similarity');
# build up a gene exon by exon
$e1 = Bio::SeqFeature::Lite->new(-start=>1,-stop=>100,-type=>'exon');
$e2 = Bio::SeqFeature::Lite->new(-start=>150,-stop=>200,-type=>'exon');
$e3 = Bio::SeqFeature::Lite->new(-start=>300,-stop=>500,-type=>'exon');
$f = Bio::SeqFeature::Lite->new(-segments=>[$e1,$e2,$e3],-type=>'gene');
DESCRIPTION
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight
feature objects for drawing.
All methods are as described in Bio::SeqFeatureI with the following additions:
The new() Constructor
$feature = Bio::SeqFeature::Lite->new(@args);
This method creates a new feature object. You can create a simple feature that contains no subfeatures, or a hierarchically nested object.
Arguments are as follows:
-seq_id the reference sequence
-start the start position of the feature
-end the stop position of the feature
-stop an alias for end
-name the feature name (returned by seqname())
-type the feature type (returned by primary_tag())
-primary_tag the same as -type
-source the source tag
-score the feature score (for GFF compatibility)
-desc a description of the feature
-segments a list of subfeatures (see below)
-subtype the type to use when creating subfeatures
-strand the strand of the feature (one of -1, 0 or +1)
-phase the phase of the feature (0..2)
-seq a dna or protein sequence string to attach to feature
-id an alias for -name
-seqname an alias for -name
-display_id an alias for -name
-display_name an alias for -name (do you get the idea the API has changed?)
-primary_id unique database ID
-url a URL to link to when rendered with Bio::Graphics
-attributes a hashref of tag value attributes, in which the key is the tag
and the value is an array reference of values
-factory a reference to a feature factory, used for compatibility with
more obscure parts of Bio::DB::GFF
The subfeatures passed in -segments may be an array of Bio::SeqFeature::Lite objects, or an array of [$start,$stop] pairs. Each pair should
be a two-element array reference. In the latter case, the feature type passed in -subtype will be used when creating the subfeatures.
If no feature type is passed, then it defaults to "feature".
Non-SeqFeatureI methods
A number of new methods are provided for compatibility with Ace::Sequence, which has a slightly different API from SeqFeatureI:
url()
Get/set the URL that the graphical rendering of this feature will link to.
add_segment(@segments)
Add one or more segments (a subfeature). Segments can either be Feature objects, or [start,stop] arrays, as in the -segments argument
to new(). The feature endpoints are automatically adjusted.
segments()
An alias for sub_SeqFeature().
get_SeqFeatures()
Alias for sub_SeqFeature()
get_all_SeqFeatures()
Alias for sub_SeqFeature()
merged_segments()
Another alias for sub_SeqFeature().
stop()
An alias for end().
name()
An alias for seqname().
exons()
An alias for sub_SeqFeature() (you don't want to know why!)
display_name
Title : display_name
Usage : $id = $obj->display_name or $obj->display_name($newid);
Function: Gets or sets the display id, also known as the common name of
the Seq object.
The semantics of this is that it is the most likely string
to be used as an identifier of the sequence, and likely to
have "human" readability. The id is equivalent to the LOCUS
field of the GenBank/EMBL databanks and the ID field of the
Swissprot/sptrembl database. In fasta format, the >(S+) is
presumed to be the id, though some people overload the id
to embed other information. Bioperl does not use any
embedded information in the ID field, and people are
encouraged to use other mechanisms (accession field for
example, or extending the sequence object) to solve this.
Notice that $seq->id() maps to this function, mainly for
legacy/convenience issues.
Returns : A string
Args : None or a new id
accession_number
Title : accession_number
Usage : $unique_biological_key = $obj->accession_number;
Function: Returns the unique biological id for a sequence, commonly
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the
unique id for the implemetation, allowing multiple objects
to have the same accession number in a particular implementation.
For sequences with no accession number, this method should return
"unknown".
Returns : A string
Args : None
alphabet
Title : alphabet
Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
Function: Returns the type of sequence being one of
'dna', 'rna' or 'protein'. This is case sensitive.
This is not called <type> because this would cause
upgrade problems from the 0.5 and earlier Seq objects.
Returns : a string either 'dna','rna','protein'. NB - the object must
make a call of the type - if there is no type specified it
has to guess.
Args : none
Status : Virtual
desc
Title : desc
Usage : $seqobj->desc($string) or $seqobj->desc()
Function: Sets or gets the description of the sequence
Example :
Returns : The description
Args : The description or none
location
Title : location
Usage : my $location = $seqfeature->location()
Function: returns a location object suitable for identifying location
of feature on sequence or parent feature
Returns : Bio::LocationI object
Args : none
location_string
Title : location_string
Usage : my $string = $seqfeature->location_string()
Function: Returns a location string in a format recognized by gbrowse
Returns : a string
Args : none
This is a convenience function used by the generic genome browser. It returns the location of the feature and its subfeatures in the
compact form "start1..end1,start2..end2,...". Use $seqfeature->location()->toFTString() to obtain a standard GenBank/EMBL location
representation.
clone
Title : clone
Usage : my $feature = $seqfeature->clone
Function: Create a deep copy of the feature
Returns : A copy of the feature
Args : none
refseq
Title : refseq
Usage : $ref = $s->refseq([$newseq] [,$newseqclass])
Function: get/set reference sequence
Returns : current reference sequence
Args : new reference sequence and class (optional)
Status : Public
This method will get or set the reference sequence. Called with no arguments, it returns the current reference sequence. Called with any
Bio::SeqFeatureI object that provides the seq_id(), start(), end() and strand() methods.
The method will generate an exception if you attempt to set the reference sequence to a sequence that has a different seq_id from the
current feature.
SEE ALSO
Bio::Graphics::Feature
AUTHOR
Lincoln Stein <lstein@cshl.edu>.
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. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 Bio::SeqFeature::Lite(3pm)