ClinicalDataAnnotator.py

#!/usr/bin/python

import sys
import re
import argparse
import logging

from AnnotatorCore import setsampleidsfileterfile
from AnnotatorCore import process_clinical_data

logging.basicConfig(level=logging.INFO)
log = logging.getLogger('ClinicalDataAnnotator')


def main(argv):
    if argv.help:
        log.info(
            '\n'
            'ClinicalDataAnnotator.py -i <input clinical file> -o <output clinical file> -a <annotated alteration files, separate by ,> [-s sample list filter]\n'
            '  Essential clinical columns:\n'
            '    SAMPLE_ID: sample ID'
        )
        sys.exit()
    if argv.sample_ids_filter:
        setsampleidsfileterfile(argv.sample_ids_filter)

    annotated_alteration_files = re.split(',|, ', argv.annotated_alteration_files)
    if argv.input_file == '' or argv.output_file == '' or len(annotated_alteration_files) == 0:
        required_params = []
        if argv.input_file == '':
            required_params.append('-i')
        if argv.output_file == '':
            required_params.append('-o')
        if len(annotated_alteration_files) == 0:
            required_params.append('-a')
        log.error('The parameter(s) ' + ', '.join(required_params) + ' can not be empty')
        log.info('for help: python ClinicalDataAnnotator.py -h')
        sys.exit(2)

    log.info('annotating %s ...' % argv.input_file)
    process_clinical_data(annotated_alteration_files, argv.input_file, argv.output_file)

    log.info('done!')


if __name__ == "__main__":
    parser = argparse.ArgumentParser(add_help=False)
    parser.add_argument('-h', dest='help', action="store_true", default=False)
    parser.add_argument('-i', dest='input_file', default='', type=str)
    parser.add_argument('-o', dest='output_file', default='', type=str)
    parser.add_argument('-s', dest='sample_ids_filter', default='', type=str)
    parser.add_argument('-a', dest='annotated_alteration_files', default='', type=str)
    parser.set_defaults(func=main)

    args = parser.parse_args()
    args.func(args)