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

Peter biopython at maubp.freeserve.co.uk
Mon Sep 7 17:34:53 UTC 2009

On Fri, Sep 4, 2009 at 4:33 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> Hi David,
> [This is a continuation of a thread on the main list, but it is much more
> suited to the dev list now.]
> ...
> 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).

I see you've switched to _EmbossCommandLine - fine.

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

Also fixed, thanks.

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


I have checked this into CVS, but did also fix an old typo (in a docstring)
and one new typo (in an argument name). Thanks David!

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.

We should put you in the CONTRIB file now too (are there any other
recent people we've missed?). Would you like to give a webpage, or
is this email address fine (be warned it may get harvested for spam)?

Thank you,


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