Bio::SeqFeature::PositionProxy(3pm) User Contributed Perl Documentation Bio::SeqFeature::PositionProxy(3pm)
NAME
Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature
SYNOPSIS
$proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc,
-parent => $basefeature);
$seq->add_SeqFeature($feat);
DESCRIPTION
PositionProxy is a Proxy Sequence Feature to handle truncation and revcomp without duplicating all the data within the sequence features.
It holds a new location for a sequence feature and the original feature it came from to provide the additional annotation information.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney
Ewan Birney <birney@sanger.ac.uk>
DEVELOPERS
This class has been written with an eye out of inheritence. The fields the actual object hash are:
_gsf_tag_hash = reference to a hash for the tags
_gsf_sub_array = reference to an array for sub arrays
_gsf_start = scalar of the start point
_gsf_end = scalar of the end point
_gsf_strand = scalar of the strand
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
parent
Title : parent
Usage : my $sf = $proxy->parent()
Function: returns the seqfeature parent of this proxy
Returns : Bio::SeqFeatureI object
Args : none
start
Title : start
Usage : $start = $feat->start
$feat->start(20)
Function: Get
Returns : integer
Args : none
end
Title : end
Usage : $end = $feat->end
$feat->end($end)
Function: get
Returns : integer
Args : none
length
Title : length
Usage :
Function:
Example :
Returns :
Args :
strand
Title : strand
Usage : $strand = $feat->strand()
$feat->strand($strand)
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : none
attach_seq
Title : attach_seq
Usage : $sf->attach_seq($seq)
Function: Attaches a Bio::Seq object to this feature. This
Bio::Seq object is for the *entire* sequence: ie
from 1 to 10000
Example :
Returns : TRUE on success
Args :
seq
Title : seq
Usage : $tseq = $sf->seq()
Function: returns the truncated sequence (if there) for this
Example :
Returns : sub seq on attached sequence bounded by start & end
Args : none
entire_seq
Title : entire_seq
Usage : $whole_seq = $sf->entire_seq()
Function: gives the entire sequence that this seqfeature is attached to
Example :
Returns :
Args :
seqname
Title : seqname
Usage : $obj->seq_id($newval)
Function: There are many cases when you make a feature that you
do know the sequence name, but do not know its actual
sequence. This is an attribute such that you can store
the seqname.
This attribute should *not* be used in GFF dumping, as
that should come from the collection in which the seq
feature was found.
Returns : value of seqname
Args : newvalue (optional)
Proxies
These functions chain back to the parent for all non sequence related stuff.
primary_tag
Title : primary_tag
Usage : $tag = $feat->primary_tag()
Function: Returns the primary tag for a feature,
eg 'exon'
Returns : a string
Args : none
source_tag
Title : source_tag
Usage : $tag = $feat->source_tag()
Function: Returns the source tag for a feature,
eg, 'genscan'
Returns : a string
Args : none
has_tag
Title : has_tag
Usage : $tag_exists = $self->has_tag('some_tag')
Function:
Returns : TRUE if the specified tag exists, and FALSE otherwise
Args :
each_tag_value
Title : each_tag_value
Usage : @values = $self->each_tag_value('some_tag')
Function:
Returns : An array comprising the values of the specified tag.
Args :
all_tags
Title : all_tags
Usage : @tags = $feat->all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args : none
perl v5.14.2 2012-03-02 Bio::SeqFeature::PositionProxy(3pm)