The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqFeature::FeaturePair

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