[Biopython-dev] Tests for Emboss Phylip wrappers

[David Winter]

>>
>> Do you fancy writing a short unit tests? e.g. test_Emboss_phylip.py
>> based on test_Emboss.py? Continuing on the github branch is fine.
>>  

Well, it didn't end up being very short but there is a test on my 
"phylo" branch (http://github.com/dwinter/biopython/tree/phylo) in  
test_PhylipNew.phy  (which uses a couple of new files in Tests/Phylip) 
that I'd welcome comments on.

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.

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.

Cheers,
David