# Path: targetexplorer/cbioportal.py
# class GatherCbioportalData(object):
# class AddCbioportalMAFData(object):
#     def __init__(self,
#                  use_existing_cbioportal_data=False,
#                  use_existing_oncotator_data=False,
#                  write_extended_mutation_txt_files=False,
#                  run_main=True,
#                  commit_to_db=True
#                  ):
#     def get_hgnc_gene_symbols_from_db(self):
#     def get_mutation_data_as_xml(self):
#     def extract_mutation_data(self):
#     def get_oncotator_data(
#             self,
#             chromosome_index,
#             chromosome_startpos,
#             chromosome_endpos,
#             reference_allele,
#             variant_allele
#             ):
#     def write_oncotator_data(self):
#     def finish(self):
# def get_cancer_studies():
# def get_genetic_profile_ids(cancer_study):
# def get_profile_data(case_set_id, genetic_profile_id, entrez_gene_ids):
# def retrieve_mutants_xml(output_xml_filepath, cancer_studies, gene_ids,
#                          write_extended_mutation_txt_files=False,
#                          verbose=False
#                          ):
# def retrieve_mutation_datatxt(case_set_id,
#                               genetic_profile_id,
#                               gene_ids,
#                               portal_version='public-portal',
#                               verbose=False,
#                               ):
# def retrieve_extended_mutation_datatxt(case_set_id,
#                                        genetic_profile_id,
#                                        gene_ids,
#                                        portal_version='public-portal',
#                                        write_to_filepath=False
#                                        ):
# def match_dual_consecutive_aa_change(aa_change_string):
# def split_dual_consecutive_aa_change(aa_change_string):
# def percent_cases_with_mutations(gene_node):
#     def __init__(self,
#                  maf_filepath=None,
#                  run_main=True,
#                  commit_to_db=True
#                  ):
#     def parse_maf_file(self):
#     def extract_mutation_data(self):
#     def finish(self):


import argparse
from targetexplorer.cbioportal import GatherCbioportalData, external_cbioportal_data_filepath


argparser = argparse.ArgumentParser(description='Gather cBioPortal data')
argparser.add_argument(
    '--use_existing_data',
    help='Only works if an existing file {0} is present.'.format(external_cbioportal_data_filepath),
    action='store_true',
    default=False

# Path: targetexplorer/cbioportal.py
# class GatherCbioportalData(object):
# class AddCbioportalMAFData(object):
#     def __init__(self,
#                  use_existing_cbioportal_data=False,
#                  use_existing_oncotator_data=False,
#                  write_extended_mutation_txt_files=False,
#                  run_main=True,
#                  commit_to_db=True
#                  ):
#     def get_hgnc_gene_symbols_from_db(self):
#     def get_mutation_data_as_xml(self):
#     def extract_mutation_data(self):
#     def get_oncotator_data(
#             self,
#             chromosome_index,
#             chromosome_startpos,
#             chromosome_endpos,
#             reference_allele,
#             variant_allele
#             ):
#     def write_oncotator_data(self):
#     def finish(self):
# def get_cancer_studies():
# def get_genetic_profile_ids(cancer_study):
# def get_profile_data(case_set_id, genetic_profile_id, entrez_gene_ids):
# def retrieve_mutants_xml(output_xml_filepath, cancer_studies, gene_ids,
#                          write_extended_mutation_txt_files=False,
#                          verbose=False
#                          ):
# def retrieve_mutation_datatxt(case_set_id,
#                               genetic_profile_id,
#                               gene_ids,
#                               portal_version='public-portal',
#                               verbose=False,
#                               ):
# def retrieve_extended_mutation_datatxt(case_set_id,
#                                        genetic_profile_id,
#                                        gene_ids,
#                                        portal_version='public-portal',
#                                        write_to_filepath=False
#                                        ):
# def match_dual_consecutive_aa_change(aa_change_string):
# def split_dual_consecutive_aa_change(aa_change_string):
# def percent_cases_with_mutations(gene_node):
#     def __init__(self,
#                  maf_filepath=None,
#                  run_main=True,
#                  commit_to_db=True
#                  ):
#     def parse_maf_file(self):
#     def extract_mutation_data(self):
#     def finish(self):


# Path: scripts/DoraGathercBioPortal.py
import argparse
from targetexplorer.cbioportal import GatherCbioportalData, external_cbioportal_data_filepath



argparser = argparse.ArgumentParser(description='Gather cBioPortal data')
argparser.add_argument(
    '--use_existing_data',
    help='Only works if an existing file {0} is present.'.format(external_cbioportal_data_filepath),
    action='store_true',
    default=False

)