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# BioPerl module for Bio::SeqFeature::SubSeq |
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# |
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# Please direct questions and support issues to |
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# |
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# Copyright Florent Angly |
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# |
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# You may distribute this module under the same terms as perl itself |
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=head1 NAME |
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Bio::SeqFeature::SubSeq - Feature representing a subsequence |
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=head1 SYNOPSIS |
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# SubSeq with implicit sequence |
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use Bio::Seq; |
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my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' ); |
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$subseq = Bio::SeqFeature::Amplicon->new( |
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-start => 6, |
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-end => 15, |
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-template => $template, |
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); |
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print "Subsequence is: ".$amplicon->seq->seq."\n"; # Should be 'CCCCCGGGGG' |
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# SubSeq with explicit sequence |
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use Bio::SeqFeature::Subseq; |
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my $subseq = Bio::SeqFeature::Amplicon->new( |
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-seq => $seq_object, |
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); |
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=head1 DESCRIPTION |
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Bio::SeqFeature::SubSeq extends L features to |
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represent a subsequence. When this feature is attached to a template sequence, |
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the sequence of feature is the subsequence of the template at this location. The |
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purpose of this class is to represent a sequence as a feature without having to |
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explictly store its sequence string. |
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Of course, you might have reasons to explicitly set a sequence. In that case, |
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note that the length of the sequence is allowed to not match the position of the |
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feature. For example, you can set sequence of length 10 in a SubSeq feature that |
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spans positions 30 to 50 of the template if you so desire. |
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=head1 FEEDBACK |
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=head2 Mailing Lists |
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User feedback is an integral part of the evolution of this and other |
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Bioperl modules. Send your comments and suggestions preferably to one |
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of the Bioperl mailing lists. Your participation is much appreciated. |
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bioperl-l@bioperl.org - General discussion |
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists |
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=head2 Support |
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Please direct usage questions or support issues to the mailing list: |
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I |
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rather than to the module maintainer directly. Many experienced and |
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reponsive experts will be able look at the problem and quickly |
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address it. Please include a thorough description of the problem |
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with code and data examples if at all possible. |
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=head2 Reporting Bugs |
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Report bugs to the Bioperl bug tracking system to help us keep track |
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the bugs and their resolution. Bug reports can be submitted via |
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the web: |
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https://github.com/bioperl/bioperl-live/issues |
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=head1 AUTHOR |
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Florent Angly |
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=head1 APPENDIX |
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The rest of the documentation details each of the object |
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methods. Internal methods are usually preceded with a _ |
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=cut |
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package Bio::SeqFeature::SubSeq; |
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use strict; |
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use base qw(Bio::SeqFeature::Generic); |
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=head2 new |
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Title : new() |
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Usage : my $subseq = Bio::SeqFeature::SubSeq( -start => 1, -end => 10, -strand => -1); |
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Function: Instantiate a new Bio::SeqFeature::SubSeq feature object |
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Args : -seq , the sequence object or sequence string of the feature (optional) |
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-template , attach the feature to the provided parent template sequence or feature (optional). |
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Note that you must specify the feature location to do this. |
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-start, -end, -location, -strand and all other L argument can be used. |
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Returns : A Bio::SeqFeature::SubSeq object |
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=cut |
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sub new { |
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my ($class, @args) = @_; |
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my $self = $class->SUPER::new(@args); |
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my ($seq, $template) = $self->_rearrange([qw(SEQ TEMPLATE)], @args); |
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if (defined $seq) { |
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# Set the subsequence explicitly |
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if (not ref $seq) { |
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# Convert string to sequence object |
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$seq = Bio::PrimarySeq->new( -seq => $seq ); |
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} else { |
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# Sanity check |
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if (not $seq->isa('Bio::PrimarySeqI')) { |
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$self->throw("Expected a sequence object but got a '".ref($seq)."'\n"); |
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} |
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} |
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$self->seq($seq); |
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} |
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if ($template) { |
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if ( not($self->start) || not($self->end) ) { |
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$self->throw('Could not attach feature to template $template because'. |
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' the feature location was not specified.'); |
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} |
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# Need to attach to parent sequence and then add sequence feature |
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my $template_seq; |
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if ($template->isa('Bio::SeqFeature::Generic')) { |
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$template_seq = $template->entire_seq; |
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} elsif ($template->isa('Bio::SeqI')) { |
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$template_seq = $template; |
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} else { |
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$self->throw("Expected a Bio::SeqFeature::Generic or Bio::SeqI object". |
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" as template, but got '$template'."); |
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} |
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$self->attach_seq($template_seq); |
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$template->add_SeqFeature($self); |
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} |
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return $self; |
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} |
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=head2 seq |
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Title : seq() |
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Usage : my $seq = $subseq->seq(); |
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Function: Get or set the sequence object of this SubSeq feature. If no sequence |
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was provided, but the subseq is attached to a sequence, get the |
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corresponding subsequence. |
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Returns : A sequence object or undef |
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Args : None. |
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=cut |
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sub seq { |
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my ($self, $value) = @_; |
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if (defined $value) { |
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# The sequence is explicit |
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if ( not(ref $value) || not $value->isa('Bio::PrimarySeqI') ) { |
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$self->throw("Expected a sequence object but got a '".ref($value)."'\n"); |
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} |
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$self->{seq} = $value; |
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} |
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my $seq = $self->{seq}; |
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if (not defined $seq) { |
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# The sequence is implied |
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$seq = $self->SUPER::seq; |
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} |
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return $seq; |
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} |
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=head2 length |
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Title : seq() |
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Usage : my $length = $subseq->seq(); |
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Function: Get the length of the SubSeq feature. It is similar to the length() |
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method of L, which computes length based |
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on the location of the feature. However, if the feature was not |
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given a location, return the length of the subsequence if possible. |
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Returns : integer or undef |
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Args : None. |
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=cut |
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sub length { |
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my ($self) = @_; |
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# Try length from location first |
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if ($self->start && $self->end) { |
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return $self->SUPER::length(); |
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} |
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# Then try length from subsequence |
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my $seq = $self->seq; |
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if (defined $seq) { |
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return length $seq->seq; |
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} |
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# We failed |
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return undef; |
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} |
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1; |