Modifying a substitution matrix by column raises an error

[davidnewman02]

From the documentation it should be possible to modify a substitution matrix like a numpy array:

import parasail
# copy a built-in matrix, then modify like a numpy array
matrix = parasail.blosum62.copy()
matrix[2,4] = 200
matrix[3,:] = 100

However row/column-wise assignment fails with the following error:

>>> matrix[3,:] = 100
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "venv/lib/python3.12/site-packages/parasail/bindings_v2.py", line 504, in __setitem__
    for c in range(key[1].start, key[1].stop, key[1].step or 1):
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object cannot be interpreted as an integer

parasail version == 1.3.4
python version == 3.12.3

[haydenji0731]

I couldn't modify the substitution matrix following the documentation either.

Instead, I had to do something like:

mat = parasail.matrix_create("ACGT", 2, 1)
mat.set_value(4, 0, 3)

The parasail.blosum62.copy() just returns a read-only numpy array, which is not so useful for modifying the matrix and using it subsequently for an alignment. You can still access elements though:

>>> matrix = parasail.blosum62.copy()
>>> matrix.matrix[2,4]
np.int32(-3)