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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
Ewan Birney <firstname.lastname@example.org>
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
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