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This repository has been archived by the owner on Oct 11, 2022. It is now read-only.
Scripts to format and harmonise scoring files for the PGS Catalog.
Validate the format and data of the scoring files.
File Formatter
usage: run_formatter.py [-h] [-f SCORING_FILE_NAME] [--dir DIR]
optional arguments:
-h, --help show this help message and exit
-f SCORING_FILE_NAME The name of the file to be processed
--dir DIR The name of the directory containing the files that
need to processed
usage: run_validator.py [-h] [-f SCORING_FILE_NAME] [--dir DIR] --log_dir
LOG_DIR
optional arguments:
-h, --help show this help message and exit
-f SCORING_FILE_NAME The path to the polygenic scoring file to be validated
(no need to use the [--dir] option)
--dir DIR The name of the directory containing the files that
need to processed (no need to use the [-f] option
--log_dir LOG_DIR The name of the log directory where the log file(s)
will be stored
usage: run_pipeline.py [-h] [-f SCORING_FILE_NAME] [--dir DIR] --log_dir
LOG_DIR
optional arguments:
-h, --help show this help message and exit
-f SCORING_FILE_NAME The path to the polygenic scoring file to be formatted
and validated (no need to use the [--dir] option)
--dir DIR The name of the directory containing the mutiple files
that need to processed (no need to use the [-f]
option)
--log_dir LOG_DIR The name of the log directory where the log file(s)
will be stored