Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature
$proxy = Bio::SeqFeature::PositionProxy->new( -loc => $loc, -parent => $basefeature); $seq->add_SeqFeature($feat);
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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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 $feat->start(20) Function: Get Returns : integer Args : none
Title : end Usage : $end = $feat->end $feat->end($end) Function: get Returns : integer Args : none
Title : length Usage : Function: Example : Returns : Args :
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
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') Function: Returns : TRUE if the specified tag exists, and FALSE otherwise Args :
Title : get_tag_values Usage : @values = $self->get_tag_values('some_tag') Function: 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