[Biopython] ‘grant’ substitution matrix error

[Peter Cock]

Do you think either of you could tweak this bit of code to cope nicely
with the U or O amino acids?

Peter

On Mon, Oct 31, 2016 at 9:01 AM, Konrad Koehler <konrad.koehler at mac.com> wrote:
> Thanks Iddo,
>
> After removing dictionary entries containing ‘U’ or ‘O’ from MatrixInfo.py,
> I can now load the ‘grant’ matrix.
>
> /Konrad
>
>
> On 27 Oct 2016, at 15:48, Iddo Friedberg <idoerg at gmail.com> wrote:
>
> Wild guess: grant & fitch are the only matrices in MatrixInfo.py to have the
> 'U" amino acid in the 2-tuples that make up the key in the dictionary
> representing the matrices.  "U" is a non-canonical single amino-acid letter
> code. Since the program fails on the following:
> .
> .
> .
>  elif all(isinstance(i, str) for i in item):
>                 row_name, col_name = item
>                 if row_name in self.names and col_name in self.names:
>                     row_index = self.names.index(row_name)
>                     col_index = self.names.index(col_name)
>                 else:
>                     raise ValueError("Item not found.")
>
> My guess is that the 'U'   is not in self.names, which triggers the
> ValueError. Try inserting a different MatrixInfo file, where keys having 'U'
> are removed.
>
> ./I
>
>
> On Thu, Oct 27, 2016 at 7:56 AM, Konrad Koehler <konrad.koehler at mac.com>
> wrote:
>>
>> Hello Everyone,
>>
>> I wanted to use the ‘grant’ substitution matrix, but when I specify this
>> matrix in DistanceCalculator, it throws a ValueError (the full error message
>> is reproduced below). I have tested all the available substitution matrices
>> and they all work with the exception of ‘fitch’ and ‘grant’. These matrices
>> are stored in the following file:
>>
>> ~/anaconda/lib/python2.7/site-packages/Bio/SubsMat/MatrixInfo.py
>>
>> The fitch and grant matrices in this file look OK and I cannot see any
>> obvious reason why these matrices are failing to load. I would be very
>> grateful for any suggesting for how to fix these matrices.
>>
>> Thanks,
>>
>> Konrad
>>
>>
>> -------------------------------------------------------------------------------------------------------------------------------------
>> The following was produced by Biopython 1.68 on Mac OS X installed using
>> pip:
>>
>> >>> from Bio.Phylo.TreeConstruction import DistanceCalculator
>> >>> calculator = DistanceCalculator('grant')
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File
>> “~/anaconda/lib/python2.7/site-packages/Bio/Phylo/TreeConstruction.py", line
>> 411, in __init__
>>     self.protein_matrices[model])
>>   File
>> “~/anaconda/lib/python2.7/site-packages/Bio/Phylo/TreeConstruction.py", line
>> 480, in _build_protein_matrix
>>     protein_matrix[aa1, aa2] = v
>>   File
>> “~/anaconda/lib/python2.7/site-packages/Bio/Phylo/TreeConstruction.py", line
>> 222, in __setitem__
>>     raise ValueError("Item not found.")
>> ValueError: Item not found.
>>
>> -------------------------------------------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>>
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>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>>----.<--.>++++++.<<<<------------------------------------.
>
>
>
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