2 * consensusseqscommand.cpp
5 * Created by westcott on 11/23/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "consensusseqscommand.h"
11 #include "sequence.hpp"
12 #include "inputdata.h"
14 //**********************************************************************************************************************
15 vector<string> ConsensusSeqsCommand::setParameters(){
17 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
18 CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
19 CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
20 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","fasta-name",false,false,true); parameters.push_back(plist);
21 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
22 CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pcutoff);
23 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
24 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
26 vector<string> myArray;
27 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
31 m->errorOut(e, "ConsensusSeqsCommand", "setParameters");
35 //**********************************************************************************************************************
36 string ConsensusSeqsCommand::getHelpString(){
38 string helpString = "";
39 helpString += "The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n";
40 helpString += "The consensus.seqs command parameters are fasta, list, name, count, cutoff and label.\n";
41 helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
42 helpString += "The list parameter allows you to enter a your list file. \n";
43 helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
44 helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
45 helpString += "The cutoff parameter allows you set a percentage of sequences that support the base. For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.\n";
46 helpString += "The consensus.seqs command should be in the following format: \n";
47 helpString += "consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n";
48 helpString += "Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n";
49 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
53 m->errorOut(e, "ConsensusSeqsCommand", "getHelpString");
57 //**********************************************************************************************************************
58 string ConsensusSeqsCommand::getOutputPattern(string type) {
62 if (type == "fasta") { pattern = "[filename],cons.fasta-[filename],[tag],cons.fasta"; }
63 else if (type == "name") { pattern = "[filename],cons.names-[filename],[tag],cons.names"; }
64 else if (type == "count") { pattern = "[filename],cons.count_table-[filename],[tag],cons.count_table"; }
65 else if (type == "summary") { pattern = "[filename],cons.summary-[filename],[tag],cons.summary"; }
66 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
71 m->errorOut(e, "ConsensusSeqsCommand", "getOutputPattern");
75 //**********************************************************************************************************************
76 ConsensusSeqsCommand::ConsensusSeqsCommand(){
78 abort = true; calledHelp = true;
80 vector<string> tempOutNames;
81 outputTypes["fasta"] = tempOutNames;
82 outputTypes["name"] = tempOutNames;
83 outputTypes["count"] = tempOutNames;
84 outputTypes["summary"] = tempOutNames;
87 m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
91 //***************************************************************************************************************
92 ConsensusSeqsCommand::ConsensusSeqsCommand(string option) {
94 abort = false; calledHelp = false;
97 //allow user to run help
98 if(option == "help") { help(); abort = true; calledHelp = true; }
99 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
103 vector<string> myArray = setParameters();
105 OptionParser parser(option);
106 map<string,string> parameters = parser.getParameters();
108 ValidParameters validParameter;
109 map<string,string>::iterator it;
111 //check to make sure all parameters are valid for command
112 for (it = parameters.begin(); it != parameters.end(); it++) {
113 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
116 //initialize outputTypes
117 vector<string> tempOutNames;
118 outputTypes["fasta"] = tempOutNames;
119 outputTypes["name"] = tempOutNames;
120 outputTypes["count"] = tempOutNames;
121 outputTypes["summary"] = 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("list");
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["list"] = 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; }
163 //check for parameters
164 fastafile = validParameter.validFile(parameters, "fasta", true);
165 if (fastafile == "not open") { abort = true; }
166 else if (fastafile == "not found") {
167 fastafile = m->getFastaFile();
168 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
169 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
170 }else { m->setFastaFile(fastafile); }
172 namefile = validParameter.validFile(parameters, "name", true);
173 if (namefile == "not open") { namefile = ""; abort = true; }
174 else if (namefile == "not found") { namefile = ""; }
175 else { m->setNameFile(namefile); }
177 countfile = validParameter.validFile(parameters, "count", true);
178 if (countfile == "not open") { abort = true; countfile = ""; }
179 else if (countfile == "not found") { countfile = ""; }
180 else { m->setCountTableFile(countfile); }
182 if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
184 listfile = validParameter.validFile(parameters, "list", true);
185 if (listfile == "not open") { abort = true; }
186 else if (listfile == "not found") { listfile = ""; }
187 else { m->setListFile(listfile); }
189 label = validParameter.validFile(parameters, "label", false);
190 if (label == "not found") { label = ""; }
192 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
193 else { allLines = 1; }
196 string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
197 m->mothurConvert(temp, cutoff);
199 //if the user changes the output directory command factory will send this info to us in the output parameter
200 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
202 if (countfile == "") {
204 vector<string> files; files.push_back(fastafile);
205 parser.getNameFile(files);
210 catch(exception& e) {
211 m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
215 //***************************************************************************************************************
217 int ConsensusSeqsCommand::execute(){
220 if (abort == true) { if (calledHelp) { return 0; } return 2; }
222 int start = time(NULL);
226 if (m->control_pressed) { return 0; }
228 if (namefile != "") { readNames(); }
229 if (countfile != "") { ct.readTable(countfile, true, false); }
231 if (m->control_pressed) { return 0; }
234 if (listfile == "") {
237 map<string, string> variables;
238 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
239 string outputSummaryFile = getOutputFileName("summary", variables);
240 m->openOutputFile(outputSummaryFile, outSummary);
241 outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
242 outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
244 outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
247 string outputFastaFile = getOutputFileName("fasta", variables);
248 m->openOutputFile(outputFastaFile, outFasta);
249 outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
251 vector< vector<float> > percentages; percentages.resize(5);
252 for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
257 for (int j = 0; j < seqLength; j++) {
259 if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
261 vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
264 for (map<string, string>::iterator it = fastaMap.begin(); it != fastaMap.end(); it++) {
266 string thisSeq = it->second;
269 if (countfile != "") { size = ct.getNumSeqs(it->first); }
271 map<string, int>::iterator itCount = nameFileMap.find(it->first);
272 if (itCount != nameFileMap.end()) {
273 size = itCount->second;
274 }else { m->mothurOut("[ERROR]: file mismatch, aborting.\n"); m->control_pressed = true; break; }
277 for (int k = 0; k < size; k++) {
278 if (thisSeq[j] == '.') { numDots++; }
280 char base = toupper(thisSeq[j]);
281 if (base == 'A') { counts[0]++; }
282 else if (base == 'T') { counts[1]++; }
283 else if (base == 'G') { counts[2]++; }
284 else if (base == 'C') { counts[3]++; }
285 else { counts[4]++; }
291 if (numDots != thisCount) { conBase = getBase(counts, thisCount); }
295 percentages[0][j] = counts[0] / (float) thisCount;
296 percentages[1][j] = counts[1] / (float) thisCount;
297 percentages[2][j] = counts[2] / (float) thisCount;
298 percentages[3][j] = counts[3] / (float) thisCount;
299 percentages[4][j] = counts[4] / (float) thisCount;
302 for (int j = 0; j < seqLength; j++) {
303 outSummary << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << thisCount << '\t' << consSeq[j] << endl;
307 outFasta << ">conseq" << endl << consSeq << endl;
309 outSummary.close(); outFasta.close();
311 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
316 InputData* input = new InputData(listfile, "list");
317 ListVector* list = input->getListVector();
319 string lastLabel = list->getLabel();
320 set<string> processedLabels;
321 set<string> userLabels = labels;
323 //as long as you are not at the end of the file or done wih the lines you want
324 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
326 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; delete input; return 0; }
328 if(allLines == 1 || labels.count(list->getLabel()) == 1){
330 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
334 processedLabels.insert(list->getLabel());
335 userLabels.erase(list->getLabel());
338 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
339 string saveLabel = list->getLabel();
343 list = input->getListVector(lastLabel);
344 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
348 processedLabels.insert(list->getLabel());
349 userLabels.erase(list->getLabel());
351 //restore real lastlabel to save below
352 list->setLabel(saveLabel);
355 lastLabel = list->getLabel();
357 delete list; list = NULL;
359 //get next line to process
360 list = input->getListVector();
364 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } if (list != NULL) { delete list; } delete input; return 0; }
366 //output error messages about any remaining user labels
367 set<string>::iterator it;
368 bool needToRun = false;
369 for (it = userLabels.begin(); it != userLabels.end(); it++) {
370 m->mothurOut("Your file does not include the label " + *it);
371 if (processedLabels.count(lastLabel) != 1) {
372 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
375 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
379 //run last label if you need to
380 if (needToRun == true) {
381 if (list != NULL) { delete list; }
383 list = input->getListVector(lastLabel);
385 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
389 delete list; list = NULL;
392 if (list != NULL) { delete list; }
396 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the consensus sequences.");
398 m->mothurOutEndLine();
399 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
400 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
401 m->mothurOutEndLine();
407 catch(exception& e) {
408 m->errorOut(e, "ConsensusSeqsCommand", "execute");
412 //***************************************************************************************************************
414 int ConsensusSeqsCommand::processList(ListVector*& list){
418 map<string, string> variables;
419 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
420 variables["[tag]"] = list->getLabel();
421 string outputSummaryFile = getOutputFileName("summary", variables);
422 m->openOutputFile(outputSummaryFile, outSummary);
423 outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
424 outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
427 string outputNameFile = getOutputFileName("name",variables);
428 m->openOutputFile(outputNameFile, outName);
429 outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
432 string outputFastaFile = getOutputFileName("fasta",variables);
433 m->openOutputFile(outputFastaFile, outFasta);
434 outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
436 outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
438 string snumBins = toString(list->getNumBins());
439 vector<string> binLabels = list->getLabels();
440 for (int i = 0; i < list->getNumBins(); i++) {
442 if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
444 string bin = list->get(i);
445 string consSeq = getConsSeq(bin, outSummary, i);
447 outFasta << ">" << binLabels[i] << endl << consSeq << endl;
448 outName << binLabels[i] << '\t' << binLabels[i] << "," << bin << endl;
451 outSummary.close(); outName.close(); outFasta.close();
456 catch(exception& e) {
457 m->errorOut(e, "ConsensusSeqsCommand", "processList");
462 //***************************************************************************************************************
463 string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, int binNumber){
470 vector<string> binNames;
471 m->splitAtComma(bin, binNames);
473 vector< vector<float> > percentages; percentages.resize(5);
474 for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
476 if (countfile != "") {
478 for (int j = 0; j < seqLength; j++) {
480 if (m->control_pressed) { return consSeq; }
482 vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
485 for (int i = 0; i < binNames.size(); i++) {
486 if (m->control_pressed) { return consSeq; }
489 map<string, string>::iterator itFasta = fastaMap.find(binNames[i]);
490 if (itFasta != fastaMap.end()) {
491 thisSeq = itFasta->second;
492 }else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
494 int size = ct.getNumSeqs(binNames[i]);
496 for (int k = 0; k < size; k++) {
497 if (thisSeq[j] == '.') { numDots++; }
499 char base = toupper(thisSeq[j]);
500 if (base == 'A') { counts[0]++; }
501 else if (base == 'T') { counts[1]++; }
502 else if (base == 'G') { counts[2]++; }
503 else if (base == 'C') { counts[3]++; }
504 else { counts[4]++; }
507 }else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
510 if (numDots != totalSize) { conBase = getBase(counts, totalSize); }
514 percentages[0][j] = counts[0] / (float) totalSize;
515 percentages[1][j] = counts[1] / (float) totalSize;
516 percentages[2][j] = counts[2] / (float) totalSize;
517 percentages[3][j] = counts[3] / (float) totalSize;
518 percentages[4][j] = counts[4] / (float) totalSize;
523 //get sequence strings for each name in the bin
525 for (int i = 0; i < binNames.size(); i++) {
527 map<string, string>::iterator it;
528 it = nameMap.find(binNames[i]);
529 if (it == nameMap.end()) {
530 if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
531 else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
534 //add sequence string to seqs vector to process below
535 map<string, string>::iterator itFasta = fastaMap.find(it->second);
537 if (itFasta != fastaMap.end()) {
538 string seq = itFasta->second;
540 }else { m->mothurOut("[ERROR]: file mismatch, aborting. \n"); }
544 if (error) { m->control_pressed = true; return consSeq; }
545 totalSize = seqs.size();
547 for (int j = 0; j < seqLength; j++) {
549 if (m->control_pressed) { return consSeq; }
551 vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
554 for (int i = 0; i < seqs.size(); i++) {
556 if (seqs[i][j] == '.') { numDots++; }
558 char base = toupper(seqs[i][j]);
559 if (base == 'A') { counts[0]++; }
560 else if (base == 'T') { counts[1]++; }
561 else if (base == 'G') { counts[2]++; }
562 else if (base == 'C') { counts[3]++; }
563 else { counts[4]++; }
567 if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
571 percentages[0][j] = counts[0] / (float) seqs.size();
572 percentages[1][j] = counts[1] / (float) seqs.size();
573 percentages[2][j] = counts[2] / (float) seqs.size();
574 percentages[3][j] = counts[3] / (float) seqs.size();
575 percentages[4][j] = counts[4] / (float) seqs.size();
582 for (int j = 0; j < seqLength; j++) {
583 outSummary << (binNumber + 1) << '\t' << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << totalSize << '\t' << consSeq[j] << endl;
589 catch(exception& e) {
590 m->errorOut(e, "ConsensusSeqsCommand", "getConsSeq");
594 //***************************************************************************************************************
596 char ConsensusSeqsCommand::getBase(vector<int> counts, int size){ //A,T,G,C,Gap
603 * Y = T C (pyrimidine)
606 * S = G C (strong bonds)
607 * W = A T (weak bonds)
608 * B = G T C (all but A)
609 * D = G A T (all but C)
610 * H = A C T (all but G)
611 * V = G C A (all but T)
612 * N = A G C T (any) */
616 //zero out counts that don't make the cutoff
617 float percentage = (100.0 - cutoff) / 100.0;
619 for (int i = 0; i < counts.size(); i++) {
620 float countPercentage = counts[i] / (float) size;
621 if (countPercentage < percentage) { counts[i] = 0; }
625 if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'n'; }
627 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'N'; }
629 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'v'; }
631 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'V'; }
633 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'h'; }
635 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'H'; }
637 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'd'; }
639 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'D'; }
641 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'b'; }
643 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'B'; }
644 //W = A T (weak bonds)
645 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'w'; }
646 //W = A T (weak bonds) no gap
647 else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'W'; }
648 //S = G C (strong bonds)
649 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 's'; }
650 //S = G C (strong bonds) no gap
651 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'S'; }
653 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'm'; }
654 //M = A C (amino) no gap
655 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'M'; }
657 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'k'; }
658 //K = G T (keto) no gap
659 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'K'; }
660 //Y = T C (pyrimidine)
661 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'y'; }
662 //Y = T C (pyrimidine) no gap
663 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'Y'; }
665 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'r'; }
666 //R = G A (purine) no gap
667 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'R'; }
669 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'a'; }
671 else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'A'; }
673 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 't'; }
675 else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'T'; }
677 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'g'; }
679 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'G'; }
681 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'c'; }
683 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'C'; }
685 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = '-'; }
686 //cutoff removed all counts
687 else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'N'; }
688 else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
693 catch(exception& e) {
694 m->errorOut(e, "ConsensusSeqsCommand", "getBase");
699 //***************************************************************************************************************
701 int ConsensusSeqsCommand::readFasta(){
705 m->openInputFile(fastafile, in);
710 if (m->control_pressed) { break; }
712 Sequence seq(in); m->gobble(in);
713 string name = seq.getName();
716 fastaMap[name] = seq.getAligned();
717 nameMap[name] = name; //set nameMap incase no names file
718 nameFileMap[name] = 1;
720 if (seqLength == 0) { seqLength = seq.getAligned().length(); }
721 else if (seqLength != seq.getAligned().length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; break; }
730 catch(exception& e) {
731 m->errorOut(e, "ConsensusSeqsCommand", "readFasta");
735 //***************************************************************************************************************
737 int ConsensusSeqsCommand::readNames(){
739 map<string, string> temp;
740 map<string, string>::iterator it;
743 m->readNames(namefile, temp); //use central buffered read
745 for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
746 string thisname, repnames;
747 thisname = itTemp->first;
748 repnames = itTemp->second;
750 it = nameMap.find(thisname);
751 if (it != nameMap.end()) { //then this sequence was in the fastafile
752 nameFileMap[thisname] = m->getNumNames(repnames); //for later when outputting the new namesFile if the list file is unique
754 vector<string> splitRepNames;
755 m->splitAtComma(repnames, splitRepNames);
757 for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
759 }else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
762 if (error) { m->control_pressed = true; }
767 catch(exception& e) {
768 m->errorOut(e, "ConsensusSeqsCommand", "readNames");
773 //***************************************************************************************************************