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# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""A Python wrapper for hmmbuild - construct HMM profiles from MSA."""
import os
import re
import subprocess
from absl import logging
from alphafold.data.tools import utils
# Internal import (7716).
class Hmmbuild(object):
"""Python wrapper of the hmmbuild binary."""
def __init__(self,
*,
binary_path: str,
singlemx: bool = False):
"""Initializes the Python hmmbuild wrapper.
Args:
binary_path: The path to the hmmbuild executable.
singlemx: Whether to use --singlemx flag. If True, it forces HMMBuild to
just use a common substitution score matrix.
Raises:
RuntimeError: If hmmbuild binary not found within the path.
"""
self.binary_path = binary_path
self.singlemx = singlemx
def build_profile_from_sto(self, sto: str, model_construction='fast') -> str:
"""Builds a HHM for the aligned sequences given as an A3M string.
Args:
sto: A string with the aligned sequences in the Stockholm format.
model_construction: Whether to use reference annotation in the msa to
determine consensus columns ('hand') or default ('fast').
Returns:
A string with the profile in the HMM format.
Raises:
RuntimeError: If hmmbuild fails.
"""
return self._build_profile(sto, model_construction=model_construction)
def build_profile_from_a3m(self, a3m: str) -> str:
"""Builds a HHM for the aligned sequences given as an A3M string.
Args:
a3m: A string with the aligned sequences in the A3M format.
Returns:
A string with the profile in the HMM format.
Raises:
RuntimeError: If hmmbuild fails.
"""
lines = []
for line in a3m.splitlines():
if not line.startswith('>'):
line = re.sub('[a-z]+', '', line) # Remove inserted residues.
lines.append(line + '\n')
msa = ''.join(lines)
return self._build_profile(msa, model_construction='fast')
def _build_profile(self, msa: str, model_construction: str = 'fast') -> str:
"""Builds a HMM for the aligned sequences given as an MSA string.
Args:
msa: A string with the aligned sequences, in A3M or STO format.
model_construction: Whether to use reference annotation in the msa to
determine consensus columns ('hand') or default ('fast').
Returns:
A string with the profile in the HMM format.
Raises:
RuntimeError: If hmmbuild fails.
ValueError: If unspecified arguments are provided.
"""
if model_construction not in {'hand', 'fast'}:
raise ValueError(f'Invalid model_construction {model_construction} - only'
'hand and fast supported.')
with utils.tmpdir_manager(base_dir='/tmp') as query_tmp_dir:
input_query = os.path.join(query_tmp_dir, 'query.msa')
output_hmm_path = os.path.join(query_tmp_dir, 'output.hmm')
with open(input_query, 'w') as f:
f.write(msa)
cmd = [self.binary_path]
# If adding flags, we have to do so before the output and input:
if model_construction == 'hand':
cmd.append(f'--{model_construction}')
if self.singlemx:
cmd.append('--singlemx')
cmd.extend([
'--amino',
output_hmm_path,
input_query,
])
logging.info('Launching subprocess %s', cmd)
process = subprocess.Popen(cmd, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
with utils.timing('hmmbuild query'):
stdout, stderr = process.communicate()
retcode = process.wait()
logging.info('hmmbuild stdout:\n%s\n\nstderr:\n%s\n',
stdout.decode('utf-8'), stderr.decode('utf-8'))
if retcode:
raise RuntimeError('hmmbuild failed\nstdout:\n%s\n\nstderr:\n%s\n'
% (stdout.decode('utf-8'), stderr.decode('utf-8')))
with open(output_hmm_path, encoding='utf-8') as f:
hmm = f.read()
return hmm
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