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

[Peter Cock]

On Sun, Dec 18, 2011 at 2:22 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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...).

Actually, I might have been worried about what to do
with the existing MutableSeq's index method (which
is list/array like not string like).

Perhaps in the short term a fix to the TM function is
easier.

Peter