def default_parser(output_dir, experiment_code, project_id): parser = default_argument_parser( output_dir=output_dir, description='Reads bcc json and writes gen3 json ({}).'.format(output_dir) ) parser.add_argument('--experiment_code', type=str, default=experiment_code, help='Name of gen3 experiment ({}).'.format(experiment_code)) parser.add_argument('--project_id', type=str, default=project_id, help='Name of gen3 program-project ({}).'.format(project_id)) parser.add_argument('--schema', type=bool, default=True, help='generate schemas (true).'.format(experiment_code)) return parser
def default_parser(): parser = default_argument_parser( output_dir=DEFAULT_OUTPUT_DIR, description='Reads bcc json and writes gen3 json ({}).'.format( DEFAULT_OUTPUT_DIR)) parser.add_argument('--experiment_code', type=str, default=DEFAULT_EXPERIMENT_CODE, help='Name of existing gen3 experiment ({}).'.format( DEFAULT_EXPERIMENT_CODE)) parser.add_argument( '--schema', type=bool, default=True, help='generate schemas (true).'.format(DEFAULT_EXPERIMENT_CODE)) return parser
python3 load/gen3_query_generator.py $PP $EP --node_type slide_image python3 load/gen3_query_generator.py $PP $EP --node_type submitted_aligned_reads python3 load/gen3_query_generator.py $PP $EP --node_type submitted_copy_number python3 load/gen3_query_generator.py $PP $EP --node_type submitted_file python3 load/gen3_query_generator.py $PP $EP --node_type submitted_methylation python3 load/gen3_query_generator.py $PP $EP --node_type submitted_somatic_mutation python3 load/gen3_query_generator.py $PP $EP --node_type submitted_unaligned_reads python3 load/gen3_query_generator.py $PP $EP --node_type hop_survey python3 load/gen3_query_generator.py $PP $EP --node_type aliquot """ if __name__ == "__main__": parser = default_argument_parser( output_dir=DEFAULT_OUTPUT_DIR, description='Reads gen3 json ({}), creates psql tsv .'.format( DEFAULT_INPUT_DIR)) parser.add_argument( '--program', type=str, default=DEFAULT_PROGRAM, help='Name of existing gen3 program ({}).'.format(DEFAULT_PROGRAM)) parser.add_argument( '--project', type=str, default=DEFAULT_PROJECT, required=True, help='Name of existing gen3 project ({}).'.format(DEFAULT_PROJECT)) parser.add_argument( '--node_type',
diagnosis['*age_at_diagnosis'] = None diagnosis['*classification_of_tumor'] = 'Unknown' diagnosis['*days_to_last_follow_up'] = None diagnosis['*days_to_last_known_disease_status'] = None diagnosis['*days_to_recurrence'] = None diagnosis['*last_known_disease_status'] = 'Unknown tumor status' diagnosis['*morphology'] = 'unknown' diagnosis['*progression_or_recurrence'] = 'unknown' diagnosis['*site_of_resection_or_biopsy'] = 'unknown' diagnosis['*tissue_or_organ_of_origin'] = 'unknown' diagnosis['*tumor_grade'] = 'unknown' diagnosis['*tumor_stage'] = 'unknown' diagnosis['*vital_status'] = 'unknown' diagnosis_emitter.write(diagnosis) samples_emitter.close() aliquots_emitter.close() diagnosis_emitter.close() if __name__ == "__main__": parser = default_argument_parser( output_dir=DEFAULT_OUTPUT_DIR, description='Reads bcc tsv and writes gen3 json ({}).'.format( DEFAULT_OUTPUT_DIR)) args = parser.parse_args() transform(output_dir=args.output_dir)
if not deleted and delete_first: delete_all(submission_client, program, project, types=[nodes[0]['type']]) deleted = True collect_result(create_node(submission_client, program, project, nodes)) # pool.apply_async(create_node, args=(submission_client, program, project, nodes), callback=collect_result) # logger.info(f'pool.close/join') # pool.close() # pool.join() # postpones the execution of next line of code until all processes in the queue are done if __name__ == "__main__": parser = default_argument_parser( description='Reads gen3 json ({}).'.format(DEFAULT_INPUT_DIR) ) parser.add_argument('--path', type=str, default=DEFAULT_PATH, help='Match these files ({}).'.format(DEFAULT_PATH)) parser.add_argument('--program', type=str, default=DEFAULT_PROGRAM, help='Name of existing gen3 program ({}).'.format(DEFAULT_PROGRAM)) parser.add_argument('--project', type=str, default=DEFAULT_PROJECT, required=True, help='Name of existing gen3 project ({}).'.format(DEFAULT_PROJECT)) parser.add_argument('--batch_size', type=int, default=DEFAULT_BATCH_SIZE, help='Number of records to send to gen3 at a time({}).'.format(DEFAULT_BATCH_SIZE))
# {"_id": "(Callset:ccle:ACH-001270:None)--CallsetFor->(Aliquot:ACH-001270)", "gid": "(Callset:ccle:ACH-001270:None)--CallsetFor->(Aliquot:ACH-001270)", "label": "CallsetFor", "from": "Callset:ccle:ACH-001270:None", "to": "Aliquot:ACH-001270", "data": {}} for line in reader('source/ccle/maf.CallsetFor.Edge.json.gz'): # *type project_id *submitter_id *aliquots.submitter_id RIN adapter_name adapter_sequence barcoding_applied base_caller_name base_caller_version experiment_name flow_cell_barcode includes_spike_ins instrument_model is_paired_end library_name library_preparation_kit_catalog_number library_preparation_kit_name library_preparation_kit_vendor library_preparation_kit_version library_selection library_strand library_strategy platform read_group_name read_length sequencing_center sequencing_date size_selection_range spike_ins_concentration spike_ins_fasta target_capture_kit_catalog_number target_capture_kit_name target_capture_kit_target_region target_capture_kit_vendor target_capture_kit_version to_trim_adapter_sequence ] read_group_submitter_id = 'read_group-{}'.format(line['from']) if read_group_submitter_id in read_groups: continue read_group = { 'type': 'read_group', '*aliquots': { 'submitter_id': line['to'] } } read_group['*submitter_id'] = read_group_submitter_id read_groups[read_group_submitter_id] = read_group for read_group in read_groups: read_groups_emitter.write(read_groups[read_group]) read_groups_emitter.close() if __name__ == "__main__": parser = default_argument_parser( output_dir=DEFAULT_OUTPUT_DIR, description= 'Reads bmeg callset json and writes gen3 read_group json ({}).'.format( DEFAULT_OUTPUT_DIR)) args = parser.parse_args() transform(output_dir=args.output_dir)
for line in reader('source/ccle/File.Vertex.json.gz'): ssm_submitter_id = line['gid'] read_group_submitter_id = read_groups[ssm_submitter_id] ssm = { 'type': 'submitted_somatic_mutation', '*read_groups': { 'submitter_id': read_group_submitter_id } } ssm['*submitter_id'] = ssm_submitter_id ssm['md5sum'] = line['data']['md5'] ssm['file_size'] = line['data']['size'] ssm['file_name'] = line['data']['path'] ssm['experimental_strategy'] = 'etl' ssm['data_type'] = 'maf like' ssm['data_format'] = 'tsv' ssm['data_category'] = 'omics' ssm_emitter.write(ssm) ssm_emitter.close() if __name__ == "__main__": parser = default_argument_parser( output_dir=DEFAULT_OUTPUT_DIR, description='Reads bmeg Files json and writes gen3 submitted_somatic_mutation json ({}).'.format(DEFAULT_OUTPUT_DIR) ) args = parser.parse_args() transform(output_dir=args.output_dir)
types=types, batch_size=batch_size) try: if drop_project: print(submission_client.delete_project(program, project), file=sys.stderr) except Exception as e: print(e) # try: # print(submission_client.delete_program(program), file=sys.stderr) # except Exception as e: # print(e) if __name__ == "__main__": parser = default_argument_parser( description='deletes all content for project') parser.add_argument( '--program', type=str, default=DEFAULT_PROGRAM, help='Name of existing gen3 program ({}).'.format(DEFAULT_PROGRAM)) parser.add_argument( '--project', type=str, default=DEFAULT_PROJECT, help='Name of existing gen3 project ({}).'.format(DEFAULT_PROJECT)) parser.add_argument( '--credentials_path', type=str, default=DEFAULT_CREDENTIALS_PATH, help='Location of gen3 path ({}).'.format(DEFAULT_CREDENTIALS_PATH))