Support ClustalW `.aln` file formats for sequence alignments

[ansumanbiswas]

Hi,
I wish to know how I can convert the following alignment file into .aln format and save it in the local directory?

Perform a multiple sequence alignment of the PB sequences

matrix = align.SubstitutionMatrix.std_protein_blocks_matrix()
alignment, order, _, _ = align.align_multiple(
structural_sequences, matrix, gap_penalty=(-500, -100), terminal_penalty=False
)
alignment = alignment[:, order.tolist()]

thanks and best,
Ansuman

[padix-key]

Hi. Unfortunately the Clustal .aln format is not supported, yet. If you are interested, it should not be too complicated to implement it yourself, as it is quite similar to the string representation of an Alignment object:

biotite/src/biotite/sequence/align/alignment.py

Lines 131 to 153 in 08e73e1

	def __str__(self):
	# Check if any of the sequences
	# has an non-single letter alphabet
	all_single_letter = True
	for seq in self.sequences:
	if not _is_single_letter(seq.alphabet):
	all_single_letter = False
	if all_single_letter:
	# First dimension: sequence number,
	# second dimension: line number
	seq_str_lines_list = []
	wrapper = textwrap.TextWrapper(break_on_hyphens=False)
	for i in range(len(self.sequences)):
	seq_str_lines_list.append(wrapper.wrap(self._gapped_str(i)))
	ali_str = ""
	for row_i in range(len(seq_str_lines_list[0])):
	for seq_j in range(len(seq_str_lines_list)):
	ali_str += seq_str_lines_list[seq_j][row_i] + "\n"
	ali_str += "\n"
	# Remove final line breaks
	return ali_str[:-2]
	else:
	return super().__str__()

Of course I am also willing to review a PR that adds this File class to Biotite 😉 .