[Biopython-dev] OBO parser & DAG

Eric Talevich eric.talevich at gmail.com
Wed Jan 8 19:18:52 UTC 2014

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.

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