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 $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$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).
The trouble about this is we are not that sure what "interesting facts" someone might want to store: the possibility is endless.
Bioperl's approach is that the "interesting facts" are represented by Bio::AnnotationI objects. The interface Bio::AnnotationI guarentees 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 info read Bio::AnnotationI docs
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, AnnotationCollectionI's are guarentee to maintain a consistent set object values 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 Bio::Annotation::Comment dblink Bio::Annotation::DBLink description Bio::Annotation::SimpleValue gene_name Bio::Annotation::SimpleValue ontology_term Bio::Annotation::OntologyTerm reference 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@bio.perl.org
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/
Email birney@ebi.ac.uk
Describe contact details here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_all_annotation_keys 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
Title : get_Annotations Usage : my @annotations = $collection->get_Annotations('key') Function: Retrieves all the Bio::AnnotationI objects for a specific key Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : string which is key for annotations
Title : get_num_of_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 Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.