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
Submodules¶
- pyani.scripts.parsers.anib_parser module
- pyani.scripts.parsers.aniblastall_parser module
- pyani.scripts.parsers.anim_parser module
- pyani.scripts.parsers.classify_parser module
- pyani.scripts.parsers.common_parser module
- pyani.scripts.parsers.createdb_parser module
- pyani.scripts.parsers.download_parser module
- pyani.scripts.parsers.index_parser module
- pyani.scripts.parsers.plot_parser module
- pyani.scripts.parsers.report_parser module
- pyani.scripts.parsers.run_common_parser module
- pyani.scripts.parsers.scheduling_parser module