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|
/*
* consensusseqscommand.cpp
* Mothur
*
* Created by westcott on 11/23/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "consensusseqscommand.h"
#include "sequence.hpp"
#include "inputdata.h"
//**********************************************************************************************************************
vector<string> ConsensusSeqsCommand::setParameters(){
try {
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", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ConsensusSeqsCommand::getHelpString(){
try {
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", "getHelpString");
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);
}
}
//**********************************************************************************************************************
ConsensusSeqsCommand::ConsensusSeqsCommand(){
try {
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, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
exit(1);
}
}
//***************************************************************************************************************
ConsensusSeqsCommand::ConsensusSeqsCommand(string option) {
try {
abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["count"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("fasta");
//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["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
//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["name"] = inputDir + it->second; }
}
it = parameters.find("list");
//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["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->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") { 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 = ""; }
else { m->setListFile(listfile); }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
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) {
m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
exit(1);
}
}
//***************************************************************************************************************
int ConsensusSeqsCommand::execute(){
try{
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, false); }
if (m->control_pressed) { return 0; }
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++) {
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++;
}
}
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;
}
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))) {
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; delete input; return 0; }
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();
delete list; list = NULL;
//get next line to process
list = input->getListVector();
}
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; }
//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);
delete list; list = NULL;
}
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 Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ConsensusSeqsCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************
int ConsensusSeqsCommand::processList(ListVector*& list){
try{
ofstream outSummary;
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 = getOutputFileName("name",variables);
m->openOutputFile(outputNameFile, outName);
outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
ofstream outFasta;
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());
vector<string> binLabels = list->getLabels();
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 consSeq = getConsSeq(bin, outSummary, i);
outFasta << ">" << binLabels[i] << endl << consSeq << endl;
outName << binLabels[i] << '\t' << binLabels[i] << "," << bin << endl;
}
outSummary.close(); outName.close(); outFasta.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ConsensusSeqsCommand", "processList");
exit(1);
}
}
//***************************************************************************************************************
string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, int binNumber){
try{
string consSeq = "";
bool error = false;
int totalSize=0;
vector<string> binNames;
m->splitAtComma(bin, binNames);
vector< vector<float> > percentages; percentages.resize(5);
for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
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;
}
return consSeq;
}
catch(exception& e) {
m->errorOut(e, "ConsensusSeqsCommand", "getConsSeq");
exit(1);
}
}
//***************************************************************************************************************
char ConsensusSeqsCommand::getBase(vector<int> counts, int size){ //A,T,G,C,Gap
try{
/* A = adenine
* C = cytosine
* G = guanine
* T = thymine
* R = G A (purine)
* Y = T C (pyrimidine)
* K = G T (keto)
* M = A C (amino)
* S = G C (strong bonds)
* W = A T (weak bonds)
* B = G T C (all but A)
* D = G A T (all but C)
* H = A C T (all but G)
* V = G C A (all but T)
* N = A G C T (any) */
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 = 'N'; }
//all but T
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'v'; }
//all but T no gap
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'V'; }
//all but G
else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'h'; }
//all but G no gap
else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'H'; }
//all but C
else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'd'; }
//all but C no gap
else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'D'; }
//all but A
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'b'; }
//all but A no gap
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'B'; }
//W = A T (weak bonds)
else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'w'; }
//W = A T (weak bonds) no gap
else if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'W'; }
//S = G C (strong bonds)
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 's'; }
//S = G C (strong bonds) no gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'S'; }
//M = A C (amino)
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'm'; }
//M = A C (amino) no gap
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'M'; }
//K = G T (keto)
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'k'; }
//K = G T (keto) no gap
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'K'; }
//Y = T C (pyrimidine)
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'y'; }
//Y = T C (pyrimidine) no gap
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'Y'; }
//R = G A (purine)
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'r'; }
//R = G A (purine) no gap
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'R'; }
//only A
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'a'; }
//only A no gap
else if ((counts[0] != 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'A'; }
//only T
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 't'; }
//only T no gap
else if ((counts[0] == 0) && (counts[1] != 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'T'; }
//only G
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = 'g'; }
//only G no gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] != 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'G'; }
//only C
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'c'; }
//only C 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;
}
catch(exception& e) {
m->errorOut(e, "ConsensusSeqsCommand", "getBase");
exit(1);
}
}
//***************************************************************************************************************
int ConsensusSeqsCommand::readFasta(){
try{
ifstream in;
m->openInputFile(fastafile, in);
seqLength = 0;
while (!in.eof()) {
if (m->control_pressed) { break; }
Sequence seq(in); m->gobble(in);
string name = seq.getName();
if (name != "") {
fastaMap[name] = seq.getAligned();
nameMap[name] = name; //set nameMap incase no names file
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; }
}
}
in.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ConsensusSeqsCommand", "readFasta");
exit(1);
}
}
//***************************************************************************************************************
int ConsensusSeqsCommand::readNames(){
try{
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);
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; }
}
if (error) { m->control_pressed = true; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "ConsensusSeqsCommand", "readNames");
exit(1);
}
}
//***************************************************************************************************************
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