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"
12 #include "deconvolutecommand.h"
14 //**********************************************************************************************************************
15 vector<string> ChimeraSlayerCommand::getValidParameters(){
17 string AlignArray[] = {"fasta", "processors","trim", "name","window", "include","template","numwanted", "ksize", "match","mismatch",
18 "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
19 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
23 m->errorOut(e, "ChimeraSlayerCommand", "getValidParameters");
27 //**********************************************************************************************************************
28 ChimeraSlayerCommand::ChimeraSlayerCommand(){
30 vector<string> tempOutNames;
31 outputTypes["chimera"] = tempOutNames;
32 outputTypes["accnos"] = tempOutNames;
33 outputTypes["fasta"] = tempOutNames;
36 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
40 //**********************************************************************************************************************
41 vector<string> ChimeraSlayerCommand::getRequiredParameters(){
43 string AlignArray[] = {"template","fasta"};
44 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
48 m->errorOut(e, "ChimeraSlayerCommand", "getRequiredParameters");
52 //**********************************************************************************************************************
53 vector<string> ChimeraSlayerCommand::getRequiredFiles(){
55 vector<string> myArray;
59 m->errorOut(e, "ChimeraSlayerCommand", "getRequiredFiles");
63 //***************************************************************************************************************
64 ChimeraSlayerCommand::ChimeraSlayerCommand(string option) {
68 //allow user to run help
69 if(option == "help") { help(); abort = true; }
72 //valid paramters for this command
73 string Array[] = {"fasta", "processors","name", "include","trim", "window", "template","numwanted", "ksize", "match","mismatch",
74 "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
75 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
77 OptionParser parser(option);
78 map<string,string> parameters = parser.getParameters();
80 ValidParameters validParameter("chimera.slayer");
81 map<string,string>::iterator it;
83 //check to make sure all parameters are valid for command
84 for (it = parameters.begin(); it != parameters.end(); it++) {
85 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
88 vector<string> tempOutNames;
89 outputTypes["chimera"] = tempOutNames;
90 outputTypes["accnos"] = tempOutNames;
91 outputTypes["fasta"] = tempOutNames;
93 //if the user changes the input directory command factory will send this info to us in the output parameter
94 string inputDir = validParameter.validFile(parameters, "inputdir", false);
95 if (inputDir == "not found"){ inputDir = ""; }
97 //check for required parameters
98 fastafile = validParameter.validFile(parameters, "fasta", false);
99 if (fastafile == "not found") { fastafile = ""; m->mothurOut("[ERROR]: fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
101 m->splitAtDash(fastafile, fastaFileNames);
103 //go through files and make sure they are good, if not, then disregard them
104 for (int i = 0; i < fastaFileNames.size(); i++) {
105 if (inputDir != "") {
106 string path = m->hasPath(fastaFileNames[i]);
107 //if the user has not given a path then, add inputdir. else leave path alone.
108 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
114 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
116 //if you can't open it, try default location
117 if (ableToOpen == 1) {
118 if (m->getDefaultPath() != "") { //default path is set
119 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
120 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
122 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
124 fastaFileNames[i] = tryPath;
128 if (ableToOpen == 1) {
129 if (m->getOutputDir() != "") { //default path is set
130 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
131 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
133 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
135 fastaFileNames[i] = tryPath;
141 if (ableToOpen == 1) {
142 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
143 //erase from file list
144 fastaFileNames.erase(fastaFileNames.begin()+i);
149 //make sure there is at least one valid file left
150 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
154 //check for required parameters
156 namefile = validParameter.validFile(parameters, "name", false);
157 if (namefile == "not found") { namefile = ""; hasName = false; }
159 m->splitAtDash(namefile, nameFileNames);
161 //go through files and make sure they are good, if not, then disregard them
162 for (int i = 0; i < nameFileNames.size(); i++) {
163 if (inputDir != "") {
164 string path = m->hasPath(nameFileNames[i]);
165 //if the user has not given a path then, add inputdir. else leave path alone.
166 if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; }
172 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
174 //if you can't open it, try default location
175 if (ableToOpen == 1) {
176 if (m->getDefaultPath() != "") { //default path is set
177 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
178 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
180 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
182 nameFileNames[i] = tryPath;
186 if (ableToOpen == 1) {
187 if (m->getOutputDir() != "") { //default path is set
188 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
189 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
191 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
193 nameFileNames[i] = tryPath;
199 if (ableToOpen == 1) {
200 m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
201 //erase from file list
202 nameFileNames.erase(nameFileNames.begin()+i);
207 //make sure there is at least one valid file left
208 if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
211 if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
213 //if the user changes the output directory command factory will send this info to us in the output parameter
214 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
218 it = parameters.find("template");
219 //user has given a template file
220 if(it != parameters.end()){
221 if (it->second == "self") { templatefile = "self"; }
223 path = m->hasPath(it->second);
224 //if the user has not given a path then, add inputdir. else leave path alone.
225 if (path == "") { parameters["template"] = inputDir + it->second; }
227 templatefile = validParameter.validFile(parameters, "template", true);
228 if (templatefile == "not open") { abort = true; }
229 else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
233 string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
234 convert(temp, processors);
236 includeAbunds = validParameter.validFile(parameters, "include", false); if (includeAbunds == "not found") { includeAbunds = "greater"; }
237 if ((includeAbunds != "greater") && (includeAbunds != "greaterequal") && (includeAbunds != "all")) { includeAbunds = "greater"; m->mothurOut("Invalid include setting. options are greater, greaterequal or all. using greater."); m->mothurOutEndLine(); }
239 temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
240 convert(temp, ksize);
242 temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; }
243 convert(temp, window);
245 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; }
246 convert(temp, match);
248 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
249 convert(temp, mismatch);
251 temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
254 temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
255 convert(temp, minSimilarity);
257 temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
258 convert(temp, minCoverage);
260 temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
261 convert(temp, minBS);
263 temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "100"; }
264 convert(temp, minSNP);
266 temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
267 convert(temp, parents);
269 temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; }
270 realign = m->isTrue(temp);
272 temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
273 trim = m->isTrue(temp);
275 search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
277 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
278 convert(temp, iters);
280 temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
281 convert(temp, increment);
283 temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
284 convert(temp, numwanted);
286 if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
289 catch(exception& e) {
290 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
294 //**********************************************************************************************************************
296 void ChimeraSlayerCommand::help(){
299 m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
300 m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
301 m->mothurOut("The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
302 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
303 m->mothurOut("The name parameter allows you to provide a name file, if you are using template=self. \n");
304 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n");
305 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n");
306 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
308 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
310 m->mothurOut("The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest peice, default=F. \n");
311 m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
312 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
313 m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
314 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n");
315 m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n");
316 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");
317 m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n");
318 m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n");
319 m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n");
320 m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
321 m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
322 m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
323 m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n");
324 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");
325 m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n");
326 m->mothurOut("The chimera.slayer command should be in the following format: \n");
327 m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
328 m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
329 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
331 catch(exception& e) {
332 m->errorOut(e, "ChimeraSlayerCommand", "help");
337 //***************************************************************************************************************
339 ChimeraSlayerCommand::~ChimeraSlayerCommand(){ /* do nothing */ }
341 //***************************************************************************************************************
343 int ChimeraSlayerCommand::execute(){
346 if (abort == true) { return 0; }
348 for (int s = 0; s < fastaFileNames.size(); s++) {
350 m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
352 int start = time(NULL);
354 if (templatefile != "self") { //you want to run slayer with a refernce template
355 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
357 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
358 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFileNames[s], search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
361 m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
363 //use unique.seqs to create new name and fastafile
364 string inputString = "fasta=" + fastaFileNames[s];
365 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
366 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
368 Command* uniqueCommand = new DeconvoluteCommand(inputString);
369 uniqueCommand->execute();
371 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
373 delete uniqueCommand;
375 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
377 string nameFile = filenames["name"][0];
378 fastaFileNames[s] = filenames["fasta"][0];
380 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFile, search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
384 if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
385 string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
386 string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.accnos";
387 string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.fasta";
389 if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
391 if (chimera->getUnaligned()) {
392 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
396 templateSeqsLength = chimera->getLength();
399 int pid, numSeqsPerProcessor;
401 vector<unsigned long int> MPIPos;
404 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
405 MPI_Comm_size(MPI_COMM_WORLD, &processors);
409 MPI_File outMPIAccnos;
410 MPI_File outMPIFasta;
412 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
413 int inMode=MPI_MODE_RDONLY;
415 char outFilename[1024];
416 strcpy(outFilename, outputFileName.c_str());
418 char outAccnosFilename[1024];
419 strcpy(outAccnosFilename, accnosFileName.c_str());
421 char outFastaFilename[1024];
422 strcpy(outFastaFilename, trimFastaFileName.c_str());
424 char inFileName[1024];
425 strcpy(inFileName, fastaFileNames[s].c_str());
427 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
428 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
429 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
430 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
432 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
434 if (pid == 0) { //you are the root process
435 m->mothurOutEndLine();
436 m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
437 m->mothurOutEndLine();
439 string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
442 int length = outTemp.length();
443 char* buf2 = new char[length];
444 memcpy(buf2, outTemp.c_str(), length);
446 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
449 MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
451 //send file positions to all processes
452 for(int i = 1; i < processors; i++) {
453 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
454 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
457 //figure out how many sequences you have to align
458 numSeqsPerProcessor = numSeqs / processors;
459 int startIndex = pid * numSeqsPerProcessor;
460 if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
463 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
465 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } 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; }
467 }else{ //you are a child process
468 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
469 MPIPos.resize(numSeqs+1);
470 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
472 //figure out how many sequences you have to align
473 numSeqsPerProcessor = numSeqs / processors;
474 int startIndex = pid * numSeqsPerProcessor;
475 if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
478 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
480 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
484 MPI_File_close(&inMPI);
485 MPI_File_close(&outMPI);
486 MPI_File_close(&outMPIAccnos);
487 if (trim) { MPI_File_close(&outMPIFasta); }
488 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
492 string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
493 m->openOutputFile(tempHeader, outHeader);
495 chimera->printHeader(outHeader);
498 vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
500 for (int i = 0; i < (positions.size()-1); i++) {
501 lines.push_back(new linePair(positions[i], positions[(i+1)]));
505 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
507 numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
509 if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
512 processIDS.resize(0);
514 numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
516 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
517 rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
518 if (trim) { rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
520 //append output files
521 for(int i=1;i<processors;i++){
522 m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
523 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
526 //append output files
527 for(int i=1;i<processors;i++){
528 m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
529 remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
533 for(int i=1;i<processors;i++){
534 m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
535 remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str());
539 if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
543 numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
545 if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
549 m->appendFiles(outputFileName, tempHeader);
551 remove(outputFileName.c_str());
552 rename(tempHeader.c_str(), outputFileName.c_str());
558 for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
560 outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
561 outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
562 if (trim) { outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
564 m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
567 m->mothurOutEndLine();
568 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
569 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
570 m->mothurOutEndLine();
575 catch(exception& e) {
576 m->errorOut(e, "ChimeraSlayerCommand", "execute");
580 //**********************************************************************************************************************
582 int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){
585 m->openOutputFile(outputFName, out);
588 m->openOutputFile(accnos, out2);
591 if (trim) { m->openOutputFile(fasta, out3); }
594 m->openInputFile(filename, inFASTA);
596 inFASTA.seekg(filePos->start);
603 if (m->control_pressed) { out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1; }
605 Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
607 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
609 if (candidateSeq->getAligned().length() != templateSeqsLength) {
610 m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
613 chimera->getChimeras(candidateSeq);
615 if (m->control_pressed) { delete candidateSeq; return 1; }
618 Sequence* trimmed = chimera->print(out, out2);
620 if (trim) { trimmed->printSequence(out3); delete trimmed; }
626 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
627 unsigned long int pos = inFASTA.tellg();
628 if ((pos == -1) || (pos >= filePos->end)) { break; }
630 if (inFASTA.eof()) { break; }
634 if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
637 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
641 if (trim) { out3.close(); }
646 catch(exception& e) {
647 m->errorOut(e, "ChimeraSlayerCommand", "driver");
651 //**********************************************************************************************************************
653 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
657 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
659 for(int i=0;i<num;i++){
661 if (m->control_pressed) { return 1; }
664 int length = MPIPos[start+i+1] - MPIPos[start+i];
666 char* buf4 = new char[length];
667 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
669 string tempBuf = buf4;
670 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
671 istringstream iss (tempBuf,istringstream::in);
675 Sequence* candidateSeq = new Sequence(iss); m->gobble(iss);
677 if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
679 if (candidateSeq->getAligned().length() != templateSeqsLength) {
680 m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
684 chimera->getChimeras(candidateSeq);
686 if (m->control_pressed) { delete candidateSeq; return 1; }
689 Sequence* trimmed = chimera->print(outMPI, outAccMPI);
692 string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
695 //write to accnos file
696 int length = outputString.length();
697 char* buf2 = new char[length];
698 memcpy(buf2, outputString.c_str(), length);
700 MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
709 if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); }
712 if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); }
717 catch(exception& e) {
718 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
724 /**************************************************************************************************/
726 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) {
728 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
732 //loop through and create all the processes you want
733 while (process != processors) {
737 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
740 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp");
742 //pass numSeqs to parent
744 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
745 m->openOutputFile(tempFile, out);
751 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
752 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
757 //force parent to wait until all the processes are done
758 for (int i=0;i<processors;i++) {
759 int temp = processIDS[i];
763 for (int i = 0; i < processIDS.size(); i++) {
765 string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp";
766 m->openInputFile(tempFile, in);
767 if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
768 in.close(); remove(tempFile.c_str());
774 catch(exception& e) {
775 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
780 /**************************************************************************************************/