def main():
global meta_config
global study_config
global janus_path
global verb
from support import helper
from generate.analysis_pipelines.MUTATION_EXTENDED import support_functions
import logging
verb = logger.isEnabledFor(
logging.INFO) # TODO replace the 'verb' switch with logger
logger.info('Transferring VCF files to temporary folder')
meta_config = helper.relocate_inputs(meta_config, study_config, verb)
logger.info(
'Ensuring both columns exist, otherwise adding UNMATCHED column ...')
support_functions.verify_dual_columns(meta_config, verb)
logger.info('Exporting vcf2maf...')
logger.info('And deleting .vcf s...')
meta_config = support_functions.export2maf(meta_config, study_config, verb)
# Generate the meta data files for mutation extended data
logger.info('Generating MUTATION_EXTENDED Meta ...')
meta.generate_meta_type(meta_config, study_config, logger)
logger.info('Cleaning MAF Files ...')
support_functions.clean_head(meta_config, verb)
logger.info('Concating MAF Files to export folder ...')
helper.concat_files(meta_config, study_config, verb)
def main():
global meta_config
global study_config
global janus_path
global logger
import logging
from support import helper
from generate import meta
from generate.analysis_pipelines.MUTATION_EXTENDED import support_functions
verb = logger.isEnabledFor(
logging.INFO) # TODO replace the 'verb' switch with logger
logger.info('Decompressing VCF files to temporary folder')
meta_config = helper.relocate_inputs(meta_config, study_config, verb)
logger.info(
'Ensuring both columns exist, otherwise adding UNMATCHED column ...')
support_functions.verify_dual_columns(meta_config, verb)
logger.info('Filtering for only PASS ...')
support_functions.filter_vcf_rejects(meta_config, verb)
logger.info('Exporting vcf2maf, and deleting .VCFs')
meta_config = support_functions.export2maf(meta_config, study_config, verb)
# Generate the meta data files for mutation extended data
logger.info('Generating MUTATION_EXTENDED Meta ...')
meta.generate_meta_type(meta_config, study_config, logger)
logger.info('Cleaning MAF Files ...')
support_functions.clean_head(meta_config, verb)
logger.info('Concating MAF Files to export folder ...')
helper.concat_files(meta_config, study_config, verb)
logger.info('Finished processing data for Mutect pipeline')