[Biopython-dev] "Features" of Bio.Clustalw

[Davide Marchignoli]

On Sat, 28 Jul 2001, Brad Chapman wrote:

> Hi Davide;
>
> Thanks for your feedback on this. If you can send patches for whatever
> you can fix, I'll take care of the rest of the bugs, and beef up the
> test suite to catch them.
>
> Thanks again!
> Brad
>

Hi Brad,

Here I send the patches I was able to cook up, these are only minor
changes, anyway I hope it will help.

I think that having a class like MultipleAlignCL is superior to passing
the alignment arguments to a function as is for blastpgp or blastall.

For first, it allow you to see which command it will be executed (for
debugging purposes it can be interesting) simply applying str to the
object.

Also it permits to build a set of parameters to be used on different
files.

Finally it is a general mechanism and could be used to give a uniform
interface to functions invoking external programs.

Do you think you would be interested in a patch implementing such
behaviour? I think one could also retain compatibilty with the current
interface.

Thanks again,

				Davide Marchignoli