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"""A Python wrapper for hmmalign from the HMMER Suite."""
from collections.abc import Mapping, Sequence
import os
import tempfile
from flax_model.alphafold3.data import parsers
from flax_model.alphafold3.data.tools import subprocess_utils
def _to_a3m(sequences: Sequence[str], name_prefix: str = 'sequence') -> str:
a3m = ''
for i, sequence in enumerate(sequences, 1):
a3m += f'> {name_prefix} {i}\n{sequence}\n'
return a3m
class Hmmalign:
"""Python wrapper of the hmmalign binary."""
def __init__(self, binary_path: str):
"""Initializes the Python hmmalign wrapper.
Args:
binary_path: Path to the hmmalign binary.
Raises:
RuntimeError: If hmmalign binary not found within the path.
"""
self._binary_path = binary_path
subprocess_utils.check_binary_exists(path=self._binary_path, name='hmmalign')
def align_sequences(
self,
sequences: Sequence[str],
profile: str,
extra_flags: Mapping[str, str] | None = None,
) -> str:
"""Aligns sequence list to the profile and returns the alignment in A3M."""
return self.align(
a3m_str=_to_a3m(sequences, name_prefix='query'),
profile=profile,
extra_flags=extra_flags,
)
def align(
self,
a3m_str: str,
profile: str,
extra_flags: Mapping[str, str] | None = None,
) -> str:
"""Aligns sequences in A3M to the profile and returns the alignment in A3M.
Args:
a3m_str: A list of sequence strings.
profile: A hmm file with the hmm profile to align the sequences to.
extra_flags: Dictionary with extra flags, flag_name: flag_value, that are
added to hmmalign.
Returns:
An A3M string with the aligned sequences.
Raises:
RuntimeError: If hmmalign fails.
"""
with tempfile.TemporaryDirectory() as query_tmp_dir:
input_profile = os.path.join(query_tmp_dir, 'profile.hmm')
input_sequences = os.path.join(query_tmp_dir, 'sequences.a3m')
output_a3m_path = os.path.join(query_tmp_dir, 'output.a3m')
with open(input_profile, 'w') as f:
f.write(profile)
with open(input_sequences, 'w') as f:
f.write(a3m_str)
cmd = [
self._binary_path,
*('-o', output_a3m_path),
*('--outformat', 'A2M'), # A2M is A3M in the HMMER suite.
]
if extra_flags:
for flag_name, flag_value in extra_flags.items():
cmd.extend([flag_name, flag_value])
cmd.extend([input_profile, input_sequences])
subprocess_utils.run(
cmd=cmd,
cmd_name='hmmalign',
log_stdout=False,
log_stderr=True,
log_on_process_error=True,
)
with open(output_a3m_path, encoding='utf-8') as f:
a3m = f.read()
return a3m
def align_sequences_to_profile(self, profile: str, sequences_a3m: str) -> str:
"""Aligns the sequences to profile and returns the alignment in A3M string.
Uses hmmalign to align the sequences to the profile, then ouputs the
sequence contatenated at the beginning of the sequences in the A3M format.
As the sequences are represented by an alignment with possible gaps ('-')
and insertions (lowercase characters), the method first removes the gaps,
then uppercases the insertions to prepare the sequences for realignment.
Sequences with gaps cannot be aligned, as '-'s are not a valid symbol to
align; lowercase characters must be uppercased to preserve the original
sequences before realignment.
Args:
profile: The Hmmbuild profile to align the sequences to.
sequences_a3m: Sequences in A3M format to align to the profile.
Returns:
An A3M string with the aligned sequences.
Raises:
RuntimeError: If hmmalign fails.
"""
deletion_table = str.maketrans('', '', '-')
sequences_no_gaps_a3m = []
for seq, desc in parsers.lazy_parse_fasta_string(sequences_a3m):
sequences_no_gaps_a3m.append(f'>{desc}')
sequences_no_gaps_a3m.append(seq.translate(deletion_table))
sequences_no_gaps_a3m = '\n'.join(sequences_no_gaps_a3m)
aligned_sequences = self.align(sequences_no_gaps_a3m, profile)
return aligned_sequences
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