FAST::Bio::AnnotationCollectionI - Interface for annotation collections
# get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an FAST::Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"\n"; # also defined hash_tree method, which allows data orientated # access into this object $hash = $value->hash_tree(); } }
Annotation Collections are a way of storing a series of "interesting facts" about something. We call an "interesting fact" in Bioperl an Annotation (this differs from a Sequence Feature, which is called a Sequence Feature and may or may not have an Annotation Collection).
A benefit of this approach is that all sorts of simple, interesting observations can be collected, the possibility is endless.
The Bioperl approach is that the "interesting facts" are represented by FAST::Bio::AnnotationI objects. The interface FAST::Bio::AnnotationI guarantees two methods
$obj->as_text(); # string formated to display to users
and
$obj->hash_tree(); # hash with defined rules for data-orientated discovery
The hash_tree method is designed to play well with XML output and other "nested-tag-of-data-values", think BoulderIO and/or Ace stuff. For more information see FAST::Bio::AnnotationI.
Annotations are stored in AnnotationCollections, each Annotation under a different "tag". The tags allow simple discovery of the available annotations, and in some cases (like the tag "gene_name") indicate how to interpret the data underneath the tag. The tag is only one tag deep and each tag can have an array of values.
In addition, AnnotationCollections are guaranteed to maintain consistent types of objects under each tag - at least that each object complies to one interface. The "standard" AnnotationCollection insists the following rules are set up:
Tag Object --- ------ comment FAST::Bio::Annotation::Comment dblink FAST::Bio::Annotation::DBLink description FAST::Bio::Annotation::SimpleValue gene_name FAST::Bio::Annotation::SimpleValue ontology_term FAST::Bio::Annotation::OntologyTerm reference FAST::Bio::Annotation::Reference
These tags are the implict tags that the SeqIO system needs to round-trip GenBank/EMBL/Swissprot.
However, you as a user and us collectively as a community can grow the "standard" tag mapping over time and specifically for a particular area.
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.
bioperl-l@bioperl.org
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:
https://redmine.open-bio.org/projects/bioperl/
Email birney@ebi.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Use these for FAST::Bio::AnnotationI object access.
Usage : $ac->get_all_annotation_keys() Function: gives back a list of annotation keys, which are simple text strings Returns : list of strings Args : none
Usage : my @annotations = $collection->get_Annotations('key') Function: Retrieves all the FAST::Bio::AnnotationI objects for a specific key Returns : list of FAST::Bio::AnnotationI - empty if no objects stored for a key Args : string which is key for annotations
Usage : $self->add_Annotation('reference',$object); $self->add_Annotation($object,'FAST::Bio::MyInterface::DiseaseI'); $self->add_Annotation($object); $self->add_Annotation('disease',$object,'FAST::Bio::MyInterface::DiseaseI'); Function: Adds an annotation for a specific key. If the key is omitted, the object to be added must provide a value via its tagname(). If the archetype is provided, this and future objects added under that tag have to comply with the archetype and will be rejected otherwise. Returns : none Args : annotation key ('disease', 'dblink', ...) object to store (must be FAST::Bio::AnnotationI compliant) [optional] object archetype to map future storage of object of these types to
Usage : Function: Remove the annotations for the specified key from this collection. Returns : an list of FAST::Bio::AnnotationI compliant objects which were stored under the given key(s) Args : the key(s) (tag name(s), one or more strings) for which to remove annotations (optional; if none given, flushes all annotations)
Usage : my $count = $collection->get_num_of_annotations() Function: Returns the count of all annotations stored in this collection Returns : integer Args : none
To install FAST, copy and paste the appropriate command in to your terminal.
cpanm
cpanm FAST
CPAN shell
perl -MCPAN -e shell install FAST
For more information on module installation, please visit the detailed CPAN module installation guide.