Convert the supplied multiple sequence alignment to an ordinary array so that reducing over rows returns one value per column. With nine sequences, fewer than 30% gaps means at most two gaps in a column:
from collections import Counter
A = np.asarray(msa_matrix)
gap_fraction = np.mean(A == ".", axis=0)
match_mask = gap_fraction < .30
match_columns = np.flatnonzero(match_mask)
print(match_columns + 1) # human-readable, one-based alignment columnsThere are 72 match states: alignment columns 1–21 and 29–79, using one-based numbering. The seven remaining columns, 22–28, form one contiguous insertion region. The strict inequality is applied to the actual fraction, rather than to rounded percentages.
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