[Biopython-dev] Phylip interface questions

Peter biopython at maubp.freeserve.co.uk
Mon Jul 27 17:24:57 UTC 2009

On Mon, Jul 27, 2009 at 6:05 PM, Marshall Hampton<mhampton at d.umn.edu> wrote:
> I am wondering if there is already an interface to the Phylip programs in
> biopython.  I am pretty sure there is not, but I wanted to ask before doing
> a chunk of work on one.  I know that AlignIO can read and write the phylip
> alignment files, but I think that is it.
> Assuming such a thing doesn't already exist, I will write some functions for
> calling various combinations of programs in phylip to make some common tasks
> easier.  Mostly this will use the pexpect module.  What is the most
> appropriate place to put such an interface within biopython?

I really wouldn't go down the route of trying to wrap the original PHYLIP
tools, it would involve piping simulated keypresses to stdin - very tricky
(even if the python module pexpect is wonderful).

I would instead wrap the EMBOSS packaged versions of the PHYLIP
suite, which have proper command line interfaces with switches etc.
In this case, Bio/Emboss/Applications.py would be the file to look at.
However, something I have been discussing with Peter Rice at EMBOSS
is using their ACD files (which define the EMBOSS tools command line
interfaces) to automatically generate the Biopython wrappers.


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