maxibor / AMDirT

AncientMetagenomeDir Toolkit

AncientMetagenomeDirCheck

A python package to check AncientMetagenomeDir.

AncientMetagenomeDirCheck will verify a dataset, in tabular format, against a json schema (and some other checks...).

Install

From PyPI using pip

pip install ancientMetagenomeDirCheck

The latest development version, directly from GitHub

pip install --upgrade --force-reinstall git+https://github.com/SPAAM-workshop/AncientMetagenomeDirCheck.git

Documentation

$ ancientMetagenomeDirCheck --help
Usage: ancientMetagenomeDirCheck [OPTIONS] DATASET SCHEMA

  ancientMetagenomeDirCheck: Performs validity check of ancientMetagenomeDir datasets
  Author: Maxime Borry
  Contact: <borry[at]shh.mpg.de>
  Homepage & Documentation: github.com/spaam-workshop/ancientMetagenomeDirCheck

  DATASET: path to tsv file of dataset to check
  SCHEMA: path to JSON schema file

Options:
  --version                       Show the version and exit.
  -v, --validity                  Turn on schema checking.
  -d, --duplicate                 Turn on line duplicate line checking.
  -i, --doi                       Turn on DOI duplicate checking.
  -m, --markdown                  Output is in markdown format
  -dc, --duplicated_entries TEXT  Commma separated list of columns to check
                                  for duplicated entries
  --help                          Show this message and exit.