def run(items): """Normalization and log2 ratio calculation plus CNV calling for full cohort. - Combine coverage of each region for each sample - Prepare read counts for each sample - Normalize coverages in cohort by gene and sample, and calculate log2 ratios - Call amplifications and deletions """ items = [utils.to_single_data(x) for x in items] work_dir = _sv_workdir(items[0]) input_backs = list(set(filter(lambda x: x is not None, [dd.get_background_cnv_reference(d, "seq2c") for d in items]))) coverage_file = _combine_coverages(items, work_dir, input_backs) read_mapping_file = _calculate_mapping_reads(items, work_dir, input_backs) normal_names = [] if input_backs: with open(input_backs[0]) as in_handle: for line in in_handle: if len(line.split()) == 2: normal_names.append(line.split()[0]) normal_names += [dd.get_sample_name(x) for x in items if population.get_affected_status(x) == 1] seq2c_calls_file = _call_cnv(items, work_dir, read_mapping_file, coverage_file, normal_names) items = _split_cnv(items, seq2c_calls_file, read_mapping_file, coverage_file) return items
def run(items): """Normalization and log2 ratio calculation plus CNV calling for full cohort. - Combine coverage of each region for each sample - Prepare read counts for each sample - Normalize coverages in cohort by gene and sample, and calculate log2 ratios - Call amplifications and deletions """ items = [utils.to_single_data(x) for x in items] work_dir = _sv_workdir(items[0]) input_backs = list( set( filter( lambda x: x is not None, [dd.get_background_cnv_reference(d, "seq2c") for d in items]))) coverage_file = _combine_coverages(items, work_dir, input_backs) read_mapping_file = _calculate_mapping_reads(items, work_dir, input_backs) normal_names = [] if input_backs: with open(input_backs[0]) as in_handle: for line in in_handle: if len(line.split()) == 2: normal_names.append(line.split()[0]) normal_names += [ dd.get_sample_name(x) for x in items if population.get_affected_status(x) == 1 ] seq2c_calls_file = _call_cnv(items, work_dir, read_mapping_file, coverage_file, normal_names) items = _split_cnv(items, seq2c_calls_file, read_mapping_file, coverage_file) return items
def find_case_control(items): """Find case/control items in a population of multiple samples. """ cases = [] controls = [] for data in items: if population.get_affected_status(data) == 1: controls.append(data) else: cases.append(data) return cases, controls
def find_case_control(items): """Find case/control items in a population of multiple samples. """ cases = [] controls = [] for data in items: if population.get_affected_status(data) == 1: controls.append(data) else: cases.append(data) return cases, controls
def run(items): """Normalization and log2 ratio calculation plus CNV calling for full cohort. - Combine coverage of each region for each sample - Prepare read counts for each sample - Normalize coverages in cohort by gene and sample, and calculate log2 ratios - Call amplifications and deletions """ items = [utils.to_single_data(x) for x in items] work_dir = _sv_workdir(items[0]) coverage_file = _combine_coverages(items, work_dir) read_mapping_file = _calculate_mapping_reads(items, work_dir) normal_names = [dd.get_sample_name(x) for x in items if population.get_affected_status(x) == 1] seq2c_calls_file = _call_cnv(items, work_dir, read_mapping_file, coverage_file, normal_names) items = _split_cnv(items, seq2c_calls_file, read_mapping_file) return items
def run(items): """Normalization and log2 ratio calculation plus CNV calling for full cohort. - Combine coverage of each region for each sample - Prepare read counts for each sample - Normalize coverages in cohort by gene and sample, and calculate log2 ratios - Call amplifications and deletions """ items = [utils.to_single_data(x) for x in items] work_dir = _sv_workdir(items[0]) coverage_file = _combine_coverages(items, work_dir) read_mapping_file = _calculate_mapping_reads(items, work_dir) normal_names = [dd.get_sample_name(x) for x in items if population.get_affected_status(x) == 1] seq2c_calls_file = _call_cnv(items, work_dir, read_mapping_file, coverage_file, normal_names) _split_cnv(items, seq2c_calls_file) return items