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2
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1 library(argparse)
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2
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3 parser <- ArgumentParser(description="Select the best TITAN cluster");
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4
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5 parser$add_argument(
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6 '--input_params', "-ip",
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7 nargs="+",
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8 required="True",
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9 help="Input parameter files from TITAN"
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10 );
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11
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12 parser$add_argument(
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13 '--input_segments', "-is",
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14 nargs="+",
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15 required="True",
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16 help="Input segment files from TITAN"
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17 );
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18
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19 parser$add_argument(
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20 "--method", "-m",
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21 choices=c('validity_index', 'validity_index_and_pga'),
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22 required="True",
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23 help="Algorithm to use for cluster selection"
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24 );
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25
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26 parser$add_argument(
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27 "--percent_genome_alteration", "-pga",
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28 metavar="PGA",
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29 type="double",
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30 default="0.8",
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31 help="Maximum percent genome alteration to accept in a cluster"
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32 );
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33
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34 parser$add_argument(
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35 "--output_param", "-op",
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36 required="True",
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37 help="Output file to store optimal parameter file"
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38 );
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39
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40 parser$add_argument(
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41 "--output_segment", "-os",
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42 required="True",
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43 help="Output file to store optimal segment file"
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44 );
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45
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46 parser$add_argument(
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47 "--cancer_genomics_functions_path", "-cgfp",
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48 required="True",
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49 help="Path to cancer genomics functions in R"
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50 )
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51
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52 args <- parser$parse_args();
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53
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54 source(paste(args$cancer_genomics_functions_path, "functions.R", sep="/"));
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55
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56 current_index <- 0;
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57 current_val_index <- 1;
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58 genome_frame <- generate_common_genome_frame();
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59 for (i in 1:length(args$input_params)) {
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60 if (args$method == "validity_index_and_pga") {
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61 titan_segs <- read_titan_cnv_file(args$input_segments[i]);
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62 pga <- calculate_percent_genome_alteration(titan_segs, genome_frame);
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63 if (pga >= args$percent_genome_alteration) {
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64 next;
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65 }
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66 }
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67
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68 titan_params <- read_titan_params_file(args$input_params[i]);
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69 val_index <- fetch_validity_index(titan_params)
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70 if (current_val_index > val_index) {
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71 current_val_index <- val_index;
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72 current_index <- i;
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73 }
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74 }
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75
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76 command_params <- paste(
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77 "cp",
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78 args$input_params[current_index],
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79 args$output_param,
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80 sep=" "
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81 );
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82
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83 system(command_params);
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84
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85
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86 command_segments <- paste(
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87 "cp",
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88 args$input_segments[current_index],
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89 args$output_segment,
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90 sep=" "
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91 );
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92
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93 system(command_params);
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