Bio::SeqFeature::SubSeq - Feature representing a subsequence
# SubSeq with implicit sequence use Bio::Seq; my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' ); $subseq = Bio::SeqFeature::Amplicon->new( -start => 6, -end => 15, -template => $template, ); print "Subsequence is: ".$amplicon->seq->seq."\n"; # Should be 'CCCCCGGGGG' # SubSeq with explicit sequence use Bio::SeqFeature::Subseq; my $subseq = Bio::SeqFeature::Amplicon->new( -seq => $seq_object, );
Bio::SeqFeature::SubSeq extends Bio::SeqFeature::Generic features to represent a subsequence. When this feature is attached to a template sequence, the sequence of feature is the subsequence of the template at this location. The purpose of this class is to represent a sequence as a feature without having to explicitly store its sequence string.
Of course, you might have reasons to explicitly set a sequence. In that case, note that the length of the sequence is allowed to not match the position of the feature. For example, you can set sequence of length 10 in a SubSeq feature that spans positions 30 to 50 of the template if you so desire.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new() Usage : my $subseq = Bio::SeqFeature::SubSeq( -start => 1, -end => 10, -strand => -1); Function: Instantiate a new Bio::SeqFeature::SubSeq feature object Args : -seq , the sequence object or sequence string of the feature (optional) -template , attach the feature to the provided parent template sequence or feature (optional). Note that you must specify the feature location to do this. -start, -end, -location, -strand and all other L<Bio::SeqFeature::Generic> argument can be used. Returns : A Bio::SeqFeature::SubSeq object
Title : seq() Usage : my $seq = $subseq->seq(); Function: Get or set the sequence object of this SubSeq feature. If no sequence was provided, but the subseq is attached to a sequence, get the corresponding subsequence. Returns : A sequence object or undef Args : None.
Title : seq() Usage : my $length = $subseq->seq(); Function: Get the length of the SubSeq feature. It is similar to the length() method of L<Bio::Generic::SeqFeature>, which computes length based on the location of the feature. However, if the feature was not given a location, return the length of the subsequence if possible. Returns : integer or undef Args : None.