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://github.com/bioperl/bioperl-live/issues

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    :

get_tag_values

Title   : get_tag_values
Usage   : @values = $self->get_tag_values('some_tag')
Function: 
Returns : An array comprising the values of the specified tag.
Args    :

get_all_tags

Title   : get_all_tags
Usage   : @tags = $feat->get_all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args    : none

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq