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OneScience-Group/flex_ddG_tutorial/scripts

Imports Python's subprocess modulePython subprocess captures output streams

SHA-256bfbb27b5bebb5923207433113fa85f137862da88b563f5543c496c05fc367cd2

Evidence

Imports Python's subprocess module lines 1–17

⋯4 lines
5import argparse
6import functools
7import subprocess
8import re
9import shutil
⋯8 lines

English function-word token "the" lines 18–25

18:7… _multiprocessing:
19    import multiprocessing
20
21# The Reporter class is useful for printing output for tasks which will take a long time
22# Really, you should just use tqdm now, but I used this before I knew about tqdm and it removes a dependency
23
24# Time in seconds function
25# Converts datetime timedelta object to num …

English function-word token "with" lines 59–65

21… al_count -= 1
60
  def report(self, n):
      with self._lock:
          self.n = n
          time_now = datetime.datetime.now()
          i …

Python lists directory entries lines 152–159

22… ruct_dbs( input_dir ):
  return_list = []
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  for path in [os.path.join(input_dir, x) for x in os.listdir( input_dir )]:
      if os.path.isdir( path ):
          return_list.extend( recursive_find_struct_dbs( path ) )
      elif os.path.isfile( path ) and os.path.basename( path ) == struct_db3_file:
          return_list.append( path ) …

Python file opened for write or append lines 172–189

29… s.path.join(working_directory, 'structure_output.txt' )
  if not use_multiprocessing:
      print(rosetta_outfile_path)
  rosetta_outfile = open( rosetta_outfile_path, 'w')
  if not use_multiprocessing:
      print( ' '.join( args ) )
  # No shell: joining the arguments into a string breaks as soon as a path contains a space.
  rosetta_process = subprocess.Popen(
      args,
      stdout=rosetta_outfile, stderr=subprocess.STDOUT, close_fds = True, cwd = working_directory,
  )
  return_code = rosetta_process.wait()
⋯6 lines