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 unifold.msa import parsers
from . import utils


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}")

    @property
    def output_format(self) -> str:
        return "hhr"

    @property
    def input_format(self) -> str:
        return "a3m"

    def query(self, a3m: str) -> str:
        """Queries the database using HHsearch using a given a3m."""
        with utils.tmpdir_manager() 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

    def get_template_hits(
        self, output_string: str, input_sequence: str
    ) -> Sequence[parsers.TemplateHit]:
        """Gets parsed template hits from the raw string output by the tool."""
        del input_sequence  # Used by hmmseach but not needed for hhsearch.
        return parsers.parse_hhr(output_string)