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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 hmmsearch - search profile against a sequence db."""
import os
import subprocess
from typing import Optional, Sequence
from absl import logging
from alphafold.data.tools import utils
# Internal import (7716).
class Hmmsearch(object):
"""Python wrapper of the hmmsearch binary."""
def __init__(self,
*,
binary_path: str,
database_path: str,
flags: Optional[Sequence[str]] = None):
"""Initializes the Python hmmsearch wrapper.
Args:
binary_path: The path to the hmmsearch executable.
database_path: The path to the hmmsearch database (FASTA format).
flags: List of flags to be used by hmmsearch.
Raises:
RuntimeError: If hmmsearch binary not found within the path.
"""
self.binary_path = binary_path
self.database_path = database_path
self.flags = flags
if not os.path.exists(self.database_path):
logging.error('Could not find hmmsearch database %s', database_path)
raise ValueError(f'Could not find hmmsearch database {database_path}')
def query(self, hmm: str) -> str:
"""Queries the database using hmmsearch using a given hmm."""
with utils.tmpdir_manager(base_dir='/tmp') as query_tmp_dir:
hmm_input_path = os.path.join(query_tmp_dir, 'query.hmm')
a3m_out_path = os.path.join(query_tmp_dir, 'output.a3m')
with open(hmm_input_path, 'w') as f:
f.write(hmm)
cmd = [
self.binary_path,
'--noali', # Don't include the alignment in stdout.
'--cpu', '8'
]
# If adding flags, we have to do so before the output and input:
if self.flags:
cmd.extend(self.flags)
cmd.extend([
'-A', a3m_out_path,
hmm_input_path,
self.database_path,
])
logging.info('Launching sub-process %s', cmd)
process = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
with utils.timing(
f'hmmsearch ({os.path.basename(self.database_path)}) query'):
stdout, stderr = process.communicate()
retcode = process.wait()
if retcode:
raise RuntimeError(
'hmmsearch failed:\nstdout:\n%s\n\nstderr:\n%s\n' % (
stdout.decode('utf-8'), stderr.decode('utf-8')))
with open(a3m_out_path) as f:
a3m_out = f.read()
return a3m_out
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