Chum::VariantSequence - A variant sequence
A sequence with an assigned allele inserted. Possess sequence flanking the allele. The position of the allele within the sequence. And the allele sequence itself. All sequences are Bio::Seq objects
Example: my $variant_sequence = new Chum::VariantSequence( 'id' => "Homo_sapiens", 'sequence' => new Bio::Seq(-id => "sequence", -seq => "CCCCCTGGGGG"), 'allele_left_flank_sequence' => new Bio::Seq(-id => "left_flank", -seq => "CCCCC"), 'allele_right_flank_sequence' => new Bio::Seq(-id => "right_flank", -seq => "GGGGG"), 'allele_sequence' => new Bio::Seq(-id => "allele", -seq => "T")); $variant_sequence->start; #Prints 5 $variant_sequence->end; #Prints 5
Stephen Montgomery (smontgom@bcsgc.bc.ca)
Usage : $variant_sequence->id;
a display name for this sequence
Returns : string
Args : none
Usage : $variant_sequence->sequence;
a sequence with the allele inserted into it
Returns : Bio::Seq
Args : none
Usage : $variant_sequence->allele_sequence;
the allele sequence
Returns : Bio::Seq
Args : none
Usage : $variant_sequence->allele_left_flank_sequence;
a 5 prime sequence flanking the allele
Returns : Bio::Seq
Args : none
Usage : $variant_sequence->allele_right_flank_sequence;
a 3 prime sequence flanking the allele
Returns : Bio::Seq
Args : none
Usage : $variant_sequence->start;
the start position of the allele in the sequence
Returns : integer
Args : none
Usage : $variant_sequence->end;
the end position of the allele in the sequence
Returns : integer
Args : none
Usage : $variant_sequence->get_sequence_from_flank;
get a flank sequence around object, must be smaller flank than half the length of the sequence
Returns : new Bio::Seq object
Args : flank, integer
Usage : $variant_sequence->is_sequence_feature_overlapping($sequence_feature);
determine if a Bio::SeqFeature object is overlapping the allele in this Chum::VariantSequence object
Returns : boolean
Args : Bio::SeqFeature
Usage : $variant_sequence->is_start_stop_overlapping(10, 20);
determine if an object's start and end is overlapping the allele in this Chum::VariantSequence object
Returns : boolean
Args : start, integer
end, integer