af_backprop/alphafold/data/tools/hhsearch.py

# 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 HHsearch from Python."""

import glob
import os
import subprocess
from typing import Sequence

from absl import logging

from alphafold.data.tools import utils
# Internal import (7716).


class HHSearch:
  """Python wrapper of the HHsearch binary."""

  def __init__(self,
               *,
               binary_path: str,
               databases: Sequence[str],
               maxseq: int = 1_000_000):
    """Initializes the Python HHsearch wrapper.

    Args:
      binary_path: The path to the HHsearch executable.
      databases: A sequence of HHsearch database paths. This should be the
        common prefix for the database files (i.e. up to but not including
        _hhm.ffindex etc.)
      maxseq: The maximum number of rows in an input alignment. Note that this
        parameter is only supported in HHBlits version 3.1 and higher.

    Raises:
      RuntimeError: If HHsearch binary not found within the path.
    """
    self.binary_path = binary_path
    self.databases = databases
    self.maxseq = maxseq

    for database_path in self.databases:
      if not glob.glob(database_path + '_*'):
        logging.error('Could not find HHsearch database %s', database_path)
        raise ValueError(f'Could not find HHsearch database {database_path}')

  def query(self, a3m: str) -> str:
    """Queries the database using HHsearch using a given a3m."""
    with utils.tmpdir_manager(base_dir='/tmp') as query_tmp_dir:
      input_path = os.path.join(query_tmp_dir, 'query.a3m')
      hhr_path = os.path.join(query_tmp_dir, 'output.hhr')
      with open(input_path, 'w') as f:
        f.write(a3m)

      db_cmd = []
      for db_path in self.databases:
        db_cmd.append('-d')
        db_cmd.append(db_path)
      cmd = [self.binary_path,
             '-i', input_path,
             '-o', hhr_path,
             '-maxseq', str(self.maxseq)
             ] + db_cmd

      logging.info('Launching subprocess "%s"', ' '.join(cmd))
      process = subprocess.Popen(
          cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
      with utils.timing('HHsearch query'):
        stdout, stderr = process.communicate()
        retcode = process.wait()

      if retcode:
        # Stderr is truncated to prevent proto size errors in Beam.
        raise RuntimeError(
            'HHSearch failed:\nstdout:\n%s\n\nstderr:\n%s\n' % (
                stdout.decode('utf-8'), stderr[:100_000].decode('utf-8')))

      with open(hhr_path) as f:
        hhr = f.read()
    return hhr