pyani download

The download subcommand controls download of genome files from the NCBI Assembly database for input to pyani.

usage: pyani download [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
                     [--citation] -o OUTDIR -t TAXON --email EMAIL
                     [--api_key API_KEYPATH] [--retries RETRIES]
                     [--batchsize BATCHSIZE] [--timeout TIMEOUT] [-f]
                     [--noclobber] [--labels LABELFNAME] [--classes CLASSFNAME]

                     [--kraken] [--dry-run]

Positional arguments

outdir

The outdir argument should be the path to a directory into which genome files will be downloaded. If the directory exists, a warning will be given and the download will not proceed, to avoid overwriting existing data. To force writing into an existing directory, use the -f option.

Flagged arguments

--api_key PATH_TO_API_KEY

The program will attempt to use an NCBI API key (see here) located at PATH_TO_API_KEY. Default: ~/.ncbi/api_key

--batchsize BATCHSIZE

The download process will attempt to download assemblies in multiples of BATCHSIZE. Default: 10000

--classes CLASSFNAME

Write a set of labels (one per downloaded genome) to the file CLASSFNAME in outdir. 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.

--dry-run

Perform all actions of the download process except for downloading files.

--email EMAIL

COMPULSORY. Provide the email address EMAIL to NCBI so that they can track problems.

-f, --force

Force use of the OUTDIR directory when downloaded genomes, even if it already exists.

-h, --help

Display usage information for pyani download.

--kraken

Add taxonomy information to the FASTA file headers of downloaded genomes. This allows the genomes to be readily used to construct databases for the Kraken software package.

-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 downloaded genome) to the file LABELFNAME in outdir. Default: labels.txt

--noclobber

Do not overwrite individual files in the outdir directory, when used with -f.

-o OUTDIR, --outdir OUTDIR

The OUTDIR argument should be the path to a directory into which genome files will be downloaded. If the directory exists, a warning will be given and the download will not proceed, to avoid overwriting existing data. To force writing into an existing directory, use the -f option.

--retries RETRIES

The download process will attempt to download each batch of assemblies a maximum of RETRIES times. Default: 20

-t TAXON, --taxon TAXON

COMPULSORY. All genomes below taxon ID TAXON of a node in the NCBI Taxonomy database will be downloaded to the location specified by outdir.

--timeout TIMEOUT

The download process will wait a amaximum of TIMEOUT seconds before abandoning a URL connection attempt. Default: 10

-v, --verbose

Provide verbose output to STDOUT