Result to a numpy / panda frame?

[jjkoehorst]

I could not find it in the documentation but what is the best / most efficient way of transforming the object to a panda or numpy dataframe? Currently writing the file to disk and loading it again but there might be a better way?

Thanks a lot for the extremely fast program!

[lkeegan]

@jjkoehorst with version 1.3.0 you should be able to directly access the distances as a 1-d numpy array

data = hammingdist.from_fasta("example.fasta")
lt_array = data.lt_array

The elements in this array are in lower-triangular order, i.e. correspond to the 2-d indices (row=1,col=0), (row=2,col=0), (row=2,col=1), ...
These indices can be generated using the numpy tril_indices function, e.g. to construct the lower-triangular distances matrix from the 1-d lt_array:

lt_matrix = np.zeros((n_seq, n_seq))
lt_matrix[np.tril_indices(n_seq, -1)] = lt_array

Hopefully that is helpful, free to re-open this issue if not.