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pubMLST Client

Usage

List available schemes

usage: pubmlst_list [-h] [--pattern PATTERN] [--exclude_pattern EXCLUDE_PATTERN] [--names_only] [--base-url BASE_URL]

optional arguments:
  -h, --help            show this help message and exit
  --pattern PATTERN, -p PATTERN
                        regex pattern to filter scheme names
  --exclude_pattern EXCLUDE_PATTERN, -e EXCLUDE_PATTERN
                        regex pattern to filter scheme names
  --names_only, -n      Only show scheme names
  --base-url BASE_URL, -b BASE_URL
                        Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db

Example Output

name id description locus_count records last_added last_updated
achromobacter 1 MLST 7 480 2020-02-20 2020-02-20
abaumannii 1 MLST (Oxford) 7 2088 2020-02-07 2020-02-07
abaumannii 2 MLST (Pasteur) 7 1438 2020-02-18 2020-02-18
aeromonas 1 MLST 6 656 2020-01-07 2020-01-08

Download schemes

usage: pubmlst_download [-h] --scheme_name SCHEME_NAME [--scheme_id SCHEME_ID] [--outdir OUTDIR] [--base-url BASE_URL]

optional arguments:
  -h, --help            show this help message and exit
  --scheme_name SCHEME_NAME, -s SCHEME_NAME
                        scheme name
  --scheme_id SCHEME_ID, -i SCHEME_ID
                        scheme id
  --outdir OUTDIR, -o OUTDIR
                        output directory
  --base-url BASE_URL, -b BASE_URL
                        Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db