[Biopython] ‘grant’ substitution matrix error

[Iddo Friedberg]

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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