4  external-alignment

The external-alignment subcommand compute pairwise ANI from given multiple-sequence-alignment (MSA) file and genome files from the indir directory, and logs comparison and run data in a local SQLite3 database.

pyani-plus external-alignment Usage

pyani-plus external-alignment [OPTIONS] FASTA 

4.1 Arguments

fasta: Directory of FASTA files (extensions .fas, .fasta, .fna). (PATH) [REQUIRED]

4.2 Options

--database: Path to pyANI-plus SQLite3 database. (FILE) [REQUIRED]

--create-db: Create database if does not exist.

--name: Run name. [Default: “N genomes using METHOD”] (TEXT)

--executor: How should the internal tools be run? [Default: local] (local|slurm)

--help, -h: Display usgae information for pyani-plus anib.

4.3 Method parameters

--alignment: FASTA format MSA of the same genomes (one sequence per genome). (PATH) [REQUIRED]

--label: How are the sequences in the MSA labelled vs the FASTA genomes? [Default: stem] (md5|filename|stem )

4.4 Debugging

--temp: Directory to use for intermediate files, which for debugging purposes will not be deleted. For clusters this must be on a shared drive. Default behaviour is to use a system specified temporary directory (specific to the compute-node when using a cluster) and remove this afterwards. (Directory)

--wtemp: Directory to use for temporary workflow coordination files, which for debugging purposes will not be deleted. For clusters this must be on shared drive. Default behaviour is to use a system specified temporary directory (for the local executor) or a temporary directory under the present direct (for clusters), and remove this afterwards. (Directory)