2 * chimeraslayercommand.cpp
5 * Created by westcott on 3/31/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "chimeraslayercommand.h"
11 #include "chimeraslayer.h"
14 //***************************************************************************************************************
16 ChimeraSlayerCommand::ChimeraSlayerCommand(string option) {
20 //allow user to run help
21 if(option == "help") { help(); abort = true; }
24 //valid paramters for this command
25 string Array[] = {"fasta", "processors", "window", "template","numwanted", "ksize", "match","mismatch",
26 "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
27 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
29 OptionParser parser(option);
30 map<string,string> parameters = parser.getParameters();
32 ValidParameters validParameter("chimera.slayer");
33 map<string,string>::iterator it;
35 //check to make sure all parameters are valid for command
36 for (it = parameters.begin(); it != parameters.end(); it++) {
37 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
40 //if the user changes the input directory command factory will send this info to us in the output parameter
41 string inputDir = validParameter.validFile(parameters, "inputdir", false);
42 if (inputDir == "not found"){ inputDir = ""; }
45 it = parameters.find("template");
46 //user has given a template file
47 if(it != parameters.end()){
48 path = hasPath(it->second);
49 //if the user has not given a path then, add inputdir. else leave path alone.
50 if (path == "") { parameters["template"] = inputDir + it->second; }
55 //check for required parameters
56 fastafile = validParameter.validFile(parameters, "fasta", false);
57 if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
59 splitAtDash(fastafile, fastaFileNames);
61 //go through files and make sure they are good, if not, then disregard them
62 for (int i = 0; i < fastaFileNames.size(); i++) {
64 string path = hasPath(fastaFileNames[i]);
65 //if the user has not given a path then, add inputdir. else leave path alone.
66 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
74 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
75 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
80 ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
82 //if you can't open it, try default location
83 if (ableToOpen == 1) {
84 if (m->getDefaultPath() != "") { //default path is set
85 string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
86 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
87 ableToOpen = openInputFile(tryPath, in, "noerror");
88 fastaFileNames[i] = tryPath;
94 for (int j = 1; j < processors; j++) {
95 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
99 MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
104 if (ableToOpen == 1) {
105 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
106 //erase from file list
107 fastaFileNames.erase(fastaFileNames.begin()+i);
112 //make sure there is at least one valid file left
113 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
116 //if the user changes the output directory command factory will send this info to us in the output parameter
117 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
119 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
122 templatefile = validParameter.validFile(parameters, "template", true);
123 if (templatefile == "not open") { abort = true; }
124 else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
126 string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
127 convert(temp, processors);
129 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
130 convert(temp, ksize);
132 temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; }
133 convert(temp, window);
135 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; }
136 convert(temp, match);
138 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
139 convert(temp, mismatch);
141 temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
144 temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
145 convert(temp, minSimilarity);
147 temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
148 convert(temp, minCoverage);
150 temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
151 convert(temp, minBS);
153 temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
154 convert(temp, minSNP);
156 temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
157 convert(temp, parents);
159 temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; }
160 realign = isTrue(temp);
162 search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
164 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
165 convert(temp, iters);
167 temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
168 convert(temp, increment);
170 temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
171 convert(temp, numwanted);
173 if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
176 catch(exception& e) {
177 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
181 //**********************************************************************************************************************
183 void ChimeraSlayerCommand::help(){
186 m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
187 m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
188 m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
189 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
190 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n");
191 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
192 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
194 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
196 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
197 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
198 m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
199 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n");
200 m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n");
201 m->mothurOut("The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n");
202 m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n");
203 m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n");
204 m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n");
205 m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
206 m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
207 m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
208 m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
209 m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
210 m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n");
211 m->mothurOut("The chimera.slayer command should be in the following format: \n");
212 m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
213 m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
214 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
216 catch(exception& e) {
217 m->errorOut(e, "ChimeraSlayerCommand", "help");
222 //***************************************************************************************************************
224 ChimeraSlayerCommand::~ChimeraSlayerCommand(){ /* do nothing */ }
226 //***************************************************************************************************************
228 int ChimeraSlayerCommand::execute(){
231 if (abort == true) { return 0; }
233 for (int s = 0; s < fastaFileNames.size(); s++) {
235 m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
237 int start = time(NULL);
239 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
241 string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras";
242 string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.accnos";
244 if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
246 if (chimera->getUnaligned()) {
247 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
251 templateSeqsLength = chimera->getLength();
254 int pid, end, numSeqsPerProcessor;
256 vector<unsigned long int> MPIPos;
259 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
260 MPI_Comm_size(MPI_COMM_WORLD, &processors);
264 MPI_File outMPIAccnos;
266 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
267 int inMode=MPI_MODE_RDONLY;
269 char outFilename[1024];
270 strcpy(outFilename, outputFileName.c_str());
272 char outAccnosFilename[1024];
273 strcpy(outAccnosFilename, accnosFileName.c_str());
275 char inFileName[1024];
276 strcpy(inFileName, fastaFileNames[s].c_str());
278 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
279 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
280 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
282 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
284 if (pid == 0) { //you are the root process
285 m->mothurOutEndLine();
286 m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
287 m->mothurOutEndLine();
289 string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
292 int length = outTemp.length();
293 char* buf2 = new char[length];
294 memcpy(buf2, outTemp.c_str(), length);
296 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
299 MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
301 //send file positions to all processes
302 for(int i = 1; i < processors; i++) {
303 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
304 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
307 //figure out how many sequences you have to align
308 numSeqsPerProcessor = numSeqs / processors;
309 int startIndex = pid * numSeqsPerProcessor;
310 if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
313 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
315 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; }
317 }else{ //you are a child process
318 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
319 MPIPos.resize(numSeqs+1);
320 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
322 //figure out how many sequences you have to align
323 numSeqsPerProcessor = numSeqs / processors;
324 int startIndex = pid * numSeqsPerProcessor;
325 if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
328 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
330 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
334 MPI_File_close(&inMPI);
335 MPI_File_close(&outMPI);
336 MPI_File_close(&outMPIAccnos);
337 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
341 string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
342 openOutputFile(tempHeader, outHeader);
344 chimera->printHeader(outHeader);
348 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
351 openInputFile(fastaFileNames[s], inFASTA);
352 getNumSeqs(inFASTA, numSeqs);
355 lines.push_back(new linePair(0, numSeqs));
357 driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
359 if (m->control_pressed) {
360 remove(outputFileName.c_str());
361 remove(tempHeader.c_str());
362 remove(accnosFileName.c_str());
363 for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
364 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
370 vector<unsigned long int> positions;
371 processIDS.resize(0);
374 openInputFile(fastaFileNames[s], inFASTA);
377 while(!inFASTA.eof()){
378 input = getline(inFASTA);
379 if (input.length() != 0) {
380 if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
385 numSeqs = positions.size();
387 int numSeqsPerProcessor = numSeqs / processors;
389 for (int i = 0; i < processors; i++) {
390 unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
391 if(i == processors - 1){
392 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
394 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
397 createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
399 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
400 rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
402 //append output files
403 for(int i=1;i<processors;i++){
404 appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
405 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
408 //append output files
409 for(int i=1;i<processors;i++){
410 appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
411 remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
414 if (m->control_pressed) {
415 remove(outputFileName.c_str());
416 remove(accnosFileName.c_str());
417 for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
418 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
427 openInputFile(fastaFileNames[s], inFASTA);
428 getNumSeqs(inFASTA, numSeqs);
430 lines.push_back(new linePair(0, numSeqs));
432 driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
434 if (m->control_pressed) {
435 remove(outputFileName.c_str());
436 remove(tempHeader.c_str());
437 remove(accnosFileName.c_str());
438 for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
439 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
446 appendFiles(outputFileName, tempHeader);
448 remove(outputFileName.c_str());
449 rename(tempHeader.c_str(), outputFileName.c_str());
455 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
457 outputNames.push_back(outputFileName);
458 outputNames.push_back(accnosFileName);
460 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
463 m->mothurOutEndLine();
464 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
465 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
466 m->mothurOutEndLine();
471 catch(exception& e) {
472 m->errorOut(e, "ChimeraSlayerCommand", "execute");
476 //**********************************************************************************************************************
478 int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string filename, string accnos){
481 openOutputFile(outputFName, out);
484 openOutputFile(accnos, out2);
487 openInputFile(filename, inFASTA);
489 inFASTA.seekg(line->start);
491 for(int i=0;i<line->numSeqs;i++){
493 if (m->control_pressed) { return 1; }
495 Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
497 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
499 if (candidateSeq->getAligned().length() != templateSeqsLength) {
500 m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
503 chimera->getChimeras(candidateSeq);
505 if (m->control_pressed) { delete candidateSeq; return 1; }
508 chimera->print(out, out2);
514 if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine(); }
517 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine(); }
525 catch(exception& e) {
526 m->errorOut(e, "ChimeraSlayerCommand", "driver");
530 //**********************************************************************************************************************
532 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
536 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
538 for(int i=0;i<num;i++){
540 if (m->control_pressed) { return 1; }
543 int length = MPIPos[start+i+1] - MPIPos[start+i];
545 char* buf4 = new char[length];
546 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
548 string tempBuf = buf4;
549 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
550 istringstream iss (tempBuf,istringstream::in);
554 Sequence* candidateSeq = new Sequence(iss); gobble(iss);
556 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
558 if (candidateSeq->getAligned().length() != templateSeqsLength) {
559 m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
563 chimera->getChimeras(candidateSeq);
565 if (m->control_pressed) { delete candidateSeq; return 1; }
566 //cout << "about to print" << endl;
568 bool isChimeric = chimera->print(outMPI, outAccMPI);
574 if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); }
577 if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); }
582 catch(exception& e) {
583 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
589 /**************************************************************************************************/
591 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) {
593 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
595 // processIDS.resize(0);
597 //loop through and create all the processes you want
598 while (process != processors) {
602 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
605 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
607 }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
610 //force parent to wait until all the processes are done
611 for (int i=0;i<processors;i++) {
612 int temp = processIDS[i];
619 catch(exception& e) {
620 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
625 /**************************************************************************************************/