2 * preclustercommand.cpp
5 * Created by westcott on 12/21/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
10 #include "preclustercommand.h"
11 #include "deconvolutecommand.h"
13 //**********************************************************************************************************************
14 vector<string> PreClusterCommand::setParameters(){
16 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
17 CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
18 CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
19 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
20 CommandParameter pdiffs("diffs", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pdiffs);
21 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
22 CommandParameter ptopdown("topdown", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptopdown);
24 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
25 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
27 vector<string> myArray;
28 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
32 m->errorOut(e, "PreClusterCommand", "setParameters");
36 //**********************************************************************************************************************
37 string PreClusterCommand::getHelpString(){
39 string helpString = "";
40 helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n";
41 helpString += "The pre.cluster command outputs a new fasta and name file.\n";
42 helpString += "The pre.cluster command parameters are fasta, name, group, count, topdown, processors and diffs. The fasta parameter is required. \n";
43 helpString += "The name parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n";
44 helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n";
45 helpString += "The count parameter allows you to provide a count file so you can cluster by group. \n";
46 helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
47 helpString += "The topdown parameter allows you to specify whether to cluster from largest abundance to smallest or smallest to largest. Default=T, meaning largest to smallest.\n";
48 helpString += "The pre.cluster command should be in the following format: \n";
49 helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
50 helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
51 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
55 m->errorOut(e, "PreClusterCommand", "getHelpString");
59 //**********************************************************************************************************************
60 string PreClusterCommand::getOutputPattern(string type) {
64 if (type == "fasta") { pattern = "[filename],precluster,[extension]"; }
65 else if (type == "name") { pattern = "[filename],precluster.names"; }
66 else if (type == "count") { pattern = "[filename],precluster.count_table"; }
67 else if (type == "map") { pattern = "[filename],precluster.map"; }
68 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
73 m->errorOut(e, "PreClusterCommand", "getOutputPattern");
77 //**********************************************************************************************************************
78 PreClusterCommand::PreClusterCommand(){
80 abort = true; calledHelp = true;
82 vector<string> tempOutNames;
83 outputTypes["fasta"] = tempOutNames;
84 outputTypes["name"] = tempOutNames;
85 outputTypes["count"] = tempOutNames;
86 outputTypes["map"] = tempOutNames;
89 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
93 //**********************************************************************************************************************
95 PreClusterCommand::PreClusterCommand(string option) {
97 abort = false; calledHelp = false;
99 //allow user to run help
100 if(option == "help") { help(); abort = true; calledHelp = true; }
101 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
104 vector<string> myArray = setParameters();
106 OptionParser parser(option);
107 map<string, string> parameters = parser.getParameters();
109 ValidParameters validParameter;
110 map<string, string>::iterator it;
112 //check to make sure all parameters are valid for command
113 for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
114 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
117 //initialize outputTypes
118 vector<string> tempOutNames;
119 outputTypes["fasta"] = tempOutNames;
120 outputTypes["name"] = tempOutNames;
121 outputTypes["map"] = tempOutNames;
122 outputTypes["count"] = tempOutNames;
124 //if the user changes the input directory command factory will send this info to us in the output parameter
125 string inputDir = validParameter.validFile(parameters, "inputdir", false);
126 if (inputDir == "not found"){ inputDir = ""; }
129 it = parameters.find("fasta");
130 //user has given a template file
131 if(it != parameters.end()){
132 path = m->hasPath(it->second);
133 //if the user has not given a path then, add inputdir. else leave path alone.
134 if (path == "") { parameters["fasta"] = inputDir + it->second; }
137 it = parameters.find("name");
138 //user has given a template file
139 if(it != parameters.end()){
140 path = m->hasPath(it->second);
141 //if the user has not given a path then, add inputdir. else leave path alone.
142 if (path == "") { parameters["name"] = inputDir + it->second; }
145 it = parameters.find("group");
146 //user has given a template file
147 if(it != parameters.end()){
148 path = m->hasPath(it->second);
149 //if the user has not given a path then, add inputdir. else leave path alone.
150 if (path == "") { parameters["group"] = inputDir + it->second; }
153 it = parameters.find("count");
154 //user has given a template file
155 if(it != parameters.end()){
156 path = m->hasPath(it->second);
157 //if the user has not given a path then, add inputdir. else leave path alone.
158 if (path == "") { parameters["count"] = inputDir + it->second; }
162 //check for required parameters
163 fastafile = validParameter.validFile(parameters, "fasta", true);
164 if (fastafile == "not found") {
165 fastafile = m->getFastaFile();
166 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
167 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
169 else if (fastafile == "not open") { abort = true; }
170 else { m->setFastaFile(fastafile); }
172 //if the user changes the output directory command factory will send this info to us in the output parameter
173 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
175 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
178 //check for optional parameter and set defaults
179 // ...at some point should added some additional type checking...
180 namefile = validParameter.validFile(parameters, "name", true);
181 if (namefile == "not found") { namefile = ""; }
182 else if (namefile == "not open") { namefile = ""; abort = true; }
183 else { m->setNameFile(namefile); }
185 groupfile = validParameter.validFile(parameters, "group", true);
186 if (groupfile == "not found") { groupfile = ""; bygroup = false; }
187 else if (groupfile == "not open") { abort = true; groupfile = ""; }
188 else { m->setGroupFile(groupfile); bygroup = true; }
190 countfile = validParameter.validFile(parameters, "count", true);
191 if (countfile == "not found") { countfile = ""; }
192 else if (countfile == "not open") { abort = true; countfile = ""; }
194 m->setCountTableFile(countfile);
195 ct.readTable(countfile, true, false);
196 if (ct.hasGroupInfo()) { bygroup = true; }
197 else { bygroup = false; }
200 if ((namefile != "") && (countfile != "")) {
201 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
204 if ((groupfile != "") && (countfile != "")) {
205 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
209 string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
210 m->mothurConvert(temp, diffs);
212 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
213 m->setProcessors(temp);
214 m->mothurConvert(temp, processors);
216 temp = validParameter.validFile(parameters, "topdown", false); if(temp == "not found"){ temp = "T"; }
217 topdown = m->isTrue(temp);
219 if (countfile == "") {
220 if (namefile == "") {
221 vector<string> files; files.push_back(fastafile);
222 parser.getNameFile(files);
228 catch(exception& e) {
229 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
233 //**********************************************************************************************************************
235 int PreClusterCommand::execute(){
238 if (abort == true) { if (calledHelp) { return 0; } return 2; }
240 int start = time(NULL);
242 string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
243 map<string, string> variables;
244 variables["[filename]"] = fileroot;
245 string newNamesFile = getOutputFileName("name",variables);
246 string newCountFile = getOutputFileName("count",variables);
247 string newMapFile = getOutputFileName("map",variables); //add group name if by group
248 variables["[extension]"] = m->getExtension(fastafile);
249 string newFastaFile = getOutputFileName("fasta", variables);
250 outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
251 if (countfile == "") { outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); }
252 else { outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile); }
255 //clear out old files
256 ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
257 ofstream outNames; m->openOutputFile(newNamesFile, outNames); outNames.close();
258 newMapFile = fileroot + "precluster.";
260 //parse fasta and name file by group
261 vector<string> groups;
262 if (countfile != "") {
263 cparser = new SequenceCountParser(countfile, fastafile);
264 groups = cparser->getNamesOfGroups();
266 if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile); }
267 else { parser = new SequenceParser(groupfile, fastafile); }
268 groups = parser->getNamesOfGroups();
271 if(processors == 1) { driverGroups(newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); }
272 else { createProcessesGroups(newFastaFile, newNamesFile, newMapFile, groups); }
274 if (countfile != "") {
275 mergeGroupCounts(newCountFile, newNamesFile, newFastaFile);
279 //run unique.seqs for deconvolute results
280 string inputString = "fasta=" + newFastaFile;
281 if (namefile != "") { inputString += ", name=" + newNamesFile; }
282 m->mothurOutEndLine();
283 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
284 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
285 m->mothurCalling = true;
287 Command* uniqueCommand = new DeconvoluteCommand(inputString);
288 uniqueCommand->execute();
290 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
292 delete uniqueCommand;
293 m->mothurCalling = false;
294 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
296 m->renameFile(filenames["fasta"][0], newFastaFile);
297 m->renameFile(filenames["name"][0], newNamesFile);
299 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
300 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
303 if (processors != 1) { m->mothurOut("When using running without group information mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
304 if (namefile != "") { readNameFile(); }
306 //reads fasta file and return number of seqs
307 int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
309 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
311 if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; }
312 if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; }
314 int count = process(newMapFile);
315 outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile);
317 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
319 m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
320 m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
321 if (countfile != "") { newNamesFile = newCountFile; }
322 printData(newFastaFile, newNamesFile, "");
324 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
327 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
329 m->mothurOutEndLine();
330 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
331 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
332 m->mothurOutEndLine();
334 //set fasta file as new current fastafile
336 itTypes = outputTypes.find("fasta");
337 if (itTypes != outputTypes.end()) {
338 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
341 itTypes = outputTypes.find("name");
342 if (itTypes != outputTypes.end()) {
343 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
346 itTypes = outputTypes.find("count");
347 if (itTypes != outputTypes.end()) {
348 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
354 catch(exception& e) {
355 m->errorOut(e, "PreClusterCommand", "execute");
359 /**************************************************************************************************/
360 int PreClusterCommand::createProcessesGroups(string newFName, string newNName, string newMFile, vector<string> groups) {
363 vector<int> processIDS;
368 if (groups.size() < processors) { processors = groups.size(); }
370 //divide the groups between the processors
371 vector<linePair> lines;
372 int remainingPairs = groups.size();
374 for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
375 int numPairs = remainingPairs; //case for last processor
376 if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
377 lines.push_back(linePair(startIndex, (startIndex+numPairs))); //startIndex, endIndex
378 startIndex = startIndex + numPairs;
379 remainingPairs = remainingPairs - numPairs;
382 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
384 //loop through and create all the processes you want
385 while (process != processors) {
389 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
393 num = driverGroups(newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
395 string tempFile = toString(getpid()) + ".outputNames.temp";
397 m->openOutputFile(tempFile, outTemp);
399 outTemp << outputNames.size();
400 for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
405 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
406 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
412 num = driverGroups(newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
414 //force parent to wait until all the processes are done
415 for (int i=0;i<processIDS.size();i++) {
416 int temp = processIDS[i];
420 for (int i = 0; i < processIDS.size(); i++) {
421 string tempFile = toString(processIDS[i]) + ".outputNames.temp";
423 m->openInputFile(tempFile, intemp);
427 for (int k = 0; k < num; k++) {
429 intemp >> name; m->gobble(intemp);
431 outputNames.push_back(name); outputTypes["map"].push_back(name);
434 m->mothurRemove(tempFile);
438 //////////////////////////////////////////////////////////////////////////////////////////////////////
439 //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
440 //Above fork() will clone, so memory is separate, but that's not the case with windows,
441 //////////////////////////////////////////////////////////////////////////////////////////////////////
443 vector<preClusterData*> pDataArray;
444 DWORD dwThreadIdArray[processors-1];
445 HANDLE hThreadArray[processors-1];
447 //Create processor worker threads.
448 for( int i=1; i<processors; i++ ){
449 // Allocate memory for thread data.
450 string extension = toString(i) + ".temp";
452 preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, topdown, i);
453 pDataArray.push_back(tempPreCluster);
454 processIDS.push_back(i);
456 //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
457 //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
458 hThreadArray[i-1] = CreateThread(NULL, 0, MyPreclusterThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
462 //using the main process as a worker saves time and memory
463 num = driverGroups(newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
465 //Wait until all threads have terminated.
466 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
468 //Close all thread handles and free memory allocations.
469 for(int i=0; i < pDataArray.size(); i++){
470 if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
471 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
473 for (int j = 0; j < pDataArray[i]->mapFileNames.size(); j++) {
474 outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]);
476 CloseHandle(hThreadArray[i]);
477 delete pDataArray[i];
482 //append output files
483 for(int i=0;i<processIDS.size();i++){
484 //newFName = m->getFullPathName(".\\" + newFName);
485 //newNName = m->getFullPathName(".\\" + newNName);
487 m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
488 m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
490 m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
491 m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
497 catch(exception& e) {
498 m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
502 /**************************************************************************************************/
503 int PreClusterCommand::driverGroups(string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
508 //precluster each group
509 for (int i = start; i < end; i++) {
513 if (m->control_pressed) { return 0; }
515 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
517 map<string, string> thisNameMap;
518 vector<Sequence> thisSeqs;
519 if (groupfile != "") {
520 thisSeqs = parser->getSeqs(groups[i]);
521 }else if (countfile != "") {
522 thisSeqs = cparser->getSeqs(groups[i]);
524 if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
526 //fill alignSeqs with this groups info.
527 numSeqs = loadSeqs(thisNameMap, thisSeqs, groups[i]);
529 if (m->control_pressed) { return 0; }
531 if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
533 int count= process(newMFile+groups[i]+".map");
534 outputNames.push_back(newMFile+groups[i]+".map"); outputTypes["map"].push_back(newMFile+groups[i]+".map");
536 if (m->control_pressed) { return 0; }
538 m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
539 m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
540 printData(newFFile, newNFile, groups[i]);
542 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
548 catch(exception& e) {
549 m->errorOut(e, "PreClusterCommand", "driverGroups");
553 /**************************************************************************************************/
554 int PreClusterCommand::process(string newMapFile){
557 m->openOutputFile(newMapFile, out);
559 //sort seqs by number of identical seqs
560 if (topdown) { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityTopDown); }
561 else { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityDownTop); }
564 int numSeqs = alignSeqs.size();
567 //think about running through twice...
568 for (int i = 0; i < numSeqs; i++) {
570 if (alignSeqs[i].active) { //this sequence has not been merged yet
572 string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
574 //try to merge it with all smaller seqs
575 for (int j = i+1; j < numSeqs; j++) {
577 if (m->control_pressed) { out.close(); return 0; }
579 if (alignSeqs[j].active) { //this sequence has not been merged yet
580 //are you within "diff" bases
581 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
583 if (mismatch <= diffs) {
585 alignSeqs[i].names += ',' + alignSeqs[j].names;
586 alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
588 chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
590 alignSeqs[j].active = 0;
591 alignSeqs[j].numIdentical = 0;
597 //remove from active list
598 alignSeqs[i].active = 0;
600 out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
603 if(i % 100 == 0) { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); }
606 map<int, string> mapFile;
607 map<int, int> originalCount;
608 map<int, int>::iterator itCount;
609 for (int i = 0; i < numSeqs; i++) { mapFile[i] = ""; originalCount[i] = alignSeqs[i].numIdentical; }
611 //think about running through twice...
612 for (int i = 0; i < numSeqs; i++) {
614 //try to merge it into larger seqs
615 for (int j = i+1; j < numSeqs; j++) {
617 if (m->control_pressed) { out.close(); return 0; }
619 if (originalCount[j] > originalCount[i]) { //this sequence is more abundant than I am
620 //are you within "diff" bases
621 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
623 if (mismatch <= diffs) {
625 alignSeqs[j].names += ',' + alignSeqs[i].names;
626 alignSeqs[j].numIdentical += alignSeqs[i].numIdentical;
628 mapFile[j] = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[i].seq.getAligned() + "\n" + mapFile[i];
629 alignSeqs[i].numIdentical = 0;
630 originalCount.erase(i);
633 j+=numSeqs; //exit search, we merged this one in.
635 }//end abundance check
638 if(i % 100 == 0) { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); }
641 for (int i = 0; i < numSeqs; i++) {
642 if (alignSeqs[i].numIdentical != 0) {
643 out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n" << mapFile[i] << endl;
650 if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
655 catch(exception& e) {
656 m->errorOut(e, "PreClusterCommand", "process");
660 /**************************************************************************************************/
661 int PreClusterCommand::readFASTA(){
666 m->openInputFile(fastafile, inFasta);
669 while (!inFasta.eof()) {
671 if (m->control_pressed) { inFasta.close(); return 0; }
673 Sequence seq(inFasta); m->gobble(inFasta);
675 if (seq.getName() != "") { //can get "" if commented line is at end of fasta file
676 if (namefile != "") {
677 itSize = sizes.find(seq.getName());
679 if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
681 seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
682 alignSeqs.push_back(tempNode);
683 lengths.insert(seq.getAligned().length());
685 }else { //no names file, you are identical to yourself
687 if (countfile != "") { numRep = ct.getNumSeqs(seq.getName()); }
688 seqPNode tempNode(numRep, seq, seq.getName());
689 alignSeqs.push_back(tempNode);
690 lengths.insert(seq.getAligned().length());
696 if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
697 else if (lengths.size() == 1) { length = *(lengths.begin()); }
699 return alignSeqs.size();
702 catch(exception& e) {
703 m->errorOut(e, "PreClusterCommand", "readFASTA");
707 /**************************************************************************************************/
708 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs, string group){
712 map<string, string>::iterator it;
714 map<string, int> thisCount;
715 if (countfile != "") { thisCount = cparser->getCountTable(group); }
717 for (int i = 0; i < thisSeqs.size(); i++) {
719 if (m->control_pressed) { return 0; }
721 if (namefile != "") {
722 it = thisName.find(thisSeqs[i].getName());
724 //should never be true since parser checks for this
725 if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
729 for(int j=0;j<(it->second).length();j++){
730 if((it->second)[j] == ','){ numReps++; }
733 seqPNode tempNode(numReps, thisSeqs[i], it->second);
734 alignSeqs.push_back(tempNode);
735 lengths.insert(thisSeqs[i].getAligned().length());
737 }else { //no names file, you are identical to yourself
739 if (countfile != "") {
740 map<string, int>::iterator it2 = thisCount.find(thisSeqs[i].getName());
742 //should never be true since parser checks for this
743 if (it2 == thisCount.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); error = true; }
744 else { numRep = it2->second; }
746 seqPNode tempNode(numRep, thisSeqs[i], thisSeqs[i].getName());
747 alignSeqs.push_back(tempNode);
748 lengths.insert(thisSeqs[i].getAligned().length());
752 if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
753 else if (lengths.size() == 1) { length = *(lengths.begin()); }
756 if (error) { m->control_pressed = true; }
760 return alignSeqs.size();
763 catch(exception& e) {
764 m->errorOut(e, "PreClusterCommand", "loadSeqs");
769 /**************************************************************************************************/
771 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
775 for (int i = 0; i < seq1.length(); i++) {
777 if (seq1[i] != seq2[i]) { numBad++; }
778 if (numBad > diffs) { return length; } //to far to cluster
783 catch(exception& e) {
784 m->errorOut(e, "PreClusterCommand", "calcMisMatches");
788 /**************************************************************************************************/
790 int PreClusterCommand::mergeGroupCounts(string newcount, string newname, string newfasta){
793 m->openInputFile(newname, inNames);
795 string group, first, second;
796 set<string> uniqueNames;
797 while (!inNames.eof()) {
798 if (m->control_pressed) { break; }
799 inNames >> group; m->gobble(inNames);
800 inNames >> first; m->gobble(inNames);
801 inNames >> second; m->gobble(inNames);
803 vector<string> names;
804 m->splitAtComma(second, names);
806 uniqueNames.insert(first);
808 int total = ct.getGroupCount(first, group);
809 for (int i = 1; i < names.size(); i++) {
810 total += ct.getGroupCount(names[i], group);
811 ct.setAbund(names[i], group, 0);
813 ct.setAbund(first, group, total);
817 vector<string> namesOfSeqs = ct.getNamesOfSeqs();
818 for (int i = 0; i < namesOfSeqs.size(); i++) {
819 if (ct.getNumSeqs(namesOfSeqs[i]) == 0) {
820 ct.remove(namesOfSeqs[i]);
824 ct.printTable(newcount);
825 m->mothurRemove(newname);
827 if (bygroup) { //if by group, must remove the duplicate seqs that are named the same
829 m->openInputFile(newfasta, in);
832 m->openOutputFile(newfasta+"temp", out);
837 if (m->control_pressed) { break; }
839 Sequence seq(in); m->gobble(in);
841 if (seq.getName() != "") {
843 if (already.count(seq.getName()) == 0) {
844 seq.printSequence(out);
845 already.insert(seq.getName());
851 m->mothurRemove(newfasta);
852 m->renameFile(newfasta+"temp", newfasta);
857 catch(exception& e) {
858 m->errorOut(e, "PreClusterCommand", "mergeGroupCounts");
863 /**************************************************************************************************/
865 void PreClusterCommand::printData(string newfasta, string newname, string group){
871 m->openOutputFileAppend(newfasta, outFasta);
872 m->openOutputFileAppend(newname, outNames);
874 m->openOutputFile(newfasta, outFasta);
875 m->openOutputFile(newname, outNames);
878 if ((countfile != "") && (group == "")) { outNames << "Representative_Sequence\ttotal\n"; }
879 for (int i = 0; i < alignSeqs.size(); i++) {
880 if (alignSeqs[i].numIdentical != 0) {
881 alignSeqs[i].seq.printSequence(outFasta);
882 if (countfile != "") {
883 if (group != "") { outNames << group << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
884 else { outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].numIdentical << endl; }
885 }else { outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
893 catch(exception& e) {
894 m->errorOut(e, "PreClusterCommand", "printData");
898 /**************************************************************************************************/
900 void PreClusterCommand::readNameFile(){
903 m->openInputFile(namefile, in);
904 string firstCol, secondCol;
907 in >> firstCol >> secondCol; m->gobble(in);
909 m->checkName(firstCol);
910 m->checkName(secondCol);
911 int size = m->getNumNames(secondCol);
913 names[firstCol] = secondCol;
914 sizes[firstCol] = size;
918 catch(exception& e) {
919 m->errorOut(e, "PreClusterCommand", "readNameFile");
924 /**************************************************************************************************/