[Biopython] Melting Point.TM_NN calculation

[Peter Cock]

This was resolved off list - a variable mix up.

Peter

On Wed, Jun 24, 2015 at 5:09 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi Ian,
>
> I don't understand where the dot/period in '.G/AT' comes from.
> Can you give some more details - a short script with the problem
> sequences would be ideal.
>
> In case it is relevant, which version of Biopython are you running?
> (It looks like this is Python 2.7 under Apple OS X).
>
> Peter
>
> On Wed, Jun 24, 2015 at 3:39 PM, Ian Stavros <ianstavros at gmail.com> wrote:
>> Hello,
>>
>> My name is Ian and I am new to the bioinformatics world. I am using the
>> biopython's melting temp TM_NN algorithm to calculate the melting temp
>> differences in wild type sequence with the complementary mutation sequence,
>> using the the the Allawi and SantaLucia (1997), Biochemistry 36: 10581-10594
>> table. I have attached a small output of the sample program for better
>> understanding, which shows the Key Error I am getting and other times I will
>> get a Value Error, meaning it can find the key but can't find the value, I
>> was wondering if
>>
>> A) if there is something else out there better suited for this problem
>>
>> B) if I need to update the table or something to get working and if so how
>> would I go about improving the dictionary being used to address the problems
>> which can be seen here
>>
>>
>> /Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931:
>> BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be wrong
>>   BiopythonWarning)
>>
>>
>> Here is the output of the code. I think that the '.' may be equivalent to
>> the regex expression of '.' meaning it could be any character in front of
>> the G. But as you can see it is not a problem for the one up above.
>>
>>
>> seq:  ['G', 'A', 'T']
>> Mutation c_seq:  ['C', 'C', 'A']
>> /Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931:
>> BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be wrong
>>   BiopythonWarning)
>> TM:  -262.480685148
>> seq:  ['G', 'A', 'T', 'A']
>> Mutation c_seq:  ['C', 'C', 'A', 'T']
>> Traceback (most recent call last):
>>   File "PrimerBuilder.py", line 333, in <module>
>>     switchList = switchBuilder(middle,basepairs,mutation)
>>   File "PrimerBuilder.py", line 56, in switchBuilder
>>     tmMismatch =
>> mt.Tm_NN(switch,strict=False,c_seq=mutation,nn_table=mt.DNA_NN3)
>>   File "/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py", line
>> 856, in Tm_NN
>>     deltaH += de_table[right_de][dH]
>> KeyError: '.G/AT'
>>
>>
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