[Bioperl-l] module announcement: Bio::OntologyIO::simplehierarchy

[Allen Day]

after a brief conversation with Hilmar yesterday, i was persuaded that I 
should announce the addition of a new OntologyIO module that I've recently 
commited, so that people not on the guts list know about it, if nothing 
else.

Anyway, the purpose of the module is to create a Bio::Ontology, as the 
DAGEdit parser already does.  It operates on simply formatted files like 
this:

term1
  term2
  term3
    term4
  term5
  term6
    term7
    term4

and creates a graph, most likely a tree.  it's producing a dag if there
are cycles (as in the above case, notice "term4" is appearing twice).

the indent string is passed at runtime.  i'm using this parser to parse
some human developmental ontology files that use an indent string of "  
".  it also works on the SANBI eVOC human disease phenotype ontology
files, which use an indent string of ",".

have a look at the at the POD docs for more details on this module.

-Allen