pyani.scripts.subcommands.subcmd_index module

Provides the index subcommand for pyani.

pyani.scripts.subcommands.subcmd_index.subcmd_index(args: argparse.Namespace) → int

Generate a file with the MD5 hash for each genome in an input directory.

Parameters:

• args – Namespace, received command-line arguments
• logger – logging object

Identify the genome files in the input directory, and generate a single MD5 for each so that <genome>.fna produces <genome>.md5

Genome files (FASTA) are identified from the file extension.