[Biopython-dev] Phylip interface questions

Marshall Hampton mhampton at d.umn.edu
Mon Jul 27 18:42:21 UTC 2009

Thanks Peter, I was unaware of the EMBOSS versions of PHYLIP.  I don't 
think using pexpect to wrap the originals is really that hard - I have 
some working fine already - but now I see its almost pointless.  I don't 
like the EMBOSS dependence, but it sounds like you are already working on 
getting rid of that.


On Mon, 27 Jul 2009, Peter wrote:

> 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.
> Peter

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