Manual Reference Pages - BIO::SEQFEATURE::SUBSEQ (3)
Bio::SeqFeature::SubSeq - Feature representing a subsequence
# SubSeq with implicit sequence
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
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
explictly 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
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.
|perl v5.20.3 ||BIO::SEQFEATURE::SUBSEQ (3) ||2016-04-05 |
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