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1 #!/usr/bin/python
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2
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3 __author__ = 'Abdelrahman Hosny'
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4
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5 import os.path
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6 import datetime
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7 import argparse
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8 import shutil
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9
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10 from cnvsim.fileio import *
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11 from cnvsim.exome_simulator import *
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12 from cnvsim.genome_simulator import *
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13
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14 def log(message):
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15 print '[CNV SIM {:%Y-%m-%d %H:%M:%S}'.format(datetime.datetime.now()) + "] " + message
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16
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17 def main():
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18 parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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19 parser.add_argument("simulation_type", type=str, choices=['genome', 'exome'], \
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20 help="simulate copy number variations in whole genome or exome regions")
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21 parser.add_argument("genome", type=file, \
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22 help="path to the referece genome file in FASTA format ")
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23 parser.add_argument("target", type=file, nargs='?', default=None, \
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24 help="path to the target regions file in BED format (if using exome)")
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25
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26 parser.add_argument("-o", "--output_dir_name",type=str, default="test", \
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27 help="a name to be used to create the output directory (overrides existing directory with the same name).")
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28 parser.add_argument("-n", "--n_reads", type=int, default=10000, \
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29 help="total number of reads without variations")
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30 parser.add_argument("-l", "--read_length", type=int, default=100, \
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31 help="read length (bp)")
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32 parser.add_argument("--cnv_list", type=file, default=None, \
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33 help="path to a CNV list file in BED format chr | start | end | variation. If not passed, it is randomly generated using CNV list parameters below")
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34
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35 cnv_sim_group = parser.add_argument_group('CNV list parameters', "parameters to be used if CNV list is not passed")
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36 cnv_sim_group.add_argument("-g", "--regions_count", type=int, default=30, \
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37 help="number of CNV regions to be randomly generated")
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38 cnv_sim_group.add_argument("-a", "--amplifications", type=float, default=0.30, \
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39 help="percentage of amplifications in range [0.0: 1.0].")
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40 cnv_sim_group.add_argument("-d", "--deletions", type=float, default=0.20, \
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41 help="percentage of deletions in range [0.0: 1.0].")
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42 cnv_sim_group.add_argument("-min", "--minimum", type=float, default=3, \
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43 help="minimum number of amplifications/deletions introduced")
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44 cnv_sim_group.add_argument("-max", "--maximum", type=float, default=10, \
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45 help="maximum number of amplifications/deletions introduced")
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46
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47 args = parser.parse_args()
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48
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49 simulation_parameters = {}
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50 simulation_parameters['type'] = args.simulation_type
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51 simulation_parameters['genome_file'] = args.genome.name
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52 if args.target is not None:
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53 simulation_parameters['target_file'] = args.target.name
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54 else:
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55 simulation_parameters['target_file'] = None
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56 simulation_parameters['output_dir'] = os.path.join(os.getcwd(), args.output_dir_name)
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57 simulation_parameters['number_of_reads'] = args.n_reads
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58 simulation_parameters['read_length'] = args.read_length
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59 if args.cnv_list is not None:
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60 simulation_parameters['cnv_list_file'] = args.cnv_list.name
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61 else:
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62 simulation_parameters['cnv_list_file'] = None
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63 simulation_parameters['tmp_dir'] = os.path.join(os.getcwd(), args.output_dir_name , "tmp")
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64
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65 cnv_list_parameters = {}
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66 cnv_list_parameters['regions_count'] = args.regions_count
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67 cnv_list_parameters['amplifications'] = args.amplifications
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68 cnv_list_parameters['deletions'] = args.deletions
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69 cnv_list_parameters['minimum_variations'] = args.minimum
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70 cnv_list_parameters['maximum_variations'] = args.maximum
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71
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72 if simulation_parameters['type'] == 'genome':
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73 simulate_genome_cnv(simulation_parameters, cnv_list_parameters)
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74 else:
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75 simulate_exome_cnv(simulation_parameters, cnv_list_parameters)
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76
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77
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78 if __name__ == '__main__':
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79 main() |
