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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. | |
"""Library to run HHblits from Python.""" | |
import glob | |
import os | |
import subprocess | |
from typing import Any, Mapping, Optional, Sequence | |
from absl import logging | |
from alphafold.data.tools import utils | |
# Internal import (7716). | |
_HHBLITS_DEFAULT_P = 20 | |
_HHBLITS_DEFAULT_Z = 500 | |
class HHBlits: | |
"""Python wrapper of the HHblits binary.""" | |
def __init__(self, | |
*, | |
binary_path: str, | |
databases: Sequence[str], | |
n_cpu: int = 4, | |
n_iter: int = 3, | |
e_value: float = 0.001, | |
maxseq: int = 1_000_000, | |
realign_max: int = 100_000, | |
maxfilt: int = 100_000, | |
min_prefilter_hits: int = 1000, | |
all_seqs: bool = False, | |
alt: Optional[int] = None, | |
p: int = _HHBLITS_DEFAULT_P, | |
z: int = _HHBLITS_DEFAULT_Z): | |
"""Initializes the Python HHblits wrapper. | |
Args: | |
binary_path: The path to the HHblits executable. | |
databases: A sequence of HHblits database paths. This should be the | |
common prefix for the database files (i.e. up to but not including | |
_hhm.ffindex etc.) | |
n_cpu: The number of CPUs to give HHblits. | |
n_iter: The number of HHblits iterations. | |
e_value: The E-value, see HHblits docs for more details. | |
maxseq: The maximum number of rows in an input alignment. Note that this | |
parameter is only supported in HHBlits version 3.1 and higher. | |
realign_max: Max number of HMM-HMM hits to realign. HHblits default: 500. | |
maxfilt: Max number of hits allowed to pass the 2nd prefilter. | |
HHblits default: 20000. | |
min_prefilter_hits: Min number of hits to pass prefilter. | |
HHblits default: 100. | |
all_seqs: Return all sequences in the MSA / Do not filter the result MSA. | |
HHblits default: False. | |
alt: Show up to this many alternative alignments. | |
p: Minimum Prob for a hit to be included in the output hhr file. | |
HHblits default: 20. | |
z: Hard cap on number of hits reported in the hhr file. | |
HHblits default: 500. NB: The relevant HHblits flag is -Z not -z. | |
Raises: | |
RuntimeError: If HHblits binary not found within the path. | |
""" | |
self.binary_path = binary_path | |
self.databases = databases | |
for database_path in self.databases: | |
if not glob.glob(database_path + '_*'): | |
logging.error('Could not find HHBlits database %s', database_path) | |
raise ValueError(f'Could not find HHBlits database {database_path}') | |
self.n_cpu = n_cpu | |
self.n_iter = n_iter | |
self.e_value = e_value | |
self.maxseq = maxseq | |
self.realign_max = realign_max | |
self.maxfilt = maxfilt | |
self.min_prefilter_hits = min_prefilter_hits | |
self.all_seqs = all_seqs | |
self.alt = alt | |
self.p = p | |
self.z = z | |
def query(self, input_fasta_path: str) -> Mapping[str, Any]: | |
"""Queries the database using HHblits.""" | |
with utils.tmpdir_manager(base_dir='/tmp') as query_tmp_dir: | |
a3m_path = os.path.join(query_tmp_dir, 'output.a3m') | |
db_cmd = [] | |
for db_path in self.databases: | |
db_cmd.append('-d') | |
db_cmd.append(db_path) | |
cmd = [ | |
self.binary_path, | |
'-i', input_fasta_path, | |
'-cpu', str(self.n_cpu), | |
'-oa3m', a3m_path, | |
'-o', '/dev/null', | |
'-n', str(self.n_iter), | |
'-e', str(self.e_value), | |
'-maxseq', str(self.maxseq), | |
'-realign_max', str(self.realign_max), | |
'-maxfilt', str(self.maxfilt), | |
'-min_prefilter_hits', str(self.min_prefilter_hits)] | |
if self.all_seqs: | |
cmd += ['-all'] | |
if self.alt: | |
cmd += ['-alt', str(self.alt)] | |
if self.p != _HHBLITS_DEFAULT_P: | |
cmd += ['-p', str(self.p)] | |
if self.z != _HHBLITS_DEFAULT_Z: | |
cmd += ['-Z', str(self.z)] | |
cmd += db_cmd | |
logging.info('Launching subprocess "%s"', ' '.join(cmd)) | |
process = subprocess.Popen( | |
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) | |
with utils.timing('HHblits query'): | |
stdout, stderr = process.communicate() | |
retcode = process.wait() | |
if retcode: | |
# Logs have a 15k character limit, so log HHblits error line by line. | |
logging.error('HHblits failed. HHblits stderr begin:') | |
for error_line in stderr.decode('utf-8').splitlines(): | |
if error_line.strip(): | |
logging.error(error_line.strip()) | |
logging.error('HHblits stderr end') | |
raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % ( | |
stdout.decode('utf-8'), stderr[:500_000].decode('utf-8'))) | |
with open(a3m_path) as f: | |
a3m = f.read() | |
raw_output = dict( | |
a3m=a3m, | |
output=stdout, | |
stderr=stderr, | |
n_iter=self.n_iter, | |
e_value=self.e_value) | |
return raw_output | |