pyani.scripts.parsers.download_parser module

Provides parser for download subcommand.

pyani.scripts.parsers.download_parser.build(subps: argparse._SubParsersAction, parents: Optional[List[argparse.ArgumentParser]] = None) → None

Return a command-line parser for the download subcommand.

Parameters:

• subps – ArgumentParser.subparser
• parents – additional Parser objects

The download subcommand takes specific arguments:

-t, –taxon (NCBI taxonomy IDs - comma-separated list, or one ID) –email (email for providing to Entrez services) –api_key (path to file containing personal API key for Entrez) –retries (number of Entrez retry attempts to make) –batchsize (number of Entrez records to download in a batch) –timeout (how long to wait for Entrez query timeout) -f, –force (allow existing directory overwrite) –noclobber (don’t replace existing files) –labels (path to write labels file) –classes (path to write classes file)