[Biopython-dev] [Bug 3066] Iterating/looping over colums/rows of a MultipleSeqAlignment

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3066





------- Comment #2 from eric.talevich at gmail.com  2010-04-28 14:29 EST -------
I don't mind having plain strings returned; Bio.Seq works well enough with them
for me.

Two things:

1. Is this implementation fast? It basically transposes the alignment as a
list-of-lists, right? So:

return zip(*self)

or:

from itertools import izip
return (''.join(col) for col in izip(*self))


2. On the topic of efficiency -- have you encountered a situation where having
an alignment as a NumPy character array would have helped?


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