- AUTHOR - Ewan Birney
Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
# Bio::SeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. # Bio::SeqI implements Bio::PrimarySeqI $seq = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); # Bio::SeqI has annotationcollections $ann = $seqobj->annotation(); # annotation object # Bio::SeqI has sequence features # features must implement Bio::SeqFeatureI @features = $seqobj->get_SeqFeatures(); # just top level @features = $seqobj->get_all_SeqFeatures(); # descend into sub features
Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guaranteed to get for any Bio::SeqI. For most users of the package the documentation (and methods) in this class are not at useful - this is a developers only class which defines what methods have to be implemented by other Perl objects to comply to the Bio::SeqI interface. Go "perldoc Bio::Seq" or "man Bio::Seq" for more information.
There aren't many method here, because too many complicated functions here would prevent implementations which are just wrappers around a database or similar delayed mechanisms.
Most of the clever stuff happens inside the SeqFeatureI system.
A good reference implementation is Bio::Seq which is a pure perl implementation of this class with a lot of extra pieces for extra manipulation. However, if you want to be able to use any sequence object in your analysis, if you can do it just using these methods, then you know you will be future proof and compatible with other implementations of Seq.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
AUTHOR - Ewan Birney
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_SeqFeatures Usage : my @feats = $seq->get_SeqFeatures(); Function: retrieve just the toplevel sequence features attached to this seq Returns : array of Bio::SeqFeatureI objects Args : none
Title : get_all_SeqFeatures Usage : my @feats = $seq->get_all_SeqFeatures(); Function: returns all SeqFeatures, including sub SeqFeatures Returns : an array of Bio::SeqFeatureI objects Args : none
Title : feature_count Usage : my $count = $seq->feature_count(); Function: Return the number of SeqFeatures attached to a sequence Returns : integer representing the number of SeqFeatures Args : none
This method comes through extension of Bio::FeatureHolderI. See Bio::FeatureHolderI for more information.
Title : seq Usage : my $string = $seq->seq(); Function: Retrieves the sequence string for the sequence object Returns : string Args : none
Title : write_GFF Usage : $seq->write_GFF(\*FILEHANDLE); Function: Convenience method to write out all the sequence features in GFF format to the provided filehandle (STDOUT by default) Returns : none Args : [optional] filehandle to write to (default is STDOUT)
Title : annotation Usage : my $ann = $seq->annotation($seq_obj); Function: retrieve the attached annotation object Returns : Bio::AnnotationCollectionI or none;
Title : species Usage : Function: Gets or sets the species Example : my $species = $seq->species(); Returns : Bio::Species object Args : Bio::Species object or none;
See Bio::Species for more information
Title : primary_seq Usage : my $primaryseq = $seq->primary_seq($newval) Function: Retrieve the underlying Bio::PrimarySeqI object if available. This is in the event one has a sequence with lots of features but want to be able to narrow the object to just one with the basics of a sequence (no features or annotations). Returns : Bio::PrimarySeqI Args : Bio::PrimarySeqI or none;
See Bio::PrimarySeqI for more information