[Biopython-dev] Tests for Emboss Phylip wrappers

[David Winter]

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 ;)
>   
>> One possibly foolish thing I did was use TreeIO to test the trees that came
>> out of these programs made sense, thinking that module would be part of the
>> next release. If the plan is for a new release soon and having a test for
>> these wrappers is important the tests could be done with Nexus.Trees but I
>> found that was difficult to use for files with multiple newick trees.
>>     
>
> I put a quick crude helper function into the unit test as discussed.
>
> 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). 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!

Cheers,
David