code: def generate_nucmer_commands(
      filenames,
      outdir=".",
      nucmer_exe=pyani_config.NUCMER_DEFAULT,
      filter_exe=pyani_config.FILTER_DEFAULT,
      maxmatch=False,
  ):
      
      nucmer_cmdlines, delta_filter_cmdlines = [], []
      for idx, fname1 in enumerate(filenames[:-1]):
          for fname2 in filenames[idx + 1 :]:
              ncmd, dcmd = construct_nucmer_cmdline(
                  fname1, fname2, outdir, nucmer_exe, filter_exe, maxmatch
              )
              nucmer_cmdlines.append(ncmd)
              delta_filter_cmdlines.append(dcmd)
      return (nucmer_cmdlines, delta_filter_cmdlines)
docs: Return a tuple of lists of NUCmer command-lines for ANIm
  
      The first element is a list of NUCmer commands, the second a list
      of delta_filter_wrapper.py commands. These are ordered such that
      commands are paired. The NUCmer commands should be run before
      the delta-filter commands.
  
      - filenames - a list of paths to input FASTA files
      - outdir - path to output directory
      - nucmer_exe - location of the nucmer binary
      - maxmatch - Boolean flag indicating to use NUCmer's -maxmatch option
  
      Loop over all FASTA files generating NUCmer command lines for each
      pairwise comparison.