[Biopython-dev] OBO parser & DAG

[Eric Talevich]

On Tue, Jan 7, 2014 at 12:51 PM, Bartek Wilczynski <bartek at rezolwenta.eu.org
> wrote:

> [...]
> We have actually evaluated networkx before implementing our library and
> thought it was unnecessary for our purposes to make it a requirement for
> biopython as the enrichment analysis is using a relatively small subset of
> graph operations.
>
> However it would be very easy to make functions for converting our
> ontologies to networkx digraphs, either with or without gene annotations as
> additional attributes.
>
> [...]
>

Chiming in briefly --

While it does make sense to avoid new dependencies in Biopython modules,
the Bio.Phylo module already uses networkx for a couple of non-core
functions. Since networkx is portable, pure Python (as far as I can tell)
and has no additional hard dependencies of its own, it would not
necessarily be a major inconvenience to the user if this new module depends
on networkx.