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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 | |