2 * chimerapintailcommand.cpp
5 * Created by westcott on 4/1/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "chimerapintailcommand.h"
13 //***************************************************************************************************************
15 ChimeraPintailCommand::ChimeraPintailCommand(string option) {
19 //allow user to run help
20 if(option == "help") { help(); abort = true; }
23 //valid paramters for this command
24 string Array[] = {"fasta","filter","processors","window" "increment","template","conservation","quantile","mask","outputdir","inputdir"};
25 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
27 OptionParser parser(option);
28 map<string,string> parameters = parser.getParameters();
30 ValidParameters validParameter;
31 map<string,string>::iterator it;
33 //check to make sure all parameters are valid for command
34 for (it = parameters.begin(); it != parameters.end(); it++) {
35 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
38 //if the user changes the input directory command factory will send this info to us in the output parameter
39 string inputDir = validParameter.validFile(parameters, "inputdir", false);
40 if (inputDir == "not found"){ inputDir = ""; }
43 it = parameters.find("fasta");
44 //user has given a template file
45 if(it != parameters.end()){
46 path = hasPath(it->second);
47 //if the user has not given a path then, add inputdir. else leave path alone.
48 if (path == "") { parameters["fasta"] = inputDir + it->second; }
51 it = parameters.find("template");
52 //user has given a template file
53 if(it != parameters.end()){
54 path = hasPath(it->second);
55 //if the user has not given a path then, add inputdir. else leave path alone.
56 if (path == "") { parameters["template"] = inputDir + it->second; }
59 it = parameters.find("conservation");
60 //user has given a template file
61 if(it != parameters.end()){
62 path = hasPath(it->second);
63 //if the user has not given a path then, add inputdir. else leave path alone.
64 if (path == "") { parameters["conservation"] = inputDir + it->second; }
67 it = parameters.find("quantile");
68 //user has given a template file
69 if(it != parameters.end()){
70 path = hasPath(it->second);
71 //if the user has not given a path then, add inputdir. else leave path alone.
72 if (path == "") { parameters["quantile"] = inputDir + it->second; }
77 //check for required parameters
78 fastafile = validParameter.validFile(parameters, "fasta", true);
79 if (fastafile == "not open") { abort = true; }
80 else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.pintail command."); m->mothurOutEndLine(); abort = true; }
82 //if the user changes the output directory command factory will send this info to us in the output parameter
83 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
85 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
88 templatefile = validParameter.validFile(parameters, "template", true);
89 if (templatefile == "not open") { abort = true; }
90 else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.pintail command."); m->mothurOutEndLine(); abort = true; }
92 consfile = validParameter.validFile(parameters, "conservation", true);
93 if (consfile == "not open") { abort = true; }
94 else if (consfile == "not found") { consfile = ""; }
96 quanfile = validParameter.validFile(parameters, "quantile", true);
97 if (quanfile == "not open") { abort = true; }
98 else if (quanfile == "not found") { quanfile = ""; }
100 maskfile = validParameter.validFile(parameters, "mask", false);
101 if (maskfile == "not found") { maskfile = ""; }
102 else if (maskfile != "default") {
103 if (inputDir != "") {
104 string path = hasPath(maskfile);
105 //if the user has not given a path then, add inputdir. else leave path alone.
106 if (path == "") { maskfile = inputDir + maskfile; }
110 int ableToOpen = openInputFile(maskfile, in);
111 if (ableToOpen == 1) { abort = true; }
116 temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
117 filter = isTrue(temp);
119 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
120 convert(temp, processors);
122 temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
123 convert(temp, window);
125 temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
126 convert(temp, increment);
129 catch(exception& e) {
130 m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand");
134 //**********************************************************************************************************************
136 void ChimeraPintailCommand::help(){
139 m->mothurOut("The chimera.pintail command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
140 m->mothurOut("This command was created using the algorythms described in the 'At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies' paper by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.\n");
141 m->mothurOut("The chimera.pintail command parameters are fasta, template, filter, mask, processors, window, increment, conservation and quantile.\n");
142 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
143 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
144 m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
145 m->mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences, by default no mask is applied. You can apply an ecoli mask by typing, mask=default. \n");
146 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
148 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
150 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=1/4 sequence length. \n");
151 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=25.\n");
152 m->mothurOut("The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n");
153 m->mothurOut("The quantile parameter allows you to enter a file containing quantiles for a template files sequences, if you use the filter the quantile file generated becomes unique to the fasta file you used.\n");
154 m->mothurOut("The chimera.pintail command should be in the following format: \n");
155 m->mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
156 m->mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");
157 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
159 catch(exception& e) {
160 m->errorOut(e, "ChimeraPintailCommand", "help");
165 //***************************************************************************************************************
167 ChimeraPintailCommand::~ChimeraPintailCommand(){ /* do nothing */ }
169 //***************************************************************************************************************
171 int ChimeraPintailCommand::execute(){
174 if (abort == true) { return 0; }
176 int start = time(NULL);
178 chimera = new Pintail(fastafile, templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
181 if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
184 string outputFileName, accnosFileName;
185 if (maskfile != "") {
186 outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".pintail.chimeras";
187 accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".pintail.accnos";
189 outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pintail.chimeras";
190 accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pintail.accnos";
192 bool hasAccnos = true;
194 if (m->control_pressed) { delete chimera; return 0; }
196 if (chimera->getUnaligned()) {
197 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
201 templateSeqsLength = chimera->getLength();
204 int pid, end, numSeqsPerProcessor;
207 MPIWroteAccnos = false;
210 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
211 MPI_Comm_size(MPI_COMM_WORLD, &processors);
215 MPI_File outMPIAccnos;
217 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
218 int inMode=MPI_MODE_RDONLY;
220 char outFilename[outputFileName.length()];
221 strcpy(outFilename, outputFileName.c_str());
223 char outAccnosFilename[accnosFileName.length()];
224 strcpy(outAccnosFilename, accnosFileName.c_str());
226 char inFileName[fastafile.length()];
227 strcpy(inFileName, fastafile.c_str());
229 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
230 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
231 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
233 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
235 if (pid == 0) { //you are the root process
237 MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
239 //send file positions to all processes
240 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
241 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
243 //figure out how many sequences you have to align
244 numSeqsPerProcessor = numSeqs / processors;
245 if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
246 int startIndex = pid * numSeqsPerProcessor;
249 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
251 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; }
253 for (int i = 1; i < processors; i++) {
255 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
256 if (tempResult != 0) { MPIWroteAccnos = true; }
258 }else{ //you are a child process
259 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
260 MPIPos.resize(numSeqs+1);
261 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
263 //figure out how many sequences you have to align
264 numSeqsPerProcessor = numSeqs / processors;
265 if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
266 int startIndex = pid * numSeqsPerProcessor;
269 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
271 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
273 MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
277 MPI_File_close(&inMPI);
278 MPI_File_close(&outMPI);
279 MPI_File_close(&outMPIAccnos);
281 //delete accnos file if blank
283 if (!MPIWroteAccnos) {
285 //MPI_File_delete(outAccnosFilename, info);
287 remove(accnosFileName.c_str());
294 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
297 openInputFile(fastafile, inFASTA);
298 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
301 lines.push_back(new linePair(0, numSeqs));
303 driver(lines[0], outputFileName, fastafile, accnosFileName);
305 if (m->control_pressed) {
306 remove(outputFileName.c_str());
307 remove(accnosFileName.c_str());
308 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
313 //delete accnos file if its blank
314 if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
317 vector<int> positions;
318 processIDS.resize(0);
321 openInputFile(fastafile, inFASTA);
324 while(!inFASTA.eof()){
325 input = getline(inFASTA);
326 if (input.length() != 0) {
327 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
332 numSeqs = positions.size();
334 int numSeqsPerProcessor = numSeqs / processors;
336 for (int i = 0; i < processors; i++) {
337 long int startPos = positions[ i * numSeqsPerProcessor ];
338 if(i == processors - 1){
339 numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
341 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
345 createProcesses(outputFileName, fastafile, accnosFileName);
347 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
349 //append output files
350 for(int i=1;i<processors;i++){
351 appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
352 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
355 vector<string> nonBlankAccnosFiles;
356 //delete blank accnos files generated with multiple processes
357 for(int i=0;i<processors;i++){
358 if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
359 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
360 }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
363 //append accnos files
364 if (nonBlankAccnosFiles.size() != 0) {
365 rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
367 for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
368 appendFiles(nonBlankAccnosFiles[h], accnosFileName);
369 remove(nonBlankAccnosFiles[h].c_str());
371 }else{ hasAccnos = false; }
373 if (m->control_pressed) {
374 remove(outputFileName.c_str());
375 remove(accnosFileName.c_str());
376 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
384 openInputFile(candidateFileNames[s], inFASTA);
385 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
387 lines.push_back(new linePair(0, numSeqs));
389 driver(lines[0], outputFileName, fastafile, accnosFileName);
391 if (m->control_pressed) {
392 remove(outputFileName.c_str());
393 remove(accnosFileName.c_str());
394 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
399 //delete accnos file if its blank
400 if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
406 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
408 m->mothurOutEndLine();
409 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
410 m->mothurOut(outputFileName); m->mothurOutEndLine();
411 if (hasAccnos) { m->mothurOut(accnosFileName); m->mothurOutEndLine(); }
412 m->mothurOutEndLine();
413 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
418 catch(exception& e) {
419 m->errorOut(e, "ChimeraPintailCommand", "execute");
423 //**********************************************************************************************************************
425 int ChimeraPintailCommand::driver(linePair* line, string outputFName, string filename, string accnos){
428 openOutputFile(outputFName, out);
431 openOutputFile(accnos, out2);
434 openInputFile(filename, inFASTA);
436 inFASTA.seekg(line->start);
438 for(int i=0;i<line->numSeqs;i++){
440 if (m->control_pressed) { return 1; }
442 Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
444 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
446 if (candidateSeq->getAligned().length() != templateSeqsLength) { //chimeracheck does not require seqs to be aligned
447 m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
450 chimera->getChimeras(candidateSeq);
452 if (m->control_pressed) { delete candidateSeq; return 1; }
455 chimera->print(out, out2);
461 if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine(); }
464 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine(); }
472 catch(exception& e) {
473 m->errorOut(e, "ChimeraPintailCommand", "driver");
477 //**********************************************************************************************************************
479 int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
484 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
486 for(int i=0;i<num;i++){
488 if (m->control_pressed) { return 1; }
491 int length = MPIPos[start+i+1] - MPIPos[start+i];
494 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
496 string tempBuf = buf4;
497 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
498 istringstream iss (tempBuf,istringstream::in);
500 Sequence* candidateSeq = new Sequence(iss); gobble(iss);
502 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
504 if (candidateSeq->getAligned().length() != templateSeqsLength) { //chimeracheck does not require seqs to be aligned
505 m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
508 chimera->getChimeras(candidateSeq);
510 if (m->control_pressed) { delete candidateSeq; return 1; }
513 bool isChimeric = chimera->print(outMPI, outAccMPI);
514 if (isChimeric) { MPIWroteAccnos = true; }
520 if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); }
523 if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); }
528 catch(exception& e) {
529 m->errorOut(e, "ChimeraPintailCommand", "driverMPI");
535 /**************************************************************************************************/
537 int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) {
539 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
541 // processIDS.resize(0);
543 //loop through and create all the processes you want
544 while (process != processors) {
548 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
551 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
553 }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
556 //force parent to wait until all the processes are done
557 for (int i=0;i<processors;i++) {
558 int temp = processIDS[i];
565 catch(exception& e) {
566 m->errorOut(e, "ChimeraPintailCommand", "createProcesses");
571 /**************************************************************************************************/