pyani.scripts package¶
Modules to support use of pyani as a script.
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exception
pyani.scripts.
PyaniScriptException
(msg='Error in pyani.py script')[source]¶ Bases:
Exception
General exception for pyani.py script.
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pyani.scripts.
make_outdir
(outdir: pathlib.Path, force: bool, noclobber: bool) → None[source]¶ Create output directory (allows for force and noclobber).
Parameters: - outdir – Path, path to output directory
- force – bool, True if an existing directory will be reused
- noclobber – bool, True if existing files are not overwritten
The intended outcomes are: outdir doesn’t exist: create outdir outdir exists: raise exception outdir exists, –force only: remove the directory tree outdir exists, –force –noclobber: continue with existing directory tree
So long as the outdir is created with this function, we need only check for args.noclobber elsewhere to see how to proceed when a file exists.
Subpackages¶
- pyani.scripts.parsers package
- 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
- Submodules
- pyani.scripts.subcommands package
- Submodules
- pyani.scripts.subcommands.subcmd_anib module
- pyani.scripts.subcommands.subcmd_aniblastall module
- pyani.scripts.subcommands.subcmd_anim module
- pyani.scripts.subcommands.subcmd_classify module
- pyani.scripts.subcommands.subcmd_createdb module
- pyani.scripts.subcommands.subcmd_download module
- pyani.scripts.subcommands.subcmd_index module
- pyani.scripts.subcommands.subcmd_plot module
- pyani.scripts.subcommands.subcmd_report module
- Submodules