old_contents: #!/usr/bin/python3
  # A program for aligning CDSs of a orthogroup.
  # USAGE: ./macse4cdsOrthofiles_TA.py
  # Author: Taruna Aggarwal
  # Affiliation: University of New Hampshire, Durham, NH, USA
  # Date: 01/27/2016
  # Purpose is
  
  import sys
  import os
  import subprocess
  import argparse
  from multiprocessing import pool
  
  
  def runMACSE(input_file, NT_output_file, AA_output_file):
      MACSE_command = "java -jar /fungi/taruna/shared/bin/MACSE/macse_v1.01b.jar "
      MACSE_command += "-prog alignSequences "
      MACSE_command += "-seq {0} -out_NT {1} -out_AA {2}".format(input_file,
              NT_output_file, AA_output_file)
      # print(MACSE_command)
      subprocess.call(MACSE_command, shell=True)
  
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser(description="This script runs aligns "
              "coding sequences in files in a given directory.")
      parser.add_argument('--root', default="/fungi/taruna/shared/testing_macse/",
              help="PATH to the directory containing CDS orthogroup files.")
      parser.add_argument('--align_NT_dir',
              default="/fungi/taruna/shared/testing_macse/NT_aligned/",
              help="PATH to the directory for NT aligned CDS orthogroup files.")
      parser.add_argument('--align_AA_dir',
              default="/fungi/taruna/shared/testing_macse/AA_aligned/",
              help="PATH to the directory for AA aligned CDS orthogroup files.")
      args = parser.parse_args()
  
      Orig_file_dir = args.root
      NT_align_file_dir = args.align_NT_dir
      AA_align_file_dir = args.align_AA_dir
  
      try:
          os.makedirs(NT_align_file_dir)
          os.makedirs(AA_align_file_dir)
      except FileExistsError as e:
          print(e)
  
      for currentFile in os.listdir(args.root):
          if currentFile.endswith(".fa"):
              runMACSE(args.root + currentFile, args.align_NT_dir + currentFile[:-3]+"_NT_aligned.fa", args.align_AA_dir + currentFile[:-3]+"_AA_aligned.fa")
  
      with Pool(10) as p:
          # this is where I get lost. I don't even know if this is correct.
  
new_contents: #!/usr/bin/python3
  # A program for aligning CDSs of a orthogroup.
  # USAGE: ./macse4cdsOrthofiles_TA.py
  # Author: Taruna Aggarwal
  # Affiliation: University of New Hampshire, Durham, NH, USA
  # Date: 01/27/2016
  # Purpose is
  
  import sys
  import os
  import subprocess
  import argparse
  from multiprocessing import pool
  
  
  def runMACSE(input_file, NT_output_file, AA_output_file):
      MACSE_command = "java -jar /fungi/taruna/shared/bin/MACSE/macse_v1.01b.jar "
      MACSE_command += "-prog alignSequences "
      MACSE_command += "-seq {0} -out_NT {1} -out_AA {2}".format(input_file,
              NT_output_file, AA_output_file)
      # print(MACSE_command)
      subprocess.call(MACSE_command, shell=True)
  
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser(description="This script runs aligns "
              "coding sequences in files in a given directory.")
      parser.add_argument('--root', default="/fungi/taruna/shared/testing_macse/",
              help="PATH to the directory containing CDS orthogroup files.")
      parser.add_argument('--align_NT_dir',
              default="/fungi/taruna/shared/testing_macse/NT_aligned/",
              help="PATH to the directory for NT aligned CDS orthogroup files.")
      parser.add_argument('--align_AA_dir',
              default="/fungi/taruna/shared/testing_macse/AA_aligned/",
              help="PATH to the directory for AA aligned CDS orthogroup files.")
      args = parser.parse_args()
  
      Orig_file_dir = args.root
      NT_align_file_dir = args.align_NT_dir
      AA_align_file_dir = args.align_AA_dir
  
      try:
          os.makedirs(NT_align_file_dir)
          os.makedirs(AA_align_file_dir)
      except FileExistsError as e:
          print(e)
  
      for currentFile in os.listdir(args.root):
          if currentFile.endswith(".fa"):
              runMACSE(args.root + currentFile, args.align_NT_dir \
              + currentFile[:-3]+"_NT_aligned.fa", args.align_AA_dir \
              + currentFile[:-3]+"_AA_aligned.fa")
  
      with Pool(10) as p:
          # this is where I get lost. I don't even know if this is correct.
  
subject: Reduce line length