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comparison ideas.R @ 152:26c26cb32137 draft

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Uploaded
author greg
date Fri, 12 Jan 2018 13:12:47 -0500
parents 3762c27d820a
children b140097a984e
comparison
equal deleted inserted replaced
151:9d34f7e6d80c 152:26c26cb32137
324 } 324 }
325 cmd = paste(cmd, "-rseed", opt$rseed, sep=" "); 325 cmd = paste(cmd, "-rseed", opt$rseed, sep=" ");
326 cmd = paste(cmd, "-thread", opt$thread, sep=" "); 326 cmd = paste(cmd, "-thread", opt$thread, sep=" ");
327 327
328 if (is.null(opt$training_iterations)) { 328 if (is.null(opt$training_iterations)) {
329 cmd = paste(cmd, "-o", output_base_name, sep=" "); 329 final_cmd = paste(cmd, "-o", output_base_name, sep=" ");
330 cmd = add_output_redirect(cmd, opt$save_ideas_log, opt$output_log, default_log_name); 330 final_cmd = add_output_redirect(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
331 run_cmd(cmd, opt$save_ideas_log, opt$output_log, default_log_name); 331 run_cmd(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
332 } else { 332 } else {
333 output_para0 = paste(output_base_name, ".para0", sep="");
334 output_profile0 = paste(output_base_name, ".profile0", sep="");
333 for (i in 1:opt$training_iterations) { 335 for (i in 1:opt$training_iterations) {
334 cmd = paste(cmd, "-o", paste(output_base_name, ".tmp.", i, sep=""), sep=" "); 336 final_cmd = paste(cmd, "-o", paste(output_base_name, ".tmp.", i, sep=""), sep=" ");
335 cmd = add_output_redirect(cmd, opt$save_ideas_log, opt$output_log, default_log_name); 337 final_cmd = add_output_redirect(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
336 run_cmd(cmd, opt$save_ideas_log, opt$output_log, default_log_name); 338 run_cmd(final_cmd, opt$save_ideas_log, opt$output_log, default_log_name);
337 } 339 }
338 tpara = combine_state(paste(output_base_name, ".tmp.", (1:opt$training_iterations), ".para", sep=""), mycut=0.5); 340 tpara = combine_state(paste(output_base_name, ".tmp.", (1:opt$training_iterations), ".para", sep=""), mycut=0.5);
339 para = tpara$para; 341 para = tpara$para;
340 write.table(tpara$profile, paste(output_base_name, ".profile0", sep=""), quote=F, row.names=F, col.names=F); 342 write.table(tpara$profile, output_profile0, quote=F, row.names=F, col.names=F);
341 para = apply(para, 1, function(x){paste(x, collapse=" ")}); 343 para = apply(para, 1, function(x){paste(x, collapse=" ")});
342 para = c(readLines(paste(output_base_name, ".tmp.1.para", sep=""), n=1), para); 344 para = c(readLines(paste(output_base_name, ".tmp.1.para", sep=""), n=1), para);
343 output_para0 = paste(output_base_name, ".para0", sep="");
344 writeLines(para, output_para0); 345 writeLines(para, output_para0);
345 } 346 cmd = c(cmd, "-otherpara", output_para0, output_profile0);
347 if (length(which(cmd == "-G")) == 0) {
348 cmd = c(cmd, "-G", length(para)-1);
349 } else {
350 tt = which(cmd == "-G");
351 cmd[tt + 1] = length(para)-1;
352 }
353 tt = which(cmd == '-C');
354 if(length(tt)>0) {
355 cmd = cmd[-c(tt, tt+1)];
356 }
357 }