[Biopython-dev] [Biopython] Phylogenetic trees with biopython?

[Peter]

Hi David,

[This is a continuation of a thread on the main list, but it is much more
suited to the dev list now.]

On Tue, Sep 1, 2009 at 11:38 PM, David Winter wrote:
> Peter wrote:
>> David - I would prefer we also put your new wrappers in
>> Bio.Emboss.Applications, and would be happy to look at adding
>> those to CVS now that Biopython 1.51 is out (I had forgotten
>> about them actually - so thanks for the reminder).
>>
>> Peter
>
> Hi Peter,
>
> I'd almost forgotten about them myself! I only put them in their own module
> because I had the PhyML wrapper as well and that's not an EMBOSS
> application.

I see you've done that on github. I had a look at merging this into CVS,
but had a few comments first.

I found you had a load of tabs in your file (please use 4 space indentation
in future). http://www.biopython.org/wiki/Contributing#Coding_conventions

I am unclear why you are subclassing _EmbossMinimalCommandLine
instead of _EmbossCommandLine since most (all?) of the new wrappers
use the "outfile" parameter. As I recall EMBOSS isn't fussy about the
presence of the equals sign (right now our wrappers mostly omit the
equals, but not all the time - which looks odd to me).

Also your code seems to me missing the __str__ / _validate changes
on the trunk.

And finally, I think you can add yourself to the copyright at the top of
the file for this work ;)

Peter