Combining PWAs and MSAs #5075
Description
Hi @manulera,
I ran the following example:
def test_mixed_input(self):
"""Test that the method works with input Alignments of mixed number of sequences"""
aligner = PairwiseAligner()
# Input sequences
reference_str = "ACGT"
seq1_str = "ACGGT"
seq2_str = "AT"
# Coordinates for an alignment of three sequences
coords = np.array([
[0, 1, 2, 3, 4, 4],
[0, 1, 2, 3, 4, 5],
[0, 1, 1, 1, 1, 2]])
# Generate input alignments
pwa = next(aligner.align(reference_str, seq1_str))
not_pairwise_alignment = Alignment([reference_str, seq1_str, seq2_str], coords)
# Use the method being tested
msa = Alignment.from_alignments_with_same_reference([pwa, not_pairwise_alignment])
This produced the following error:
# Concatenate all indices vertically
> all_indices = np.concatenate(
[all_indices[0], *[ind[1:] for ind in all_indices[1:]]], axis=0
)
E ValueError: all the input array dimensions except for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 5 and the array at index 1 has size 4
Bio/Align/__init__.py:1231: ValueError
I added a print statement right before the line that produced the error
print([ind.shape for ind in all_indices])
to see that the dimensions of the two coordinates arrays were [(3, 5), (3, 4)].