changeset 2:7edf4d48a350 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/select_optimal_cluster.R	Sun Dec 04 15:57:18 2016 -0500
@@ -0,0 +1,93 @@
+library(argparse)
+
+parser <- ArgumentParser(description="Select the best TITAN cluster");
+
+parser$add_argument(
+    '--input_params', "-ip",
+    nargs="+",
+    required="True",
+    help="Input parameter files from TITAN"
+    );
+
+parser$add_argument(
+    '--input_segments', "-is",
+    nargs="+",
+    required="True",
+    help="Input segment files from TITAN"
+    );
+
+parser$add_argument(
+    "--method", "-m",
+    choices=c('validity_index', 'validity_index_and_pga'),
+    required="True",
+    help="Algorithm to use for cluster selection"
+    );
+
+parser$add_argument(
+    "--percent_genome_alteration", "-pga",
+    metavar="PGA",
+    type="double",
+    default="0.8",
+    help="Maximum percent genome alteration to accept in a cluster"
+    );
+
+parser$add_argument(
+    "--output_param", "-op",
+    required="True",
+    help="Output file to store optimal parameter file"
+    );
+
+parser$add_argument(
+    "--output_segment", "-os",
+    required="True",
+    help="Output file to store optimal segment file"
+    );
+
+parser$add_argument(
+    "--cancer_genomics_functions_path", "-cgfp",
+    required="True",
+    help="Path to cancer genomics functions in R"
+    )
+
+args <- parser$parse_args();
+
+source(paste(args$cancer_genomics_functions_path, "functions.R", sep="/"));
+
+current_index <- 0;
+current_val_index <- 1;
+genome_frame <- generate_common_genome_frame();
+for (i in 1:length(args$input_params)) {
+    if (args$method == "validity_index_and_pga") {
+        titan_segs <- read_titan_cnv_file(args$input_segments[i]);
+        pga <- calculate_percent_genome_alteration(titan_segs, genome_frame);
+        if (pga >= args$percent_genome_alteration) {
+            next;
+            }
+        }
+
+    titan_params <- read_titan_params_file(args$input_params[i]);
+    val_index <- fetch_validity_index(titan_params)
+    if (current_val_index > val_index) {
+        current_val_index <- val_index;
+        current_index <- i;
+        }
+    }
+
+command_params <- paste(
+    "cp",
+    args$input_params[current_index],
+    args$output_param,
+    sep=" "
+    );
+
+system(command_params);
+
+
+command_segments <- paste(
+    "cp",
+    args$input_segments[current_index],
+    args$output_segment,
+    sep=" "
+    );
+
+system(command_params);