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Mean score value by ID over a defined genomic region
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Bio::SeqFeature::FeaturePair(3pm) User Contributed Perl Documentation Bio::SeqFeature::FeaturePair(3pm) NAME
Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits SYNOPSIS
my $feat = Bio::SeqFeature::FeaturePair->new(-feature1 => $f1, -feature2 => $f2, ); # Bio::SeqFeatureI methods can be used my $start = $feat->start; my $end = $feat->end; # Bio::FeaturePair methods can be used my $hstart = $feat->hstart; my $hend = $feat->hend; my $feature1 = $feat->feature1; # returns feature1 object DESCRIPTION
A sequence feature object where the feature is itself a feature on another sequence - e.g. a blast hit where residues 1-40 of a protein sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence HS120G22. The genomic sequence coordinates are used to create one sequence feature $f1 and the protein coordinates are used to create feature $f2. A FeaturePair object can then be made my $fp = Bio::SeqFeature::FeaturePair->new(-feature1 => $f1, # genomic -feature2 => $f2, # protein ); This object can be used as a standard Bio::SeqFeatureI in which case my $gstart = $fp->start # returns start coord on feature1 - genomic seq. my $gend = $fp->end # returns end coord on feature1. In general standard Bio::SeqFeatureI method calls return information in feature1. Data in the feature 2 object are generally obtained using the standard methods prefixed by h (for hit!) my $pstart = $fp->hstart # returns start coord on feature2 = protein seq. my $pend = $fp->hend # returns end coord on feature2. If you wish to swap feature1 and feature2 around : $feat->invert so... $feat->start # etc. returns data in $feature2 object No sub_SeqFeatures or tags can be stored in this object directly. Any features or tags are expected to be stored in the contained objects feature1, and feature2. CONTACT
Ewan Birney <birney@sanger.ac.uk> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : Function: Constructor for this module. Accepts the following parameters: -feature1 Bio::SeqFeatureI-compliant object -feature2 Bio::SeqFeatureI-compliant object -feature_factory Bio::Factory::ObjectFactoryI compliant object to be used when feature1 and/or feature2 are accessed without explicitly set before. This is mostly useful for derived classes who want to set their preferred class for feature objects. Example : Returns : Args : see above feature1 Title : feature1 Usage : $f = $featpair->feature1 $featpair->feature1($feature) Function: Get/set for the query feature Returns : Bio::SeqFeatureI Args : Bio::SeqFeatureI feature2 Title : feature2 Usage : $f = $featpair->feature2 $featpair->feature2($feature) Function: Get/set for the hit feature Returns : Bio::SeqFeatureI Args : Bio::SeqFeatureI start Title : start Usage : $start = $featpair->start $featpair->start(20) Function: Get/set on the start coordinate of feature1 Returns : integer Args : [optional] beginning of feature end Title : end Usage : $end = $featpair->end $featpair->end($end) Function: get/set on the end coordinate of feature1 Returns : integer Args : [optional] ending point of feature 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 : [optional] strand information to set location Title : location Usage : $location = $featpair->location $featpair->location($location) Function: Get/set location object (using feature1) Returns : Bio::LocationI object Args : [optional] LocationI to store score Title : score Usage : $score = $feat->score() $feat->score($score) Function: get/set on score information Returns : float Args : none if get, the new value if set frame Title : frame Usage : $frame = $feat->frame() $feat->frame($frame) Function: get/set on frame information Returns : 0,1,2 Args : none if get, the new value if set primary_tag Title : primary_tag Usage : $ptag = $featpair->primary_tag Function: get/set on the primary_tag of feature1 Returns : 0,1,2 Args : none if get, the new value if set source_tag Title : source_tag Usage : $tag = $feat->source_tag() $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none 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) hseqname Title : hseqname Usage : $featpair->hseqname($newval) Function: Get/set method for the name of feature2. Returns : value of $feature2->seq_id Args : newvalue (optional) hstart Title : hstart Usage : $start = $featpair->hstart $featpair->hstart(20) Function: Get/set on the start coordinate of feature2 Returns : integer Args : none hend Title : hend Usage : $end = $featpair->hend $featpair->hend($end) Function: get/set on the end coordinate of feature2 Returns : integer Args : none hstrand Title : hstrand 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 hscore Title : hscore Usage : $score = $feat->score() $feat->score($score) Function: get/set on score information Returns : float Args : none if get, the new value if set hframe Title : hframe Usage : $frame = $feat->frame() $feat->frame($frame) Function: get/set on frame information Returns : 0,1,2 Args : none if get, the new value if set hprimary_tag Title : hprimary_tag Usage : $ptag = $featpair->hprimary_tag Function: Get/set on the primary_tag of feature2 Returns : 0,1,2 Args : none if get, the new value if set hsource_tag Title : hsource_tag Usage : $tag = $feat->hsource_tag() $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none invert Title : invert Usage : $tag = $feat->invert Function: Swaps feature1 and feature2 around Returns : Nothing Args : none feature_factory Title : feature_factory Usage : $obj->feature_factory($newval) Function: Get/set the feature object factory for this feature pair. The feature object factory will be used to create a feature object if feature1() or feature2() is called in get mode without having been set before. The default is an instance of Bio::Factory::ObjectFactory and hence allows the type to be changed dynamically at any time. Example : Returns : The feature object factory in use (a Bio::Factory::ObjectFactoryI compliant object) Args : on set, a Bio::Factory::ObjectFactoryI compliant object perl v5.14.2 2012-03-02 Bio::SeqFeature::FeaturePair(3pm)
