[Biopython] ‘grant’ substitution matrix error

[Konrad Koehler]

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

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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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