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comparison ideas.R @ 175:2b6b5e2769f5 draft

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author greg
date Thu, 25 Jan 2018 13:38:06 -0500
parents b0ca3591242e
children f32f15562a82
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174:b0ca3591242e 175:2b6b5e2769f5
2 2
3 suppressPackageStartupMessages(library("data.table")) 3 suppressPackageStartupMessages(library("data.table"))
4 suppressPackageStartupMessages(library("optparse")) 4 suppressPackageStartupMessages(library("optparse"))
5 5
6 option_list <- list( 6 option_list <- list(
7 make_option(c("--burnin_num"), action="store", dest="burnin_num", type="integer", help="Number of burnin steps"), 7 make_option(c("--burnin_num"), action="store", dest="burnin_num", type="integer", help="Number of burnin steps"),
8 make_option(c("--bychr"), action="store_true", dest="bychr", default=FALSE, help="Output chromosomes in separate files"), 8 make_option(c("--bychr"), action="store_true", dest="bychr", default=FALSE, help="Output chromosomes in separate files"),
9 make_option(c("--chrom_bed_input"), action="store", dest="chrom_bed_input", default=NULL, help="Chromosome windows positions file"), 9 make_option(c("--chrom_bed_input"), action="store", dest="chrom_bed_input", default=NULL, help="Chromosome windows positions file"),
10 make_option(c("--chromosome_windows"), action="store", dest="chromosome_windows", default=NULL, help="Windows positions by chroms config file"), 10 make_option(c("--chromosome_windows"), action="store", dest="chromosome_windows", default=NULL, help="Windows positions by chroms config file"),
11 make_option(c("--hp"), action="store_true", dest="hp", default=FALSE, help="Discourage state transition across chromosomes"), 11 make_option(c("--hp"), action="store_true", dest="hp", default=FALSE, help="Discourage state transition across chromosomes"),
12 make_option(c("--initial_states"), action="store", dest="initial_states", type="integer", default=NULL, help="Initial number of states"), 12 make_option(c("--initial_states"), action="store", dest="initial_states", type="integer", default=NULL, help="Initial number of states"),
13 make_option(c("--input"), action="store", dest="input", help="IdeasPre input dataset"), 13 make_option(c("--input_files_path"), action="store", dest="input_files_path", help="IdeasPre input dataset extra files path"),
14 make_option(c("--input_files_path"), action="store", dest="input_files_path", help="IdeasPre input dataset extra files path"), 14 make_option(c("--ideas_input_config"), action="store", dest="ideas_input_config", help="IDEAS_input_config file"),
15 make_option(c("--ideas_input_config"), action="store", dest="ideas_input_config", help="IDEAS_input_config file"), 15 make_option(c("--log2"), action="store", dest="log2", type="double", default=NULL, help="log2 transformation"),
16 make_option(c("--log2"), action="store", dest="log2", type="double", default=NULL, help="log2 transformation"), 16 make_option(c("--maxerr"), action="store", dest="maxerr", type="double", default=NULL, help="Maximum standard deviation for the emission Gaussian distribution"),
17 make_option(c("--maxerr"), action="store", dest="maxerr", type="double", default=NULL, help="Maximum standard deviation for the emission Gaussian distribution"), 17 make_option(c("--max_cell_type_clusters"), action="store", dest="max_cell_type_clusters", type="integer", default=NULL, help="Maximum number of cell type clusters allowed"),
18 make_option(c("--max_cell_type_clusters"), action="store", dest="max_cell_type_clusters", type="integer", default=NULL, help="Maximum number of cell type clusters allowed"), 18 make_option(c("--max_position_classes"), action="store", dest="max_position_classes", type="integer", default=NULL, help="Maximum number of position classes to be inferred"),
19 make_option(c("--max_position_classes"), action="store", dest="max_position_classes", type="integer", default=NULL, help="Maximum number of position classes to be inferred"), 19 make_option(c("--max_states"), action="store", dest="max_states", type="double", default=NULL, help="Maximum number of states to be inferred"),
20 make_option(c("--max_states"), action="store", dest="max_states", type="double", default=NULL, help="Maximum number of states to be inferred"), 20 make_option(c("--mcmc_num"), action="store", dest="mcmc_num", type="integer", help="Number of maximization steps"),
21 make_option(c("--mcmc_num"), action="store", dest="mcmc_num", type="integer", help="Number of maximization steps"), 21 make_option(c("--minerr"), action="store", dest="minerr", type="double", default=NULL, help="Minimum standard deviation for the emission Gaussian distribution"),
22 make_option(c("--minerr"), action="store", dest="minerr", type="double", default=NULL, help="Minimum standard deviation for the emission Gaussian distribution"), 22 make_option(c("--output_dir"), action="store", dest="output_dir", help="Output directory, used only if job ends in error and process log needs saving"),
23 make_option(c("--output_dir"), action="store", dest="output_dir", help="Output directory, used only if job ends in error and process log needs saving"), 23 make_option(c("--output_log"), action="store", dest="output_log", default=NULL, help="Output log file path"),
24 make_option(c("--output_log"), action="store", dest="output_log", default=NULL, help="Output log file path"), 24 make_option(c("--prior_concentration"), action="store", dest="prior_concentration", type="double", default=NULL, help="Prior concentration"),
25 make_option(c("--prior_concentration"), action="store", dest="prior_concentration", type="double", default=NULL, help="Prior concentration"), 25 make_option(c("--project_name"), action="store", dest="project_name", help="Outputs will have this base name"),
26 make_option(c("--project_name"), action="store", dest="project_name", help="Outputs will have this base name"), 26 make_option(c("--rseed"), action="store", dest="rseed", type="integer", help="Seed for IDEAS model initialization"),
27 make_option(c("--rseed"), action="store", dest="rseed", type="integer", help="Seed for IDEAS model initialization"), 27 make_option(c("--save_ideas_log"), action="store", dest="save_ideas_log", default=NULL, help="Flag to save IDEAS process log"),
28 make_option(c("--save_ideas_log"), action="store", dest="save_ideas_log", default=NULL, help="Flag to save IDEAS process log"), 28 make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"),
29 make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"), 29 make_option(c("--thread"), action="store", dest="thread", type="integer", help="Process threads"),
30 make_option(c("--thread"), action="store", dest="thread", type="integer", help="Process threads"), 30 make_option(c("--training_iterations"), action="store", dest="training_iterations", type="integer", default=NULL, help="Number of training iterations"),
31 make_option(c("--training_iterations"), action="store", dest="training_iterations", type="integer", default=NULL, help="Number of training iterations"), 31 make_option(c("--training_windows"), action="store", dest="training_windows", type="integer", default=NULL, help="Number of training iterations")
32 make_option(c("--training_windows"), action="store", dest="training_windows", type="integer", default=NULL, help="Number of training iterations")
33 ) 32 )
34 33
35 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 34 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
36 args <- parse_args(parser, positional_arguments=TRUE) 35 args <- parse_args(parser, positional_arguments=TRUE)
37 opt <- args$options 36 opt <- args$options
284 base_cmd = paste(base_cmd, "-rseed", rseed, sep=" "); 283 base_cmd = paste(base_cmd, "-rseed", rseed, sep=" ");
285 base_cmd = paste(base_cmd, "-thread", thread, sep=" "); 284 base_cmd = paste(base_cmd, "-thread", thread, sep=" ");
286 return(base_cmd); 285 return(base_cmd);
287 } 286 }
288 287
289 get_file_path <- function(dir, fname) {
290 if (is.null(fname)) {
291 return(fname);
292 } else {
293 return(paste(dir, fname, sep="/"));
294 }
295 }
296
297 get_mean <- function(n) { 288 get_mean <- function(n) {
298 N = NULL; 289 N = NULL;
299 for(i in sort(unique(n[,1]))) { 290 for(i in sort(unique(n[,1]))) {
300 t = which(n[,1]==i); 291 t = which(n[,1]==i);
301 N = rbind(N, apply(array(n[t,], dim=c(length(t), dim(n)[2])), 2, sum)[-1]); 292 N = rbind(N, apply(array(n[t,], dim=c(length(t), dim(n)[2])), 2, sum)[-1]);
347 unlink(f); 338 unlink(f);
348 } 339 }
349 } 340 }
350 341
351 run_cmd <- function(cmd, save_ideas_log, output_log, output_dir) { 342 run_cmd <- function(cmd, save_ideas_log, output_log, output_dir) {
352 cat("save_ideas_log: ", save_ideas_log, "\n");
353 cat("output_log: ", output_log, "\n");
354 cat("output_dir: ", output_dir, "\n");
355 cat("\nRunning cmd:\n", cmd, "\n\n");
356 rc = system(cmd); 343 rc = system(cmd);
357 if (rc != 0) { 344 if (rc != 0) {
358 if (is.null(save_ideas_log)) { 345 if (is.null(save_ideas_log)) {
359 to_path = paste(output_dir, output_log, sep="/"); 346 to_path = paste(output_dir, output_log, sep="/");
360 file.rename(output_log, to_path); 347 file.rename(output_log, to_path);
367 if (is.null(opt$save_ideas_log)) { 354 if (is.null(opt$save_ideas_log)) {
368 output_log = "ideas_log.txt"; 355 output_log = "ideas_log.txt";
369 } else { 356 } else {
370 output_log = opt$output_log; 357 output_log = opt$output_log;
371 } 358 }
372 # Get full path of chromosomes.bed if not NULL. 359 if (is.null(opt$chromosome_windows)) {
373 chrom_bed_input = get_file_path(opt$input_files_path, opt$chrom_bed_input);
374 cat("chrom_bed_input: ", chrom_bed_input, "\n");
375 # Get full path of chromosome_windows.txt if not NULL.
376 chromosome_windows = get_file_path(opt$input_files_path, opt$chromosome_windows);
377 cat("chromosome_windows: ", chromosome_windows, "\n");
378 if (is.null(chromosome_windows)) {
379 windows_by_chrom = NULL; 360 windows_by_chrom = NULL;
380 } else { 361 } else {
381 # Read chromosome_windows.txt into memory. 362 # Read chromosome_windows.txt into memory.
382 windows_by_chrom = get_windows_by_chrom(chromosome_windows); 363 windows_by_chrom = get_windows_by_chrom(chromosome_windows);
383 } 364 }
384 ideas_input_config = get_file_path(opt$input_files_path, opt$ideas_input_config); 365 base_cmd = get_base_cmd(opt$ideas_input_config, opt$chrom_bed_input, opt$training_iterations, opt$bychr, opt$hp,
385 cat("ideas_input_config: ", ideas_input_config, "\n");
386 base_cmd = get_base_cmd(ideas_input_config, chrom_bed_input, opt$training_iterations, opt$bychr, opt$hp,
387 opt$standardize_datasets, opt$log2, opt$max_states, opt$initial_states, opt$max_position_classes, 366 opt$standardize_datasets, opt$log2, opt$max_states, opt$initial_states, opt$max_position_classes,
388 opt$max_cell_type_clusters, opt$prior_concentration, opt$burnin_num, opt$mcmc_num, opt$minerr, 367 opt$max_cell_type_clusters, opt$prior_concentration, opt$burnin_num, opt$mcmc_num, opt$minerr,
389 opt$maxerr, opt$rseed, opt$thread); 368 opt$maxerr, opt$rseed, opt$thread);
390 cat("base_cmd: ", base_cmd, "\n");
391 output_base_name = opt$project_name; 369 output_base_name = opt$project_name;
392 cat("output_base_name: ", output_base_name, "\n"); 370 # Perform analysis.
393
394 if (is.null(opt$training_iterations)) { 371 if (is.null(opt$training_iterations)) {
395 # Not performing training. 372 # Not performing training.
396 if (is.null(windows_by_chrom)) { 373 if (is.null(windows_by_chrom)) {
397 # Not performing windows by chromosome. 374 # Not performing windows by chromosome.
398 output_name = output_base_name; 375 output_name = output_base_name;
413 cmd = add_output_redirect(cmd, output_log); 390 cmd = add_output_redirect(cmd, output_log);
414 run_cmd(cmd, opt$save_ideas_log, output_log, opt$output_dir); 391 run_cmd(cmd, opt$save_ideas_log, output_log, opt$output_dir);
415 } 392 }
416 } 393 }
417 } else { 394 } else {
418 # performing training. 395 # Performing training.
419 output_para0 = paste(output_base_name, "para0", sep="."); 396 output_para0 = paste(output_base_name, "para0", sep=".");
420 output_profile0 = paste(output_base_name, "profile0", sep="."); 397 output_profile0 = paste(output_base_name, "profile0", sep=".");
421 for (i in 1:opt$training_iterations) { 398 for (i in 1:opt$training_iterations) {
422 cmd = paste(base_cmd, "-o", paste(output_base_name, ".tmp.", i, sep=""), sep=" "); 399 cmd = paste(base_cmd, "-o", paste(output_base_name, ".tmp.", i, sep=""), sep=" ");
423 cmd = add_output_redirect(cmd, output_log); 400 cmd = add_output_redirect(cmd, output_log);