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        "description": "# Summary Statistics TSV file Validator\n\nA file validator for validating GWAS summary statistics TSV files prior to and post [harmonisation](https://github.com/EBISPOT/sum-stats-formatter/tree/master/harmonisation) using [pandas_schema](https://tmiguelt.github.io/PandasSchema/). The purpose is to validate files before their [conversion to HDF5](https://github.com/EBISPOT/SumStats/). \n\n## Installation\n- `pip install ss-validate`\n\n## Running the validator\nTo run the validator on a file:\n- `ss-validate -f <file_to_validate.tsv> --logfile <logfile_name>`\n\nInformation and errors are logged to the console and errors logged to the file specified. A console output might look like:\n```\n(INFO): Filename is good!\n(INFO): Validating file...\n(ERROR): Length of row 7 is: 16 instead of 15\n(ERROR): Please fix the table. Some rows have different numbers of columns to the header\n(INFO): Rows with different numbers of columns to the header are not validated\n(ERROR): {row: 1, column: \"p_value\"}: \"-99\" was not in the range [0, 1)\n```\nThe errors from the output tell us that row seven has too many columns and row one does not have a valid pvalue. If these rows are not fixed, they will later be dropped and not converted to HDF5. \n\n### Addional options\n- `--drop-bad-lines` : _bool, default False_\n\n   Drops the the lines with errors from the file and writes it to a new file called <file_to_validate.tsv.valid>\n- `--stage` : _{'standard', 'harmonised', 'curated'}, default 'standard'_\n\n   The stage the file is in. It is either standard format ('standard'), harmonised ('harmonised') or pre-standard in the custom curated format ('curated')\n\n\n",
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