#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getValidParameters(){
+vector<string> ConsensusSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "list", "name", "label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","fasta-name",false,false,true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getValidParameters");
+ m->errorOut(e, "ConsensusSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ConsensusSeqsCommand::ConsensusSeqsCommand(){
+string ConsensusSeqsCommand::getHelpString(){
try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ string helpString = "";
+ 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";
+ helpString += "The consensus.seqs command parameters are fasta, list, name, count, cutoff and label.\n";
+ 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";
+ helpString += "The list parameter allows you to enter a your list file. \n";
+ helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
+ helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ 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";
+ helpString += "The consensus.seqs command should be in the following format: \n";
+ helpString += "consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n";
+ helpString += "Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
+ m->errorOut(e, "ConsensusSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta", "list"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getRequiredParameters");
- exit(1);
- }
+string ConsensusSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],cons.fasta-[filename],[tag],cons.fasta"; }
+ else if (type == "name") { pattern = "[filename],cons.names-[filename],[tag],cons.names"; }
+ else if (type == "count") { pattern = "[filename],cons.count_table-[filename],[tag],cons.count_table"; }
+ else if (type == "summary") { pattern = "[filename],cons.summary-[filename],[tag],cons.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getRequiredFiles(){
+ConsensusSeqsCommand::ConsensusSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
exit(1);
}
}
//***************************************************************************************************************
ConsensusSeqsCommand::ConsensusSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","list","name","label", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
//check for parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the consensus.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; m->mothurOut("list is a required parameter for the consensus.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else { allLines = 1; }
}
+ string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, cutoff);
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
-
+
+ if (countfile == "") {
+ if (namefile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
catch(exception& e) {
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ConsensusSeqsCommand::help(){
- try {
- m->mothurOut("The consensus.seqs command reads a fastafile and listfile and creates a consensus sequence for each otu. Sequences must be aligned.\n");
- m->mothurOut("The consensus.seqs command parameters are fasta, list, name and label.\n");
- m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
- m->mothurOut("The list parameter allows you to enter a your list file. \n");
- m->mothurOut("The name parameter allows you to enter a names file associated with the fasta file. \n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
- m->mothurOut("The consensus.seqs command should be in the following format: \n");
- m->mothurOut("consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n");
- m->mothurOut("Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-ConsensusSeqsCommand::~ConsensusSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int ConsensusSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ int start = time(NULL);
+
readFasta();
if (m->control_pressed) { return 0; }
if (namefile != "") { readNames(); }
+ if (countfile != "") { ct.readTable(countfile, true); }
if (m->control_pressed) { return 0; }
- InputData* input = new InputData(listfile, "list");
- ListVector* list = input->getListVector();
-
- string lastLabel = list->getLabel();
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete list; delete input; return 0; }
-
- if(allLines == 1 || labels.count(list->getLabel()) == 1){
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ if (listfile == "") {
+
+ ofstream outSummary;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputSummaryFile = getOutputFileName("summary", variables);
+ m->openOutputFile(outputSummaryFile, outSummary);
+ outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
+ outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
+
+ outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
+
+ ofstream outFasta;
+ string outputFastaFile = getOutputFileName("fasta", variables);
+ m->openOutputFile(outputFastaFile, outFasta);
+ outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
+
+ vector< vector<float> > percentages; percentages.resize(5);
+ for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
+
+ string consSeq = "";
+ int thisCount;
+ //get counts
+ for (int j = 0; j < seqLength; j++) {
- processList(list);
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
+ thisCount = 0;
+ for (map<string, string>::iterator it = fastaMap.begin(); it != fastaMap.end(); it++) {
+
+ string thisSeq = it->second;
+ int size = 0;
+
+ if (countfile != "") { size = ct.getNumSeqs(it->first); }
+ else {
+ map<string, int>::iterator itCount = nameFileMap.find(it->first);
+ if (itCount != nameFileMap.end()) {
+ size = itCount->second;
+ }else { m->mothurOut("[ERROR]: file mismatch, aborting.\n"); m->control_pressed = true; break; }
+ }
+
+ for (int k = 0; k < size; k++) {
+ if (thisSeq[j] == '.') { numDots++; }
+
+ char base = toupper(thisSeq[j]);
+ if (base == 'A') { counts[0]++; }
+ else if (base == 'T') { counts[1]++; }
+ else if (base == 'G') { counts[2]++; }
+ else if (base == 'C') { counts[3]++; }
+ else { counts[4]++; }
+ thisCount++;
+ }
+ }
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
+ char conBase = '.';
+ if (numDots != thisCount) { conBase = getBase(counts, thisCount); }
+
+ consSeq += conBase;
+
+ percentages[0][j] = counts[0] / (float) thisCount;
+ percentages[1][j] = counts[1] / (float) thisCount;
+ percentages[2][j] = counts[2] / (float) thisCount;
+ percentages[3][j] = counts[3] / (float) thisCount;
+ percentages[4][j] = counts[4] / (float) thisCount;
+ }
+
+ for (int j = 0; j < seqLength; j++) {
+ 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;
}
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
- delete list;
+ outFasta << ">conseq" << endl << consSeq << endl;
+
+ outSummary.close(); outFasta.close();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ }else {
+
+
+ InputData* input = new InputData(listfile, "list");
+ ListVector* list = input->getListVector();
+
+ string lastLabel = list->getLabel();
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- list = input->getListVector(lastLabel);
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; delete input; return 0; }
- processList(list);
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processList(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+
+ list = input->getListVector(lastLabel);
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processList(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
+ delete list; list = NULL;
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
+ //get next line to process
+ list = input->getListVector();
}
- lastLabel = list->getLabel();
- delete list; list = NULL;
+ 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; }
- //get next line to process
- list = input->getListVector();
- }
-
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
}
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
- list = input->getListVector(lastLabel);
-
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
- processList(list);
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+
+ list = input->getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processList(list);
+
+ delete list; list = NULL;
+ }
- delete list; list = NULL;
+ if (list != NULL) { delete list; }
+ delete input;
}
- if (list != NULL) { delete list; }
- delete input;
-
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the consensus sequences.");
+
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
try{
ofstream outSummary;
- string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.summary";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[tag]"] = list->getLabel();
+ string outputSummaryFile = getOutputFileName("summary", variables);
m->openOutputFile(outputSummaryFile, outSummary);
outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
ofstream outName;
- string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.names";
+ string outputNameFile = getOutputFileName("name",variables);
m->openOutputFile(outputNameFile, outName);
outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
ofstream outFasta;
- string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.fasta";
+ string outputFastaFile = getOutputFileName("fasta",variables);
m->openOutputFile(outputFastaFile, outFasta);
outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
+ outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
+
+ string snumBins = toString(list->getNumBins());
for (int i = 0; i < list->getNumBins(); i++) {
if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
string bin = list->get(i);
-
- string newName = "";
- string consSeq = getConsSeq(bin, outSummary, newName, i);
-
- outFasta << ">seq" << (i+1) << endl << consSeq << endl;
- outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << newName << endl;
+ string consSeq = getConsSeq(bin, outSummary, i);
+
+ string seqName = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { seqName += "0"; }
+ }
+ seqName += sbinNumber;
+
+ outFasta << ">" << seqName << endl << consSeq << endl;
+ outName << seqName << '\t' << seqName << "," << bin << endl;
}
outSummary.close(); outName.close(); outFasta.close();
}
//***************************************************************************************************************
-//made this smart enough to owrk with unique or non unique list file
-string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, string& name, int binNumber){
+string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, int binNumber){
try{
string consSeq = "";
bool error = false;
-
- //the whole bin is the second column if no names file, otherwise build it
- name = bin;
- if (namefile != "") { name = ""; }
-
+ int totalSize=0;
+
vector<string> binNames;
m->splitAtComma(bin, binNames);
-
- //get sequence strings for each name in the bin
- vector<string> seqs;
-
- set<string> addedAlready;
- int seqLength = 0;
- for (int i = 0; i < binNames.size(); i++) {
-
- map<string, string>::iterator it;
-
- it = nameMap.find(binNames[i]);
- if (it == nameMap.end()) {
- if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
- else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
- break;
- }else {
-
- //add sequence string to seqs vector to process below
- string seq = fastaMap[it->second];
- seqs.push_back(seq);
-
- if (seqLength == 0) { seqLength = seq.length(); }
- else if (seqLength != seq.length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); error = true; break; }
-
- if (namefile != "") {
- //did we add this line from name file already?
- if (addedAlready.count(it->second) == 0) {
- name += "," + nameFileMap[it->second];
- addedAlready.insert(it->second);
- }
- }
-
- }
- }
-
- if (error) { m->control_pressed = true; return consSeq; }
-
- if (namefile != "") { name = name.substr(1); }
-
- vector< vector<float> > percentages; percentages.resize(5);
+
+ vector< vector<float> > percentages; percentages.resize(5);
for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
-
- //get counts
- for (int j = 0; j < seqLength; j++) {
-
- if (m->control_pressed) { return consSeq; }
-
- vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
- int numDots = 0;
-
- for (int i = 0; i < seqs.size(); i++) {
-
- if (seqs[i][j] == '.') { numDots++; }
-
- char base = toupper(seqs[i][j]);
- if (base == 'A') { counts[0]++; }
- else if (base == 'T') { counts[1]++; }
- else if (base == 'G') { counts[2]++; }
- else if (base == 'C') { counts[3]++; }
- else { counts[4]++; }
- }
-
- char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts); }
-
- consSeq += conBase;
-
- percentages[0][j] = counts[0] / (float) seqs.size();
- percentages[1][j] = counts[1] / (float) seqs.size();
- percentages[2][j] = counts[2] / (float) seqs.size();
- percentages[3][j] = counts[3] / (float) seqs.size();
- percentages[4][j] = counts[4] / (float) seqs.size();
-
+
+ if (countfile != "") {
+ //get counts
+ for (int j = 0; j < seqLength; j++) {
+
+ if (m->control_pressed) { return consSeq; }
+
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
+ totalSize = 0;
+ for (int i = 0; i < binNames.size(); i++) {
+ if (m->control_pressed) { return consSeq; }
+
+ string thisSeq = "";
+ map<string, string>::iterator itFasta = fastaMap.find(binNames[i]);
+ if (itFasta != fastaMap.end()) {
+ thisSeq = itFasta->second;
+ }else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ int size = ct.getNumSeqs(binNames[i]);
+ if (size != 0) {
+ for (int k = 0; k < size; k++) {
+ if (thisSeq[j] == '.') { numDots++; }
+
+ char base = toupper(thisSeq[j]);
+ if (base == 'A') { counts[0]++; }
+ else if (base == 'T') { counts[1]++; }
+ else if (base == 'G') { counts[2]++; }
+ else if (base == 'C') { counts[3]++; }
+ else { counts[4]++; }
+ totalSize++;
+ }
+ }else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+ char conBase = '.';
+ if (numDots != totalSize) { conBase = getBase(counts, totalSize); }
+
+ consSeq += conBase;
+
+ percentages[0][j] = counts[0] / (float) totalSize;
+ percentages[1][j] = counts[1] / (float) totalSize;
+ percentages[2][j] = counts[2] / (float) totalSize;
+ percentages[3][j] = counts[3] / (float) totalSize;
+ percentages[4][j] = counts[4] / (float) totalSize;
+ }
+
+ }else {
+
+ //get sequence strings for each name in the bin
+ vector<string> seqs;
+ for (int i = 0; i < binNames.size(); i++) {
+
+ map<string, string>::iterator it;
+ it = nameMap.find(binNames[i]);
+ if (it == nameMap.end()) {
+ if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
+ else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
+ break;
+ }else {
+ //add sequence string to seqs vector to process below
+ map<string, string>::iterator itFasta = fastaMap.find(it->second);
+
+ if (itFasta != fastaMap.end()) {
+ string seq = itFasta->second;
+ seqs.push_back(seq);
+ }else { m->mothurOut("[ERROR]: file mismatch, aborting. \n"); }
+ }
+ }
+
+ if (error) { m->control_pressed = true; return consSeq; }
+ totalSize = seqs.size();
+ //get counts
+ for (int j = 0; j < seqLength; j++) {
+
+ if (m->control_pressed) { return consSeq; }
+
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
+
+ for (int i = 0; i < seqs.size(); i++) {
+
+ if (seqs[i][j] == '.') { numDots++; }
+
+ char base = toupper(seqs[i][j]);
+ if (base == 'A') { counts[0]++; }
+ else if (base == 'T') { counts[1]++; }
+ else if (base == 'G') { counts[2]++; }
+ else if (base == 'C') { counts[3]++; }
+ else { counts[4]++; }
+ }
+
+ char conBase = '.';
+ if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
+
+ consSeq += conBase;
+
+ percentages[0][j] = counts[0] / (float) seqs.size();
+ percentages[1][j] = counts[1] / (float) seqs.size();
+ percentages[2][j] = counts[2] / (float) seqs.size();
+ percentages[3][j] = counts[3] / (float) seqs.size();
+ percentages[4][j] = counts[4] / (float) seqs.size();
+
+ }
+ }
+
+
+
+ for (int j = 0; j < seqLength; j++) {
+ 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;
}
-
- outSummary << ">seq" << (binNumber + 1) << endl;
- outSummary << "A" << '\t';
- for (int j = 0; j < seqLength; j++) { outSummary << percentages[0][j] << '\t'; }
- outSummary << endl;
- outSummary << "T" << '\t';
- for (int j = 0; j < seqLength; j++) { outSummary << percentages[1][j] << '\t'; }
- outSummary << endl;
- outSummary << "G" << '\t';
- for (int j = 0; j < seqLength; j++) { outSummary << percentages[2][j] << '\t'; }
- outSummary << endl;
- outSummary << "C" << '\t';
- for (int j = 0; j < seqLength; j++) { outSummary << percentages[3][j] << '\t'; }
- outSummary << endl;
- outSummary << "Gap" << '\t';
- for (int j = 0; j < seqLength; j++) { outSummary << percentages[4][j] << '\t'; }
- outSummary << endl;
-
return consSeq;
}
//***************************************************************************************************************
-char ConsensusSeqsCommand::getBase(vector<int> counts){ //A,T,G,C,Gap
+char ConsensusSeqsCommand::getBase(vector<int> counts, int size){ //A,T,G,C,Gap
try{
/* A = adenine
* C = cytosine
char conBase = 'N';
+ //zero out counts that don't make the cutoff
+ float percentage = (100.0 - cutoff) / 100.0;
+
+ for (int i = 0; i < counts.size(); i++) {
+ float countPercentage = counts[i] / (float) size;
+ if (countPercentage < percentage) { counts[i] = 0; }
+ }
+
//any
if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'n'; }
//any no gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'C'; }
//only gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = '-'; }
+ //cutoff removed all counts
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'N'; }
else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
return conBase;
ifstream in;
m->openInputFile(fastafile, in);
-
+ seqLength = 0;
+
while (!in.eof()) {
if (m->control_pressed) { break; }
if (name != "") {
fastaMap[name] = seq.getAligned();
nameMap[name] = name; //set nameMap incase no names file
- nameFileMap[name] = name;
+ nameFileMap[name] = 1;
+
+ if (seqLength == 0) { seqLength = seq.getAligned().length(); }
+ else if (seqLength != seq.getAligned().length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; break; }
}
}
int ConsensusSeqsCommand::readNames(){
try{
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, string>::iterator it;
-
- bool error = false;
-
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
+ map<string, string> temp;
+ map<string, string>::iterator it;
+ bool error = false;
+
+ m->readNames(namefile, temp); //use central buffered read
+
+ for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
+ string thisname, repnames;
+ thisname = itTemp->first;
+ repnames = itTemp->second;
+
+ it = nameMap.find(thisname);
if (it != nameMap.end()) { //then this sequence was in the fastafile
-
+ nameFileMap[thisname] = m->getNumNames(repnames); //for later when outputting the new namesFile if the list file is unique
+
vector<string> splitRepNames;
m->splitAtComma(repnames, splitRepNames);
- nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
}else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-
- m->gobble(in);
- }
-
- in.close();
-
+ }
+
if (error) { m->control_pressed = true; }
return 0;
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