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Christopher Fields > BioPerl > Bio::SeqFeature::PositionProxy



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Module Version: 1.007002   Source  


Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature


   $proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc,
                                                 -parent => $basefeature);



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.


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AUTHOR - Ewan Birney ^

Ewan Birney <>


This class has been written with an eye out of inheritance. 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


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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


 Title   : parent
 Usage   : my $sf = $proxy->parent()
 Function: returns the seqfeature parent of this proxy
 Returns : Bio::SeqFeatureI object
 Args    : none


 Title   : start
 Usage   : $start = $feat->start
 Function: Get
 Returns : integer
 Args    : none


 Title   : end
 Usage   : $end = $feat->end
 Function: get
 Returns : integer
 Args    : none


 Title   : length
 Usage   :
 Example :
 Returns :
 Args    :


 Title   : strand
 Usage   : $strand = $feat->strand()
 Function: get/set on strand information, being 1,-1 or 0
 Returns : -1,1 or 0
 Args    : none


 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    :


 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


 Title   : entire_seq
 Usage   : $whole_seq = $sf->entire_seq()
 Function: gives the entire sequence that this seqfeature is attached to
 Example :
 Returns :
 Args    :


 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)


These functions chain back to the parent for all non sequence related stuff.


 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
 Function: Returns the primary tag for a feature,
           eg 'exon'
 Returns : a string 
 Args    : none


 Title   : source_tag
 Usage   : $tag = $feat->source_tag()
 Function: Returns the source tag for a feature,
           eg, 'genscan' 
 Returns : a string 
 Args    : none


 Title   : has_tag
 Usage   : $tag_exists = $self->has_tag('some_tag')
 Returns : TRUE if the specified tag exists, and FALSE otherwise
 Args    :


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


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