| Previous changeset 16:7e8047d291e4 (2016-09-07) Next changeset 18:eca72016b5b3 (2016-09-07) |
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modified:
cnvsim/exome_simulator.py |
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| diff -r 7e8047d291e4 -r e4ebf3435054 cnvsim/exome_simulator.py --- a/cnvsim/exome_simulator.py Wed Sep 07 09:34:53 2016 -0400 +++ b/cnvsim/exome_simulator.py Wed Sep 07 09:36:31 2016 -0400 |
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| @@ -20,7 +20,7 @@ return os.path.dirname(os.path.realpath(__file__)) -def _generateCNVMatrix(targets_list, regions_count): +def _generateCNVMatrix(targets_list, regions_count, region_min_length, region_max_length): ''' A function to randomly divide sequential exonic targets into whole CNV regions :param targets_list: a list of target exons loaded from the file provided by the user @@ -28,22 +28,25 @@ ''' regions_count -= 1 number_of_targets = len(targets_list) - comine_size = number_of_targets / regions_count - cnv_matrix = [] + combine_size = number_of_targets / regions_count + cnv_regions = [] i = 0 while True: if i == len(targets_list): break - first_target = i - i += comine_size + region_start = targets_list[i][1] + region_end = region_start + random.randint(region_min_length, region_max_length) - 1 + cnv_regions.append((targets_list[i][0], region_start, region_end)) + + i += combine_size if i > len(targets_list): i = len(targets_list) - last_target = i - cnv_matrix.append(targets_list[first_target:last_target]) - return cnv_matrix + cnv_matrix = _loadCNVMatrix(targets_list, cnv_regions) + + return cnv_matrix, cnv_regions def _loadCNVMatrix(targets_list, cnv_regions): @@ -64,8 +67,12 @@ target_chromosome = target[0] target_start = target[1] target_end = target[2] - if target_chromosome == region_chromosome and target_start >= region_start and target_end <= region_end: - region_targets.append(target) + if target_chromosome == region_chromosome and target_start >= region_start: + if target_end <= region_end: + region_targets.append(target) + elif target_start <= region_end: + truncated_target = (target_chromosome, target_start, region_end) + region_targets.append(truncated_target) cnv_matrix.append(region_targets) @@ -187,7 +194,7 @@ :param simulation_parameters: a dictionary containing parameters for simulation :return: simulation status {'simulation_status': bool, 'message': str} ''' - _log('simulation type: whole exome') + _log('simulation type: targeted exome sequencing') # create a temporary directory for intermediate files if not os.path.exists(simulation_parameters['tmp_dir']): @@ -198,7 +205,7 @@ os.makedirs(simulation_parameters['output_dir']) if simulation_parameters['target_file'] is None: - _log("ERROR: target file cannot be None for whole exome simulation!") + _log("ERROR: target file cannot be None for target exome simulation!") fileio.clean(simulation_parameters['output_dir']) fileio.clean(simulation_parameters['tmp_dir']) exit() @@ -231,19 +238,24 @@ if simulation_parameters['cnv_list_file'] is None: # CNV list file - cnv_list_file = os.path.join(simulation_parameters['output_dir'], "CNVList.bed") + cnv_list_file = os.path.join(simulation_parameters['output_dir'], "copynumber.bed") _log("generating CNV list ..") - cnv_matrix = _generateCNVMatrix(targets, cnv_list_parameters['regions_count']) + cnv_matrix, cnv_regions = _generateCNVMatrix(targets, cnv_list_parameters['regions_count'], \ + cnv_list_parameters['minimum_length'], cnv_list_parameters['maximum_length']) mask = _generateCNVMask(len(cnv_matrix), cnv_list_parameters['amplifications'], \ cnv_list_parameters['deletions'], cnv_list_parameters['minimum_variations'], \ cnv_list_parameters['maximum_variations']) with open(cnv_list_file, 'w') as f: - for i, cnv_region in enumerate(cnv_matrix): - line = cnv_region[0][0] + '\t' \ - + `cnv_region[0][1]` + '\t' \ - + `cnv_region[-1][2]` + '\t' \ + line = 'chrom\tchr_start\tchrom_stop\tnum_positions\tcopy_number\n' + f.write(line) + for i, cnv_region in enumerate(cnv_regions): + num_positions = cnv_region[2] - cnv_region[1] + 1 + line = cnv_region[0] + '\t' \ + + `cnv_region[1]` + '\t' \ + + `cnv_region[2]` + '\t' \ + + `num_positions` + '\t' \ + `mask[i]` + '\n' f.write(line) _log("randomly generated CNV list saved to " + cnv_list_file) @@ -252,8 +264,9 @@ with open(simulation_parameters['cnv_list_file'], "r") as f: cnv_list = [] lines = f.readlines() + lines.pop(0) for line in lines: - chromosome, region_start, region_end, variation = line.strip().split("\t") + chromosome, region_start, region_end, num_positions, variation = line.strip().split("\t") cnv_list.append((chromosome, int(region_start), int(region_end), int(variation))) cnv_matrix = _loadCNVMatrix(targets, cnv_list) |