kalign.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.

"""A Python wrapper for Kalign."""
import os
import subprocess
from typing import Sequence

from absl import logging

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


def _to_a3m(sequences: Sequence[str]) -> str:
  """Converts sequences to an a3m file."""
  names = ['sequence %d' % i for i in range(1, len(sequences) + 1)]
  a3m = []
  for sequence, name in zip(sequences, names):
    a3m.append(u'>' + name + u'\n')
    a3m.append(sequence + u'\n')
  return ''.join(a3m)


class Kalign:
  """Python wrapper of the Kalign binary."""

  def __init__(self, *, binary_path: str):
    """Initializes the Python Kalign wrapper.

    Args:
      binary_path: The path to the Kalign binary.

    Raises:
      RuntimeError: If Kalign binary not found within the path.
    """
    self.binary_path = binary_path

  def align(self, sequences: Sequence[str]) -> str:
    """Aligns the sequences and returns the alignment in A3M string.

    Args:
      sequences: A list of query sequence strings. The sequences have to be at
        least 6 residues long (Kalign requires this). Note that the order in
        which you give the sequences might alter the output slightly as
        different alignment tree might get constructed.

    Returns:
      A string with the alignment in a3m format.

    Raises:
      RuntimeError: If Kalign fails.
      ValueError: If any of the sequences is less than 6 residues long.
    """
    logging.info('Aligning %d sequences', len(sequences))

    for s in sequences:
      if len(s) < 6:
        raise ValueError('Kalign requires all sequences to be at least 6 '
                         'residues long. Got %s (%d residues).' % (s, len(s)))

    with utils.tmpdir_manager() as query_tmp_dir:
      input_fasta_path = os.path.join(query_tmp_dir, 'input.fasta')
      output_a3m_path = os.path.join(query_tmp_dir, 'output.a3m')

      with open(input_fasta_path, 'w') as f:
        f.write(_to_a3m(sequences))

      cmd = [
          self.binary_path,
          '-i', input_fasta_path,
          '-o', output_a3m_path,
          '-format', 'fasta',
      ]

      logging.info('Launching subprocess "%s"', ' '.join(cmd))
      process = subprocess.Popen(cmd, stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE)

      with utils.timing('Kalign query'):
        stdout, stderr = process.communicate()
        retcode = process.wait()
        logging.info('Kalign stdout:\n%s\n\nstderr:\n%s\n',
                     stdout.decode('utf-8'), stderr.decode('utf-8'))

      if retcode:
        raise RuntimeError('Kalign failed\nstdout:\n%s\n\nstderr:\n%s\n'
                           % (stdout.decode('utf-8'), stderr.decode('utf-8')))

      with open(output_a3m_path) as f:
        a3m = f.read()

      return a3m