[Biopython-dev] Bio.SeqUtils.MeltingTemp Tm_staluc does not accept sequence object

[Peter Cock]

On Sat, Dec 17, 2011 at 10:33 PM, Markus Piotrowski
<Markus.Piotrowski at ruhr-uni-bochum.de> wrote:
> Dear Biophython developers,
>
> It seems that modul Tm_staluc from Bio.SeqUtils does not
> accept sequence objects as input but 'just' strings.

Well spotted, but the important information missing from your
email was what goes wrong:

>>> from Bio.Seq import Seq
>>> from Bio.SeqUtils.MeltingTemp import Tm_staluc
>>> Tm_staluc(Seq("ACGT"))
Traceback (most recent call last):
...
    i = st.index(p,x)
AttributeError: 'Seq' object has no attribute 'index'
>>> "ACGT".index("G")

That looks like an oversight in the Seq object, which
is easily fixed (the unit tests need a bit more work...).

> I think that is somewhat unusal for a 'SeqUtil', shouldn't sequence utilities
> accept sequence objects?
>
> I also think that the modul name 'Tm_staluc' is not self-explanatory. Obviously
> the name is derived from the corresponding author of the paper which describes
> this Tm calculation, SantaLucia. The method is better known (and described so in
> the documentation) as nearest neighbor thermodynamics, so it would better be
> called something like Tm_nn (nearest neighbour).

The doctoring could be expand to explain that. Would
you like to suggest an improvement?

> However, taking into consideration that more Tm methods will be added
> in future, they may just be numbered?

Numbered how? Tm_nn1, Tm_nn2, ... seems a bad idea.

Peter