Python code to validate the spreadsheets containing M. tuberculosis AST data donated to the project. Likely to expand in future.
To install as a module so seqtreat-spreadsheet-validate.py
is in yoru ``$PATH` (and will dynamically update if you do a
$ git clone https://github.com/philipwfowler/seqtreat.git
$ cd seqtreat
$ python setup.py develop --user
Then this should work
$ seqtreat-spreadsheet-validate.py --help
usage: seqtreat-spreadsheet-validate.py [-h] --spreadsheet SPREADSHEET
--tables_path TABLES_PATH
optional arguments:
-h, --help show this help message and exit
--spreadsheet SPREADSHEET
the path to the Seq&Treat spreadsheet to validate
--tables_path TABLES_PATH
the path to the folder containing SITES.csv,
COUNTRIES_LOOKUP.csv etc (cryptic-tables/ will work)