[Biopython-dev] Tests for Emboss Phylip wrappers

[Peter]

On Tue, Sep 22, 2009 at 6:14 AM, David Winter
<winda002 at student.otago.ac.nz> wrote:
> Peter wrote:
>>>
>>> Writing them actually exposed a bug in the code already in CVS,
>>> the FProtParsCommandline option "-intreefile" isn't mandatory so
>>> "is_required" should be set to 0 rather than 1. In my defence the
>>> emboss documentation has it listed as being both mandatory and
>>> optional.
>>
>> Fixed in CVS - does this affect any of the other tools using this
>> argument?
>
> Nope, I only slipped on this one ;)

Great. It looks like the tests have been useful already :)

>> The unit test is working nicely on Linux with EMBOSS PHYLIP
>> from CVS, I presume you are testing against an official release?
>> If you could the CVS code works fine on your setup before the
>> release that would be great.
>
> Finally got in front of the right computer to do this. The tests in the
> (Biopython) CVS work fine with the official EMBOSS 6.1.0 release
> (on ubuntu if that helps).

Great - thank you.

> I'd offer to try it out on windows but I don't
> have EMBOSS, a compiler or and of the libraries that I'd need to
> do that!

Hmm - EMBOSS only provide a Windows installer for the core
EMBOSS suite, not the extras like PHYLIP. I do have a C
compiler and cygwin setup on my Windows machine, so it may
work. We'll see...

Peter