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 <[email protected]>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