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.COPY_NUMBER_ALTERATION.support_functions import fix_chrom, fix_seg_id
verb = logger.isEnabledFor(logging.INFO) # TODO replace the 'verb' switch with logger
logger.info('Gathering and decompressing SEG files into temporary folder, and updating config')
meta_config = helper.relocate_inputs(meta_config, study_config, verb)
logger.info('Done.')
logger.info('Fixing Chromosome numbering ...')
fix_chrom(meta_config, study_config, logger)
logger.info('Done.')
logger.info('Fixing .SEG IDs')
fix_seg_id(meta_config, study_config, logger)
logger.info('Done.')
logger.info('Concatenating SEG Files to export folder')
helper.concat_files(meta_config, study_config, verb)
logger.info('Done.')
logger.info('Generating segments Meta ...')
meta.generate_meta_type(meta_config,study_config,logger)
logger.info('Done.')
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 verb
helper.working_on(
verb,
message='Gathering and decompressing SEG files into temporary folder')
helper.decompress_to_temp(meta_config, study_config, verb)
helper.working_on(verb)
helper.working_on(
verb,
message=
'Fixing HMMCopy formatting, chromosome, and chromosome max-length ...')
fix_hmmcopy_tsv(meta_config, study_config, verb)
fix_chrom(meta_config, study_config, verb)
### fix_hmmcopy_max_chrom fixes the maximum chromosome length AND imputes the num.mark value
fix_hmmcopy_max_chrom(meta_config, study_config, janus_path, verb)
helper.working_on(verb)
helper.working_on(verb, message='Fixing .SEG IDs')
fix_seg_id(meta_config, study_config, verb)
helper.working_on(verb)
helper.working_on(verb, message='Concating SEG Files to export folder')
helper.concat_files(meta_config, study_config, verb)
helper.working_on(verb)
def main():
global meta_config
global study_config
global janus_path
global logger
import logging
import os
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('Started processing data for CAP_mutation pipeline')
# Decompress MAF files to temp folder
logger.info('Decompressing MAF files to temporary folder')
meta_config = helper.relocate_inputs(meta_config, study_config, verb)
# Clean MAF files
logger.info('Cleaning MAF Files ...')
support_functions.clean_head(meta_config, verb)
# Concatenate MAF files
logger.info('Concatenating MAF Files to export folder ...')
helper.concat_files(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)
#Filtering MAF Files
logger.info('Filtering MAF Files ...')
support_functions.maf_filter(
meta_config, study_config, meta_config.config_map['Mutation_Type'],
meta_config.config_map['Filter_Exception'],
meta_config.config_map['Minimum_Tumour_Depth'],
meta_config.config_map['Minimum_Tumour_AF'],
meta_config.config_map['Maximum_gnomAD_AF'],
meta_config.config_map['Maximum_Local_Freq'])
#oncokb-annotation
logger.info('Annotating MAF files ...')
support_functions.oncokb_annotation(
meta_config, study_config, meta_config.config_map['oncokb_api_token'],
verb)
#TGL Pipe Filtering
logger.info('Filtering TGL pipe ...')
try:
support_functions.TGL_filter(meta_config, study_config)
except FileNotFoundError as err: # eg. failure to read vep_keep_columns.txt
logger.error("Cannot read file: {0}".format(err))
raise
logger.info('Finished processing data for CAP_mutation pipeline')
def test_concatenate_files(self):
test_name = 'concatenate_files'
input_dir = os.path.join(self.dataDir, test_name)
out_dir = os.path.join(self.tmp.name, test_name)
os.mkdir(out_dir)
inputs = ['foo.tsv', 'bar.tsv', 'baz.tsv']
df = pd.DataFrame({'FILE_NAME': inputs})
exports_config = mock_legacy_config({'input_folder': input_dir}, df)
study_config = mock_legacy_config({'output_folder': out_dir})
concat_files(exports_config, study_config, True)
checksums = {
'data_mock_concat.txt': 'd5f4cd22aed26f6e5022571ad5f3d745'
}
self.verify_checksums(checksums, out_dir)
def main():
global meta_config
global study_config
global janus_path
global verb
helper.working_on(verb, message='Gathering and decompressing SEG files into temporary folder')
helper.decompress_to_temp(meta_config, study_config, verb)
helper.working_on(verb)
helper.working_on(verb, message='Fixing Chromosome numbering ...')
fix_chrom(meta_config, study_config, verb)
helper.working_on(verb)
helper.working_on(verb, message='Fixing .SEG IDs')
fix_seg_id(meta_config, study_config, verb)
helper.working_on(verb)
helper.working_on(verb, message='Concating SEG Files to export folder')
helper.concat_files(meta_config, study_config, verb)
helper.working_on(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')
def main():
global meta_config
global study_config
global janus_path
global logger
import logging
import os
from support import helper
from generate.analysis_pipelines.COPY_NUMBER_ALTERATION.support_functions import fix_chrom, fix_seg_id, preProcCNA, ProcCNA
from generate import meta
from utilities.constants import DATA_DIRNAME
AP_NAME = 'analysis_pipelines'
CNA_NAME = 'COPY_NUMBER_ALTERATION'
verb = logger.isEnabledFor(
logging.INFO) # TODO replace the 'verb' switch with logger
# note that __file__ is the path to the executing module components.py, not this script
if meta_config.config_map.get('genebed'):
genebed = meta_config.config_map.get('genebed')
else:
genebed = os.path.join(os.path.dirname(__file__), AP_NAME, CNA_NAME,
DATA_DIRNAME, 'ncbi_genes_hg19_canonical.bed')
if meta_config.config_map.get('genelist'):
genelist = meta_config.config_map.get('genelist')
else:
genelist = os.path.join(os.path.dirname(__file__), AP_NAME, CNA_NAME,
DATA_DIRNAME, 'targeted_genelist.txt')
logger.info('Transferring SEG files to temporary folder')
meta_config = helper.relocate_inputs(meta_config, study_config, verb)
logger.info('Done.')
logger.info('Fixing Chromosome numbering ...')
fix_chrom(meta_config, study_config, logger)
logger.info('Done.')
logger.info('Fixing .SEG IDs')
fix_seg_id(meta_config, study_config, logger)
logger.info('Done.')
logger.info('Concatenating SEG Files to export folder')
helper.concat_files(meta_config, study_config, verb)
logger.info('Done.')
#Call preProcCNA.r to generate reduced seg files
logger.info('Generating reduced SEG files ...')
preProcCNA(meta_config, study_config, genebed, genelist,
meta_config.config_map['gain'], meta_config.config_map['ampl'],
meta_config.config_map['htzd'], meta_config.config_map['hmzd'],
logger)
logger.info('Done.')
logger.info('Generating CNA and log2CNA files ...')
ProcCNA(meta_config, study_config, genebed, genelist,
meta_config.config_map['gain'], meta_config.config_map['ampl'],
meta_config.config_map['htzd'], meta_config.config_map['hmzd'],
meta_config.config_map['oncokb_api_token'], verb)
logger.info('Done.')
# TODO legacy metadata generation left in place for now. But does it make sense for data to be *both* discrete and continuous?
logger.info('Generating segments Meta ...')
meta.generate_meta_type(meta_config, study_config, logger)
logger.info('Done.')
if meta_config.config_map.get('DISCRETE'):
logger.info('Generating DISCRETE Meta ...')
meta_config.datahandler = 'DISCRETE'
meta.generate_meta_type(meta_config, study_config, logger)
logger.info('Done.')
if meta_config.config_map.get('CONTINUOUS'):
logger.info('Generating CONTINUOUS Meta ...')
meta_config.datahandler = 'CONTINUOUS'
meta.generate_meta_type(meta_config, study_config, logger)
logger.info('Done.')
