[Biopython-dev] Phylip interface questions

Peter biopython at maubp.freeserve.co.uk
Tue Jul 28 09:26:30 UTC 2009

On Tue, Jul 28, 2009 at 2:56 AM, David
Winter<winda002 at student.otago.ac.nz> wrote:
> Hi Marshall,
> 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.
> I wrote a few for my own use (I presumed no one else was doing stuff like
> this) which I've now uploaded as module (Bio.Phylo) here:
> http://github.com/dwinter/biopython/tree/phylo
> They are for the 'new phylip' version ('f' prefixed not 'e') in EMBOSS's
> 'embassy' packages (which take different arguments than the classes already
> in the EMBOSS module...). They also depend on the cool stuff that Brad and
> Peter have done for applications in biopython 1.51. Hopefully they will
> cover some of the same ground that you want to, or at least prevent you
> having to start from scratch.

Cool. I would double check that _EmbossCommandLine is still
appropriate - especially with regards the outfile parameter. I
changed a few things recently for seqret (which doesn't have
an outfile parameter).


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