/rmlst_api

Run rmlst API through python script

Primary LanguagePythonMIT LicenseMIT

rmlst_api

Run rmlst API through python script for species identification of a bacterial assembly.

usage: rmlst.py [-h] -i INPUT [-l LOG] [--output_tab OUTPUT_TAB]
                [--output_json OUTPUT_JSON]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        assembly file
  -l LOG, --log LOG     log file. default is <input>_rmlst.log
  --output_tab OUTPUT_TAB
                        rMLST tab output. default is <input>_rmlst.tab
  --output_json OUTPUT_JSON
                        rMLST json output. default is <input>_rmlst.json

API source: https://pubmlst.org/species-id/species-identification-via-api.