diff variant_effect_predictor/Bio/SeqFeature/FeaturePair.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/FeaturePair.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,475 @@
+# $Id: FeaturePair.pm,v 1.17 2002/10/08 08:38:31 lapp Exp $
+#
+# BioPerl module for Bio::SeqFeature::FeaturePair
+#
+# Cared for by Ewan Birney <[e-mail]>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits
+
+=head1 SYNOPSIS
+
+    my $feat  = new Bio::SeqFeature::FeaturePair(-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
+
+=head1 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 = new Bio::SeqFeature::FeaturePair(-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 $feature2 object
+
+
+No sub_SeqFeatures or tags can be stored in this object directly.  Any
+features or tags are expected to be stored in the contained objects
+feature1, and feature2.
+
+=head1 CONTACT
+
+Ewan Birney E<lt>[e-mail]<gt>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::SeqFeature::FeaturePair;
+use vars qw(@ISA);
+use strict;
+
+use Bio::SeqFeatureI;
+use Bio::SeqFeature::Generic;
+
+@ISA = qw(Bio::SeqFeature::Generic);
+
+sub new {
+    my ($class, @args) = @_;
+    my $self = $class->SUPER::new(@args);
+    
+    my ($feature1,$feature2) = 
+	$self->_rearrange([qw(FEATURE1
+			      FEATURE2
+			      )],@args);
+    
+    # Store the features in the object
+    $feature1 && $self->feature1($feature1);
+    $feature2 && $self->feature2($feature2);
+    return $self;
+}
+
+=head2 feature1
+
+ Title   : feature1
+ Usage   : $f = $featpair->feature1
+           $featpair->feature1($feature)
+ Function: Get/set for the query feature
+ Returns : Bio::SeqFeatureI
+ Args    : Bio::SeqFeatureI
+
+
+=cut
+
+sub feature1 {
+    my ($self,$arg) = @_;    
+    if ( defined($arg) || !defined $self->{'feature1'} ) {
+	$arg = new Bio::SeqFeature::Generic() unless( defined $arg);
+	$self->throw("Argument [$arg] must be a Bio::SeqFeatureI") 
+	    unless (ref($arg) && $arg->isa("Bio::SeqFeatureI"));
+	$self->{'feature1'} = $arg;
+    }
+    return $self->{'feature1'};
+}
+
+=head2 feature2
+
+ Title   : feature2
+ Usage   : $f = $featpair->feature2
+           $featpair->feature2($feature)
+ Function: Get/set for the hit feature
+ Returns : Bio::SeqFeatureI
+ Args    : Bio::SeqFeatureI
+
+
+=cut
+
+sub feature2 {
+    my ($self,$arg) = @_;
+
+    if ( defined($arg) || ! defined $self->{'feature2'}) {
+	$arg = new Bio::SeqFeature::Generic unless( defined $arg);
+	$self->throw("Argument [$arg] must be a Bio::SeqFeatureI") 
+	    unless (ref($arg) && $arg->isa("Bio::SeqFeatureI"));
+	$self->{'feature2'} = $arg;
+    }
+    return $self->{'feature2'};
+}
+
+=head2 start
+
+ Title   : start
+ Usage   : $start = $featpair->start
+           $featpair->start(20)
+ Function: Get/set on the start coordinate of feature1
+ Returns : integer
+ Args    : [optional] beginning of feature
+
+=cut
+
+sub start {
+    my ($self,$value) = @_;    
+    return $self->feature1->start($value);
+}
+
+=head2 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
+
+
+=cut
+
+sub end{
+    my ($self,$value) = @_;    
+    return $self->feature1->end($value);    
+}
+
+=head2 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
+
+
+=cut
+
+sub strand{
+    my ($self,$arg) = @_;
+    return $self->feature1->strand($arg);    
+}
+
+=head2 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
+
+=cut
+
+sub location {
+    my ($self,$value) = @_;    
+    return $self->feature1->location($value);
+}
+
+=head2 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
+
+
+=cut
+
+sub score {
+    my ($self,$arg) = @_;
+    return $self->feature1->score($arg);    
+}
+
+=head2 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
+
+
+=cut
+
+sub frame {
+    my ($self,$arg) = @_;
+    return $self->feature1->frame($arg);    
+}
+
+=head2 primary_tag
+
+ Title   : primary_tag
+ Usage   : $ptag = $featpair->primary_tag
+ Function: get/set on the primary_tag of feature1
+ Returns : 0,1,2
+ Args    : none if get, the new value if set
+
+
+=cut
+
+sub primary_tag{
+    my ($self,$arg) = @_;
+    return $self->feature1->primary_tag($arg);    
+}
+
+=head2 source_tag
+
+ Title   : source_tag
+ Usage   : $tag = $feat->source_tag()
+           $feat->source_tag('genscan');
+ Function: Returns the source tag for a feature,
+           eg, 'genscan' 
+ Returns : a string 
+ Args    : none
+
+
+=cut
+
+sub source_tag{
+    my ($self,$arg) = @_;
+    return $self->feature1->source_tag($arg);    
+}
+
+=head2 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)
+
+
+=cut
+
+sub seqname{
+    my ($self,$arg) = @_;
+    return $self->feature1->seq_id($arg);    
+}
+
+=head2 hseqname
+
+ Title   : hseqname
+ Usage   : $featpair->hseqname($newval)
+ Function: Get/set method for the name of
+           feature2.
+ Returns : value of $feature2->seq_id
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub hseqname {
+    my ($self,$arg) = @_;
+    return $self->feature2->seq_id($arg);
+}
+
+
+=head2 hstart
+
+ Title   : hstart
+ Usage   : $start = $featpair->hstart
+           $featpair->hstart(20)
+ Function: Get/set on the start coordinate of feature2
+ Returns : integer
+ Args    : none
+
+=cut
+
+sub hstart {
+    my ($self,$value) = @_;
+    return $self->feature2->start($value);    
+}
+
+=head2 hend
+
+ Title   : hend
+ Usage   : $end = $featpair->hend
+           $featpair->hend($end)
+ Function: get/set on the end coordinate of feature2
+ Returns : integer
+ Args    : none
+
+
+=cut
+
+sub hend{
+    my ($self,$value) = @_;
+    return $self->feature2->end($value);    
+}
+
+
+=head2 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
+
+
+=cut
+
+sub hstrand{
+    my ($self,$arg) = @_;
+    return $self->feature2->strand($arg);
+}
+
+=head2 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
+
+
+=cut
+
+sub hscore {
+    my ($self,$arg) = @_;
+    return $self->feature2->score($arg);    
+}
+
+=head2 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
+
+
+=cut
+
+sub hframe {
+    my ($self,$arg) = @_;
+    return $self->feature2->frame($arg);    
+}
+
+=head2 hprimary_tag
+
+ Title   : hprimary_tag
+ Usage   : $ptag = $featpair->hprimary_tag
+ Function: Get/set on the primary_tag of feature2
+ Returns : 0,1,2
+ Args    : none if get, the new value if set
+
+
+=cut
+
+sub hprimary_tag{
+    my ($self,$arg) = @_;
+    return $self->feature2->primary_tag($arg);    
+}
+
+=head2 hsource_tag
+
+ Title   : hsource_tag
+ Usage   : $tag = $feat->hsource_tag()
+           $feat->source_tag('genscan');
+ Function: Returns the source tag for a feature,
+           eg, 'genscan' 
+ Returns : a string 
+ Args    : none
+
+
+=cut
+
+sub hsource_tag{
+    my ($self,$arg) = @_;
+    return $self->feature2->source_tag($arg);
+}
+
+=head2 invert
+
+ Title   : invert
+ Usage   : $tag = $feat->invert
+ Function: Swaps feature1 and feature2 around
+ Returns : Nothing
+ Args    : none
+
+
+=cut
+
+sub invert {
+    my ($self) = @_;
+
+    my $tmp = $self->feature1;
+    
+    $self->feature1($self->feature2);
+    $self->feature2($tmp);
+    return undef;
+}
+
+1;