# Path: alphafold/data/parsers.py
# class Msa:
# class TemplateHit:
# class HitMetadata:
#   def __post_init__(self):
#   def __len__(self):
#   def truncate(self, max_seqs: int):
# def parse_fasta(fasta_string: str) -> Tuple[Sequence[str], Sequence[str]]:
# def parse_stockholm(stockholm_string: str) -> Msa:
# def parse_a3m(a3m_string: str) -> Msa:
# def _convert_sto_seq_to_a3m(
#     query_non_gaps: Sequence[bool], sto_seq: str) -> Iterable[str]:
# def convert_stockholm_to_a3m(stockholm_format: str,
#                              max_sequences: Optional[int] = None,
#                              remove_first_row_gaps: bool = True) -> str:
# def _keep_line(line: str, seqnames: Set[str]) -> bool:
# def truncate_stockholm_msa(stockholm_msa_path: str, max_sequences: int) -> str:
# def remove_empty_columns_from_stockholm_msa(stockholm_msa: str) -> str:
# def deduplicate_stockholm_msa(stockholm_msa: str) -> str:
# def _get_hhr_line_regex_groups(
#     regex_pattern: str, line: str) -> Sequence[Optional[str]]:
# def _update_hhr_residue_indices_list(
#     sequence: str, start_index: int, indices_list: List[int]):
# def _parse_hhr_hit(detailed_lines: Sequence[str]) -> TemplateHit:
# def parse_hhr(hhr_string: str) -> Sequence[TemplateHit]:
# def parse_e_values_from_tblout(tblout: str) -> Dict[str, float]:
# def _get_indices(sequence: str, start: int) -> List[int]:
# def _parse_hmmsearch_description(description: str) -> HitMetadata:
# def parse_hmmsearch_a3m(query_sequence: str,
#                         a3m_string: str,
#                         skip_first: bool = True) -> Sequence[TemplateHit]:
# 
# Path: alphafold/data/tools/utils.py
# def tmpdir_manager(base_dir: Optional[str] = None):
# def timing(msg: str):


from concurrent import futures
from typing import Any, Callable, Mapping, Optional, Sequence
from urllib import request
from absl import logging
from alphafold.data import parsers
from alphafold.data.tools import utils
import glob
import os
import subprocess
        cmd_flags.extend(['--domE', str(self.dom_e)])

      if self.incdom_e is not None:
        cmd_flags.extend(['--incdomE', str(self.incdom_e)])

      cmd = [self.binary_path] + cmd_flags + [input_fasta_path,
                                              database_path]

      logging.info('Launching subprocess "%s"', ' '.join(cmd))
      process = subprocess.Popen(
          cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
      with utils.timing(
          f'Jackhmmer ({os.path.basename(database_path)}) query'):
        _, stderr = process.communicate()
        retcode = process.wait()

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

      # Get e-values for each target name
      tbl = ''
      if self.get_tblout:
        with open(tblout_path) as f:
          tbl = f.read()

      if max_sequences is None:
        with open(sto_path) as f:
          sto = f.read()
      else:

# Path: alphafold/data/parsers.py
# class Msa:
# class TemplateHit:
# class HitMetadata:
#   def __post_init__(self):
#   def __len__(self):
#   def truncate(self, max_seqs: int):
# def parse_fasta(fasta_string: str) -> Tuple[Sequence[str], Sequence[str]]:
# def parse_stockholm(stockholm_string: str) -> Msa:
# def parse_a3m(a3m_string: str) -> Msa:
# def _convert_sto_seq_to_a3m(
#     query_non_gaps: Sequence[bool], sto_seq: str) -> Iterable[str]:
# def convert_stockholm_to_a3m(stockholm_format: str,
#                              max_sequences: Optional[int] = None,
#                              remove_first_row_gaps: bool = True) -> str:
# def _keep_line(line: str, seqnames: Set[str]) -> bool:
# def truncate_stockholm_msa(stockholm_msa_path: str, max_sequences: int) -> str:
# def remove_empty_columns_from_stockholm_msa(stockholm_msa: str) -> str:
# def deduplicate_stockholm_msa(stockholm_msa: str) -> str:
# def _get_hhr_line_regex_groups(
#     regex_pattern: str, line: str) -> Sequence[Optional[str]]:
# def _update_hhr_residue_indices_list(
#     sequence: str, start_index: int, indices_list: List[int]):
# def _parse_hhr_hit(detailed_lines: Sequence[str]) -> TemplateHit:
# def parse_hhr(hhr_string: str) -> Sequence[TemplateHit]:
# def parse_e_values_from_tblout(tblout: str) -> Dict[str, float]:
# def _get_indices(sequence: str, start: int) -> List[int]:
# def _parse_hmmsearch_description(description: str) -> HitMetadata:
# def parse_hmmsearch_a3m(query_sequence: str,
#                         a3m_string: str,
#                         skip_first: bool = True) -> Sequence[TemplateHit]:
# 
# Path: alphafold/data/tools/utils.py
# def tmpdir_manager(base_dir: Optional[str] = None):
# def timing(msg: str):


# Path: alphafold/data/tools/jackhmmer.py
from concurrent import futures
from typing import Any, Callable, Mapping, Optional, Sequence
from urllib import request
from absl import logging
from alphafold.data import parsers
from alphafold.data.tools import utils
import glob
import os
import subprocess

        cmd_flags.extend(['--domE', str(self.dom_e)])

      if self.incdom_e is not None:
        cmd_flags.extend(['--incdomE', str(self.incdom_e)])

      cmd = [self.binary_path] + cmd_flags + [input_fasta_path,
                                              database_path]

      logging.info('Launching subprocess "%s"', ' '.join(cmd))
      process = subprocess.Popen(
          cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
      with utils.timing(
          f'Jackhmmer ({os.path.basename(database_path)}) query'):
        _, stderr = process.communicate()
        retcode = process.wait()

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

      # Get e-values for each target name
      tbl = ''
      if self.get_tblout:
        with open(tblout_path) as f:
          tbl = f.read()

      if max_sequences is None:
        with open(sto_path) as f:
          sto = f.read()
      else:

        sto = parsers.truncate_stockholm_msa(sto_path, max_sequences)