[Biopython-dev] Newick Parser

[Nigel Delaney]

I had a couple questions on the newick parser I was hoping someone might
know the answer to.

 

First, it fails when there are BOMs in the file, though in general it seems
that UTF encoding with BOMs should be allowed.  Is there a standard way that
BOM in files are handled in biopython?

 

Second, does anyone know what the consensus is on newick files that have
placements for data but no data.  For example:

 

((A,B):Name:.0235)C)

 

Defines a name and length for the A,B node.  However, 

 

((A,B)::)C)

 

Has positions for name and length but no length or name data, which seems
like it should be an error, though currently is just skipped.