- AUTHOR - Ewan Birney
Bio::SeqI - Abstract Interface of Sequence (with features)
# get a Bio::SeqI somehow, eg, via SeqIO. See SeqIO info # for more information $seqio = Bio::SeqIO->new ( '-format' => 'Fasta' , -file => 'myfile.fasta'); $seqobj = $seqio->next_seq(); # features must implement Bio::SeqFeatureI @features = $seqobj->top_SeqFeatures(); # just top level @features = $seqobj->all_SeqFeatures(); # descend into sub features $seq = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); $ann = $seqobj->annotation(); # annotation object
SeqI is the abstract interface of annotated Sequence. These methods are those which you can be guarenteed to get for any annseq. There aren't many here, because too many complicated functions here 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 alot 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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : top_SeqFeatures Usage : Function: Example : Returns : Args :
Title : all_SeqFeatures Usage : @features = $annseq->all_SeqFeatures() Function: returns all SeqFeatures, included sub SeqFeatures Returns : an array Args : none
Title : seq Usage : Function: Example : Returns : Args :
Title : write_GFF Usage : Function: Example : Returns : Args :
Title : annotation Usage : $obj->annotation($seq_obj) Function: Example : Returns : value of annotation Args : newvalue (optional)
Title : primary_seq Usage : $obj->primary_seq($newval) Function: Example : Returns : value of primary_seq Args : newvalue (optional)
Title : feature_count Usage : $seq->feature_count() Function: Return the number of SeqFeatures attached to a sequence Example : Returns : number of SeqFeatures Args : none
Title : species Usage : Function: Gets or sets the species Example : $species = $self->species(); Returns : Bio::Species object Args : Bio::Species object or none;