[BioPython] named tuples for biopython?

[Peter]

On Fri, Oct 17, 2008 at 11:03 AM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> Hi,
> python 2.6 is going to implement a new kind of data (like lists, strings,
> etc..) called 'named_tuple'.  It is intended to be a better data format to
> be used when parsing record files and databases.

I'd just seen this today actually via another mailing list.  Here is a
short example which actually works on python 2.6 (the details have
changed slightly from your quote),

>>> from collections import namedtuple
>>> Person = namedtuple("Person", "name surname")
>>> x = Person("Albert", "Einstein")
>>> x
Person(name='Albert', surname='Einstein')
>>> x.name
'Albert'
>>> x.surname
'Einstein'
>>> x.keys()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'Person' object has no attribute 'keys'
>>> x["name"]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: tuple indices must be integers, not str
>>> x[0]
'Albert'
>>> x[1]
'Einstein'

So this doesn't act much like a dictionary (in terms of the x[...]
usage), so we can't use it as a drop in enhancement for existing
dictionaries in Biopython.  I expect there are some places where a
namedtuple would make sense (although using it might break backwards
compatibility).

Also, if we did want to use NamedTuple in Biopython we'd have to
include a copy for use on older versions of python.  This is probably
possible under the python license... but would require an
implementation that still worked on pre 2.6.

Peter