original_docstring: Parse command-line arguments for script.
docstring: Parse command-line arguments for script.
docstring_tokens: Parse command - line arguments for script .
code: def parse_cmdline(args):
      """Parse command-line arguments for script."""
      parser = ArgumentParser(prog="average_nucleotide_identity.py")
      parser.add_argument("-o", "--outdir", dest="outdirname",
                          action="store", default=None,
                          help="Output directory")
      parser.add_argument("-i", "--indir", dest="indirname",
                          action="store", default=None,
                          help="Input directory name")
      parser.add_argument("-v", "--verbose", dest="verbose",
                          action="store_true", default=False,
                          help="Give verbose output")
      parser.add_argument("-f", "--force", dest="force",
                          action="store_true", default=False,
                          help="Force file overwriting")
      parser.add_argument("-s", "--fragsize", const="fragsize",
                          action="store_const", default=pyani_config.FRAGSIZE,
                          help="Sequence fragment size for ANIb")
      parser.add_argument("-l", "--logfile", dest="logfile",
                          action="store", default=None,
                          help="Logfile location")
      parser.add_argument("--skip_nucmer", dest="skip_nucmer",
                          action="store_true", default=False,
                          help="Skip NUCmer runs, for testing " +
                          "(e.g. if output already present)")
      parser.add_argument("--skip_blastn", dest="skip_blastn",
                          action="store_true", default=False,
                          help="Skip BLASTN runs, for testing " +
                          "(e.g. if output already present)")
      parser.add_argument("--noclobber", dest="noclobber",
                          action="store_true", default=False,
                          help="Don't nuke existing files")
      parser.add_argument("-g", "--graphics", dest="graphics",
                          action="store_true", default=False,
                          help="Generate heatmap of ANI")
      parser.add_argument("--gformat", dest="gformat",
                          action="store", default="pdf,png,eps",
                          help="Graphics output format(s) [pdf|png|jpg|svg]")
      parser.add_argument("--gmethod", dest="gmethod",
                          action="store", default="mpl",
                          help="Graphics output method [mpl|R]")
      parser.add_argument("--labels", dest="labels",
                          action="store", default=None,
                          help="Path to file containing sequence labels")
      parser.add_argument("--classes", dest="classes",
                          action="store", default=None,
                          help="Path to file containing sequence classes")
      parser.add_argument("-m", "--method", dest="method",
                          action="store", default="ANIm",
                          help="ANI method [ANIm|ANIb|ANIblastall|TETRA]")
      parser.add_argument("--scheduler", dest="scheduler",
                          action="store", default="multiprocessing",
                          help="Job scheduler [multiprocessing|SGE]")
      parser.add_argument("--maxmatch", dest="maxmatch",
                          action="store_true", default=False,
                          help="Override MUMmer to allow all NUCmer matches")
      parser.add_argument("--nucmer_exe", dest="nucmer_exe",
                          action="store", default=pyani_config.NUCMER_DEFAULT,
                          help="Path to NUCmer executable")
      parser.add_argument("--blastn_exe", dest="blastn_exe",
                          action="store", default=pyani_config.BLASTN_DEFAULT,
                          help="Path to BLASTN+ executable")
      parser.add_argument("--makeblastdb_exe", dest="makeblastdb_exe",
                          action="store",
                          default=pyani_config.MAKEBLASTDB_DEFAULT,
                          help="Path to BLAST+ makeblastdb executable")
      parser.add_argument("--blastall_exe", dest="blastall_exe",
                          action="store", default=pyani_config.BLASTALL_DEFAULT,
                          help="Path to BLASTALL executable")
      parser.add_argument("--formatdb_exe", dest="formatdb_exe",
                          action="store",
                          default=pyani_config.FORMATDB_DEFAULT,
                          help="Path to BLAST formatdb executable")
      parser.add_argument("--write_excel", dest="write_excel",
                          action="store_true",
                          default=False,
                          help="Write Excel format output tables")
      return parser.parse_args()
code_tokens: def parse_cmdline ( args ) : parser = ArgumentParser ( prog = "average_nucleotide_identity.py" ) parser . add_argument ( "-o" , "--outdir" , dest = "outdirname" , action = "store" , default = None , help = "Output directory" ) parser . add_argument ( "-i" , "--indir" , dest = "indirname" , action = "store" , default = None , help = "Input directory name" ) parser . add_argument ( "-v" , "--verbose" , dest = "verbose" , action = "store_true" , default = False , help = "Give verbose output" ) parser . add_argument ( "-f" , "--force" , dest = "force" , action = "store_true" , default = False , help = "Force file overwriting" ) parser . add_argument ( "-s" , "--fragsize" , const = "fragsize" , action = "store_const" , default = pyani_config . FRAGSIZE , help = "Sequence fragment size for ANIb" ) parser . add_argument ( "-l" , "--logfile" , dest = "logfile" , action = "store" , default = None , help = "Logfile location" ) parser . add_argument ( "--skip_nucmer" , dest = "skip_nucmer" , action = "store_true" , default = False , help = "Skip NUCmer runs, for testing " + "(e.g. if output already present)" ) parser . add_argument ( "--skip_blastn" , dest = "skip_blastn" , action = "store_true" , default = False , help = "Skip BLASTN runs, for testing " + "(e.g. if output already present)" ) parser . add_argument ( "--noclobber" , dest = "noclobber" , action = "store_true" , default = False , help = "Don't nuke existing files" ) parser . add_argument ( "-g" , "--graphics" , dest = "graphics" , action = "store_true" , default = False , help = "Generate heatmap of ANI" ) parser . add_argument ( "--gformat" , dest = "gformat" , action = "store" , default = "pdf,png,eps" , help = "Graphics output format(s) [pdf|png|jpg|svg]" ) parser . add_argument ( "--gmethod" , dest = "gmethod" , action = "store" , default = "mpl" , help = "Graphics output method [mpl|R]" ) parser . add_argument ( "--labels" , dest = "labels" , action = "store" , default = None , help = "Path to file containing sequence labels" ) parser . add_argument ( "--classes" , dest = "classes" , action = "store" , default = None , help = "Path to file containing sequence classes" ) parser . add_argument ( "-m" , "--method" , dest = "method" , action = "store" , default = "ANIm" , help = "ANI method [ANIm|ANIb|ANIblastall|TETRA]" ) parser . add_argument ( "--scheduler" , dest = "scheduler" , action = "store" , default = "multiprocessing" , help = "Job scheduler [multiprocessing|SGE]" ) parser . add_argument ( "--maxmatch" , dest = "maxmatch" , action = "store_true" , default = False , help = "Override MUMmer to allow all NUCmer matches" ) parser . add_argument ( "--nucmer_exe" , dest = "nucmer_exe" , action = "store" , default = pyani_config . NUCMER_DEFAULT , help = "Path to NUCmer executable" ) parser . add_argument ( "--blastn_exe" , dest = "blastn_exe" , action = "store" , default = pyani_config . BLASTN_DEFAULT , help = "Path to BLASTN+ executable" ) parser . add_argument ( "--makeblastdb_exe" , dest = "makeblastdb_exe" , action = "store" , default = pyani_config . MAKEBLASTDB_DEFAULT , help = "Path to BLAST+ makeblastdb executable" ) parser . add_argument ( "--blastall_exe" , dest = "blastall_exe" , action = "store" , default = pyani_config . BLASTALL_DEFAULT , help = "Path to BLASTALL executable" ) parser . add_argument ( "--formatdb_exe" , dest = "formatdb_exe" , action = "store" , default = pyani_config . FORMATDB_DEFAULT , help = "Path to BLAST formatdb executable" ) parser . add_argument ( "--write_excel" , dest = "write_excel" , action = "store_true" , default = False , help = "Write Excel format output tables" ) return parser . parse_args ( )
short_docstring: Parse command-line arguments for script.
short_docstring_tokens: Parse command - line arguments for script .
comment: """Parse command-line arguments for script."""