pyani.scripts.parsers package

Module providing command-line parser definitions.

pyani.scripts.parsers.parse_cmdline(argv: Optional[List[T]] = None) → argparse.Namespace[source]

Parse command-line arguments for script.

Parameters:argv – Namespace, command-line arguments

The script offers a single main parser, with subcommands for the actions:

  • download
    download all available NCBI assemblies below the passed taxonomy ID
  • index
    index genome sequence files in a subdirectory, for analysis
  • createdb
    generate SQLite database for data and analysis results
  • anim
    conduct ANIm analysis
  • anib
    conduct ANIb analysis
  • aniblastall
    conduct ANIblastall analysis
  • fastani
    conduct fastANI analysis
  • report
    generate output describing analyses, genomes, and results
  • plot
    generate graphical output describing results
  • classify
    produce graph-based classification of genomes on the basis of ANI analysis