Bio::Annotation - A generic object for annotations
# get an annotation somehow in $ann # description is a simple, one line description print "Description is ",$ann->description "\n"; foreach $comment ( $ann->each_Comment ) { # $comment is a Bio::Annotation::Comment object print "Comment: ", $comment->text(), "\n" } } foreach $link ( $ann->each_DBLink ) { # link is a Bio::Annotation::DBLink object print "Link to ",$link->primary_id, " in database", $link->db "\n"; } foreach $ref ( $ann->each_Reference ) { # link is a Bio::Annotation::Reference object print "Reference title ", $ref->title , "\n"; } # # Making an annotation object from scratch # $ann = Bio::Pfam::Annotation->new(); $ann->description("Description text"); print "Annotation description is ", $ann->description, "\n";
The object represents generic biological annotation of an object. It has the ability to provide
a brief, one line description free text comments links to other biological objects references to literature
It does not have the following abilities
The basis (experimental/non experimental/homology) of the annotation. This is considered to be part of the object which owns the annotation. This is because the type of relevant basis is usually dependent on the object The previous revisions of the object This should be a property of whatever database this object comes from
Mail birney@sanger.ac.uk with any queries
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : description Usage : $obj->description($newval) Function: Example : Returns : value of description Args : newvalue (optional)
Title : gene_name Usage : $obj->gene_name($newval) Function: Example : Returns : value of gene name Args : newvalue (optional)
Title : add_Reference Usage : $self->add_Reference($ref) Function: adds a reference object Example : Returns : Args :
Title : each_Reference Usage : foreach $ref ( $self->each_Reference() ) Function: gets an array of reference Example : Returns : Args :
Title : add_Comment Usage : $self->add_Comment($ref) Function: adds a Comment object Example : Returns : Args :
Title : each_Comment Usage : foreach $ref ( $self->each_Comment() ) Function: gets an array of Comment of objects Example : Returns : Args :
Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args :
Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : Args :
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.