pyani index

The index subcommand will index the genome files it finds the passed directory INDIR, generating label and class files, and files that contain an MD5 hash of the nucleotide sequence of each genome.

usage: pyani index [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
                  [--citation] -i INDIR [--labels LABELFNAME]
                  [--classes CLASSFNAME]

Flagged arguments

--classes CLASSFNAME

Write a set of labels (one per genome sequence file) to the file CLASSFNAME in INDIR. Default: classes.txt

--disable_tqdm

Disable the tqdm progress bar while the download process runs. This is useful when testing to avoid aesthetic problems with test output.

-h, --help

Display usage information for pyani index.

-i INDIR, --indir INDIR

The INDIR argument should be the path to a directory containing genome sequence data as FASTA files (one per genome assembly).

-l LOGFILE, --logfile LOGFILE

Provide the location LOGFILE to which a logfile of the download process will be written.

--labels LABELFNAME

Write a set of labels (one per genome sequence file) to the file LABELFNAME in INDIR. Default: labels.txt

-v, --verbose

Provide verbose output to STDOUT