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|
/*
* seqerrorcommand.cpp
* Mothur
*
* Created by Pat Schloss on 7/15/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "seqerrorcommand.h"
#include "alignreport.hpp"
#include "qualityscores.h"
#include "refchimeratest.h"
//**********************************************************************************************************************
vector<string> SeqErrorCommand::setParameters(){
try {
CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none","errorType",false,true,true); parameters.push_back(pquery);
CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(preference);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(pqfile);
CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(preport);
CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pignorechimeras);
CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pthreshold);
CommandParameter paligned("aligned", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(paligned);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["errorsummary"] = tempOutNames;
outputTypes["errorseq"] = tempOutNames;
outputTypes["errorquality"] = tempOutNames;
outputTypes["errorqualforward"] = tempOutNames;
outputTypes["errorqualreverse"] = tempOutNames;
outputTypes["errorforward"] = tempOutNames;
outputTypes["errorreverse"] = tempOutNames;
outputTypes["errorcount"] = tempOutNames;
outputTypes["errormatrix"] = tempOutNames;
outputTypes["errorchimera"] = tempOutNames;
outputTypes["errorref-query"] = tempOutNames;
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, "SeqErrorCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string SeqErrorCommand::getHelpString(){
try {
string helpString = "";
helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n";
helpString += "The fasta parameter allows you to provide your dataset's fasta file.\n";
helpString += "The reference parameter contains the Mock sequences.\n";
helpString += "The qfile parameter ...\n";
helpString += "The report parameter...\n";
helpString += "The name parameter allows you to provide a name file associated with the fasta file.\n";
helpString += "The count parameter allows you to provide a count file associated with the fasta file.\n";
helpString += "The ignorechimeras parameter...\n";
helpString += "The threshold parameter...\n";
helpString += "Example seq.error(...).\n";
;
helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string SeqErrorCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "errorsummary") { pattern = "[filename],error.summary"; }
else if (type == "errorseq") { pattern = "[filename],error.seq"; }
else if (type == "errorquality") { pattern = "[filename],error.quality"; }
else if (type == "errorqualforward") { pattern = "[filename],error.qual.forward"; }
else if (type == "errorqualreverse") { pattern = "[filename],error.qual.reverse"; }
else if (type == "errorforward") { pattern = "[filename],error.seq.forward"; }
else if (type == "errorreverse") { pattern = "[filename],error.seq.reverse"; }
else if (type == "errorcount") { pattern = "[filename],error.count"; }
else if (type == "errormatrix") { pattern = "[filename],error.matrix"; }
else if (type == "errorchimera") { pattern = "[filename],error.chimera"; }
else if (type == "errorref-query") { pattern = "[filename],error.ref-query"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "getOutputPattern");
exit(1);
}
}
//***************************************************************************************************************
SeqErrorCommand::SeqErrorCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
queryFileName = validParameter.validFile(parameters, "fasta");
if (queryFileName == "not found") {
queryFileName = current->getFastaFile();
if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("You have no current fasta file and the fasta parameter is required.\n"); abort = true; }
}
else if (queryFileName == "not open") { queryFileName = ""; abort = true; }
else { current->setFastaFile(queryFileName); }
referenceFileName = validParameter.validFile(parameters, "reference");
if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command.\n"); abort = true; }
else if (referenceFileName == "not open") { abort = true; }
//check for optional parameters
namesFileName = validParameter.validFile(parameters, "name");
if(namesFileName == "not found"){ namesFileName = ""; }
else if (namesFileName == "not open") { namesFileName = ""; abort = true; }
else { current->setNameFile(namesFileName); }
//check for optional parameters
countfile = validParameter.validFile(parameters, "count");
if(countfile == "not found"){ countfile = ""; }
else if (countfile == "not open") { countfile = ""; abort = true; }
else { current->setCountFile(countfile); }
qualFileName = validParameter.validFile(parameters, "qfile");
if(qualFileName == "not found"){ qualFileName = ""; }
else if (qualFileName == "not open") { qualFileName = ""; abort = true; }
else { current->setQualFile(qualFileName); }
reportFileName = validParameter.validFile(parameters, "report");
if(reportFileName == "not found"){ reportFileName = ""; }
else if (reportFileName == "not open") { reportFileName = ""; abort = true; }
if (outputdir == ""){
outputdir = util.hasPath(queryFileName); }
if ((countfile != "") && (namesFileName != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name.\n"); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp = validParameter.valid(parameters, "threshold"); if (temp == "not found") { temp = "1.00"; }
util.mothurConvert(temp, threshold);
temp = validParameter.valid(parameters, "ignorechimeras"); if (temp == "not found") { temp = "T"; }
ignoreChimeras = util.isTrue(temp);
temp = validParameter.valid(parameters, "aligned"); if (temp == "not found"){ temp = "t"; }
aligned = util.isTrue(temp);
if(aligned ){
if((reportFileName != "" && qualFileName == "") || (reportFileName == "" && qualFileName != "")){
m->mothurOut("if you use either a qual file or a report file, you have to have both.");
m->mothurOutEndLine();
abort = true;
}
}
else{
if(reportFileName != ""){
m->mothurOut("we are ignoring the report file if your sequences are not aligned. we will check that the sequences in your fasta and and qual file are the same length.");
m->mothurOutEndLine();
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
exit(1);
}
}
//***************************************************************************************************************
int SeqErrorCommand::execute(){
try{
if (abort) { if (calledHelp) { return 0; } return 2; }
long start = time(nullptr);
maxLength = 5000;
totalBases = 0;
totalMatches = 0;
substitutionMatrix.resize(6);
for(int i=0;i<6;i++){ substitutionMatrix[i].resize(6,0); }
string fileNameRoot = outputdir + util.getRootName(util.getSimpleName(queryFileName));
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
string errorSummaryFileName = getOutputFileName("errorsummary",variables);
outputNames.push_back(errorSummaryFileName); outputTypes["errorsummary"].push_back(errorSummaryFileName);
string errorSeqFileName = getOutputFileName("errorseq",variables);
outputNames.push_back(errorSeqFileName); outputTypes["errorseq"].push_back(errorSeqFileName);
string errorChimeraFileName = getOutputFileName("errorchimera",variables);
outputNames.push_back(errorChimeraFileName); outputTypes["errorchimera"].push_back(errorChimeraFileName);
vector<Sequence> referenceSeqs = getReferences(referenceFileName); //read in reference sequences - make sure there's no ambiguous bases
if (m->getControl_pressed()) { return 0; }
long long numSeqs = process(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, referenceSeqs);
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
if(qualFileName != ""){
printErrorQuality(qScoreErrorMap);
printQualityFR(qualForwardMap, qualReverseMap);
}
printErrorFRFile(errorForward, errorReverse);
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
string errorCountFileName = getOutputFileName("errorcount",variables);
ofstream errorCountFile;
util.openOutputFile(errorCountFileName, errorCountFile);
outputNames.push_back(errorCountFileName); outputTypes["errorcount"].push_back(errorCountFileName);
m->mothurOut("\nMultiply error rate by 100 to obtain the percent sequencing errors.\n");
m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n");
m->mothurOut("Errors\tSequences\n");
errorCountFile << "Errors\tSequences\n";
for(int i=0;i<misMatchCounts.size();i++){
m->mothurOut(toString(i) + '\t' + toString(misMatchCounts[i]) + '\n');
errorCountFile << i << '\t' << misMatchCounts[i] << endl;
}
errorCountFile.close();
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
printSubMatrix(substitutionMatrix);
string megAlignmentFileName = getOutputFileName("errorref-query",variables);
ofstream megAlignmentFile;
util.openOutputFile(megAlignmentFileName, megAlignmentFile);
outputNames.push_back(megAlignmentFileName); outputTypes["errorref-query"].push_back(megAlignmentFileName);
for(int i=0;i<numRefs;i++){
megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
megAlignmentFile << megaAlignVector[i] << endl;
}
megAlignmentFile.close();
m->mothurOut("It took " + toString(time(nullptr) - start) + " secs to check " + toString(numSeqs) + " sequences.\n");
bool extraOutput = false;
if (extraOutput) {
//read error.chimera
ifstream in; util.openInputFile(errorChimeraFileName, in);
int chimeraCount = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
string line = util.getline(in); gobble(in);
vector<string> pieces = util.splitWhiteSpace(line);
if (pieces.size() != 0) {
if (pieces[pieces.size()-1] == "2") {
chimeraCount++;
}
}
}
in.close();
m->mothurOut("\nTrue chimeras found: " + toString(chimeraCount) + "\n");
m->mothurOut("\nReference names for chimeras:\n\n");
//read error.summary to extract names of parents
ifstream in2; util.openInputFile(errorSummaryFileName, in2);
while (!in2.eof()) {
if (m->getControl_pressed()) { break; }
string line = util.getline(in2); gobble(in2);
vector<string> pieces = util.splitWhiteSpace(line);
if (pieces.size() != 0) {
if (pieces[pieces.size()-1] == "2") {
cout << pieces[1] << endl;
}
}
}
in2.close();
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]+"\n"); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************
Compare getErrors(Sequence query, Sequence reference, MothurOut* m){
try {
Compare errors;
if(query.getAlignLength() != reference.getAlignLength()){ m->mothurOut("[WARNING]: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n"); }
int alignLength = query.getAlignLength();
string q = query.getAligned();
string r = reference.getAligned();
int started = 0;
errors.sequence = "";
for(int i=0;i<alignLength;i++){
if(q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){ // no missing data and no double gaps
if(r[i] != 'N'){
started = 1;
if(q[i] == 'A'){
if(r[i] == 'A'){ errors.AA++; errors.matches++; errors.sequence += 'm'; }
if(r[i] == 'T'){ errors.AT++; errors.sequence += 's'; }
if(r[i] == 'G'){ errors.AG++; errors.sequence += 's'; }
if(r[i] == 'C'){ errors.AC++; errors.sequence += 's'; }
if(r[i] == '-'){ errors.Ai++; errors.sequence += 'i'; }
}
else if(q[i] == 'T'){
if(r[i] == 'A'){ errors.TA++; errors.sequence += 's'; }
if(r[i] == 'T'){ errors.TT++; errors.matches++; errors.sequence += 'm'; }
if(r[i] == 'G'){ errors.TG++; errors.sequence += 's'; }
if(r[i] == 'C'){ errors.TC++; errors.sequence += 's'; }
if(r[i] == '-'){ errors.Ti++; errors.sequence += 'i'; }
}
else if(q[i] == 'G'){
if(r[i] == 'A'){ errors.GA++; errors.sequence += 's'; }
if(r[i] == 'T'){ errors.GT++; errors.sequence += 's'; }
if(r[i] == 'G'){ errors.GG++; errors.matches++; errors.sequence += 'm'; }
if(r[i] == 'C'){ errors.GC++; errors.sequence += 's'; }
if(r[i] == '-'){ errors.Gi++; errors.sequence += 'i'; }
}
else if(q[i] == 'C'){
if(r[i] == 'A'){ errors.CA++; errors.sequence += 's'; }
if(r[i] == 'T'){ errors.CT++; errors.sequence += 's'; }
if(r[i] == 'G'){ errors.CG++; errors.sequence += 's'; }
if(r[i] == 'C'){ errors.CC++; errors.matches++; errors.sequence += 'm'; }
if(r[i] == '-'){ errors.Ci++; errors.sequence += 'i'; }
}
else if(q[i] == 'N'){
if(r[i] == 'A'){ errors.NA++; errors.sequence += 'a'; }
if(r[i] == 'T'){ errors.NT++; errors.sequence += 'a'; }
if(r[i] == 'G'){ errors.NG++; errors.sequence += 'a'; }
if(r[i] == 'C'){ errors.NC++; errors.sequence += 'a'; }
if(r[i] == '-'){ errors.Ni++; errors.sequence += 'a'; }
}
else if(q[i] == '-' && r[i] != '-'){
if(r[i] == 'A'){ errors.dA++; errors.sequence += 'd'; }
if(r[i] == 'T'){ errors.dT++; errors.sequence += 'd'; }
if(r[i] == 'G'){ errors.dG++; errors.sequence += 'd'; }
if(r[i] == 'C'){ errors.dC++; errors.sequence += 'd'; }
}
errors.total++;
}
else{
if(q[i] == '-'){
errors.sequence += 'd'; errors.total++;
}
else{
errors.sequence += 'r';
}
}
}
else if(q[i] == '.' && r[i] != '.'){ // reference extends beyond query
if(started == 1){ break; }
}
else if(q[i] != '.' && r[i] == '.'){ // query extends beyond reference
if(started == 1){ break; }
}
else if(q[i] == '.' && r[i] == '.'){ // both are missing data
if(started == 1){ break; }
}
}
errors.mismatches = errors.total-errors.matches;
if(errors.total != 0){ errors.errorRate = (double)(errors.total-errors.matches) / (double)errors.total; }
else{ errors.errorRate = 0; }
errors.queryName = query.getName();
errors.refName = reference.getName();
return errors;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "getErrors");
exit(1);
}
}
//***************************************************************************************************************
void printErrorData(Compare error, int numParentSeqs, ofstream& summaryFile, ofstream& errorFile, vector<vector<int> >& substitutionMatrix, bool ignoreChimeras){
string summaryOutput = error.queryName + '\t' + error.refName + '\t' + toString(error.weight) + '\t';
summaryOutput += toString(error.AA) + '\t' + toString(error.AT) + '\t' + toString(error.AG) + '\t' + toString(error.AC) + '\t';
summaryOutput += toString(error.TA) + '\t' + toString(error.TT) + '\t' + toString(error.TG) + '\t' + toString(error.TC) + '\t';
summaryOutput += toString(error.GA) + '\t' + toString(error.GT) + '\t' + toString(error.GG) + '\t' + toString(error.GC) + '\t';
summaryOutput += toString(error.CA) + '\t' + toString(error.CT) + '\t' + toString(error.CG) + '\t' + toString(error.CC) + '\t';
summaryOutput += toString(error.NA) + '\t' + toString(error.NT) + '\t' + toString(error.NG) + '\t' + toString(error.NC) + '\t';
summaryOutput += toString(error.Ai) + '\t' + toString(error.Ti) + '\t' + toString(error.Gi) + '\t' + toString(error.Ci) + '\t' + toString(error.Ni) + '\t';
summaryOutput += toString(error.dA) + '\t' + toString(error.dT) + '\t' + toString(error.dG) + '\t' + toString(error.dC) + '\t';
summaryOutput += toString(error.Ai + error.Ti + error.Gi + error.Ci) + '\t'; //insertions
summaryOutput += toString(error.dA + error.dT + error.dG + error.dC) + '\t'; //deletions
summaryOutput += toString(error.mismatches - (error.Ai + error.Ti + error.Gi + error.Ci) - (error.dA + error.dT + error.dG + error.dC) - (error.NA + error.NT + error.NG + error.NC + error.Ni)) + '\t'; //substitutions
summaryOutput += toString(error.NA + error.NT + error.NG + error.NC + error.Ni) + '\t'; //ambiguities
summaryOutput += toString(error.matches) + '\t' + toString(error.mismatches) + '\t' + toString(error.total) + '\t' + toString(error.errorRate) + '\t' + toString(numParentSeqs) + "\n";
summaryFile << (summaryOutput);
summaryOutput = '>' + error.queryName + "\tref:" + error.refName + '\n' + error.sequence + '\n';
errorFile << (summaryOutput);
int a=0; int t=1; int g=2; int c=3;
int gap=4; int n=5;
if(numParentSeqs == 1 || !ignoreChimeras){
substitutionMatrix[a][a] += error.weight * error.AA;
substitutionMatrix[a][t] += error.weight * error.TA;
substitutionMatrix[a][g] += error.weight * error.GA;
substitutionMatrix[a][c] += error.weight * error.CA;
substitutionMatrix[a][gap] += error.weight * error.dA;
substitutionMatrix[a][n] += error.weight * error.NA;
substitutionMatrix[t][a] += error.weight * error.AT;
substitutionMatrix[t][t] += error.weight * error.TT;
substitutionMatrix[t][g] += error.weight * error.GT;
substitutionMatrix[t][c] += error.weight * error.CT;
substitutionMatrix[t][gap] += error.weight * error.dT;
substitutionMatrix[t][n] += error.weight * error.NT;
substitutionMatrix[g][a] += error.weight * error.AG;
substitutionMatrix[g][t] += error.weight * error.TG;
substitutionMatrix[g][g] += error.weight * error.GG;
substitutionMatrix[g][c] += error.weight * error.CG;
substitutionMatrix[g][gap] += error.weight * error.dG;
substitutionMatrix[g][n] += error.weight * error.NG;
substitutionMatrix[c][a] += error.weight * error.AC;
substitutionMatrix[c][t] += error.weight * error.TC;
substitutionMatrix[c][g] += error.weight * error.GC;
substitutionMatrix[c][c] += error.weight * error.CC;
substitutionMatrix[c][gap] += error.weight * error.dC;
substitutionMatrix[c][n] += error.weight * error.NC;
substitutionMatrix[gap][a] += error.weight * error.Ai;
substitutionMatrix[gap][t] += error.weight * error.Ti;
substitutionMatrix[gap][g] += error.weight * error.Gi;
substitutionMatrix[gap][c] += error.weight * error.Ci;
substitutionMatrix[gap][n] += error.weight * error.Ni;
}
}
//**********************************************************************************************************************
long long SeqErrorCommand::process(string filename, string qFileName, string rFileName, string summaryFileName, string errorOutputFileName, string chimeraOutputFileName, vector<Sequence>& referenceSeqs) {
try {
map<string, int> weights;
if(namesFileName != "") { weights = util.readNames(namesFileName); }
else if (countfile != "") { CountTable ct; ct.readTable(countfile, false, false); weights = ct.getNameMap(); }
bool hasNameMap = false;
if (weights.size() > 0) { hasNameMap = true; }
int maxMismatch = 0;
AlignReport report;
QualityScores quality;
misMatchCounts.resize(11, 0);
map<string, int>::iterator it;
qScoreErrorMap['m'].assign(101, 0);
qScoreErrorMap['s'].assign(101, 0);
qScoreErrorMap['i'].assign(101, 0);
qScoreErrorMap['a'].assign(101, 0);
errorForward['m'].assign(maxLength,0);
errorForward['s'].assign(maxLength,0);
errorForward['i'].assign(maxLength,0);
errorForward['d'].assign(maxLength,0);
errorForward['a'].assign(maxLength,0);
errorReverse['m'].assign(maxLength,0);
errorReverse['s'].assign(maxLength,0);
errorReverse['i'].assign(maxLength,0);
errorReverse['d'].assign(maxLength,0);
errorReverse['a'].assign(maxLength,0);
//open inputfiles and go to beginning place for this processor
ifstream queryFile;
util.openInputFile(filename, queryFile);
ifstream reportFile; ifstream qualFile;
if((qFileName != "" && rFileName != "" && aligned)){
util.openInputFile(qFileName, qualFile);
//gobble headers
util.openInputFile(reportFileName, reportFile);
report.readHeaders(reportFile);
qualForwardMap.resize(maxLength);
qualReverseMap.resize(maxLength);
for(int i=0;i<maxLength;i++){
qualForwardMap[i].assign(101,0);
qualReverseMap[i].assign(101,0);
}
}
else if(qFileName != "" && !aligned){
util.openInputFile(qFileName, qualFile);
qualForwardMap.resize(maxLength);
qualReverseMap.resize(maxLength);
for(int i=0;i<maxLength;i++){
qualForwardMap[i].assign(101,0);
qualReverseMap[i].assign(101,0);
}
}
RefChimeraTest chimeraTest = RefChimeraTest(referenceSeqs, aligned);
string chimeraHeader = chimeraTest.getHeader();
int numRefs = referenceSeqs.size();
megaAlignVector.assign(numRefs, "");
ofstream out;
util.openOutputFile(summaryFileName, out); out.precision(6); out.setf(ios::fixed, ios::showpoint);
out << "query\treference\tweight\tAA\tAT\tAG\tAC\tTA\tTT\tTG\tTC\tGA\tGT\tGG\tGC\tCA\tCT\tCG\tCC\tNA\tNT\tNG\tNC\tAi\tTi\tGi\tCi\tNi\tdA\tdT\tdG\tdC\tinsertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\tnumparents\n";
ofstream outChimera;
util.openOutputFile(chimeraOutputFileName, outChimera);
outChimera << chimeraHeader;
ofstream outError;
util.openOutputFile(errorOutputFileName, outError);
int index = 0;
bool ignoreSeq = 0;
bool moreSeqs = 1;
while (moreSeqs) {
Sequence query(queryFile);
int numParentSeqs = -1;
int closestRefIndex = -1;
string querySeq = query.getAligned();
if (!aligned) { querySeq = query.getUnaligned(); }
string output = "";
numParentSeqs = chimeraTest.analyzeQuery(query.getName(), querySeq, output);
outChimera << (output);
closestRefIndex = chimeraTest.getClosestRefIndex();
Sequence reference = referenceSeqs[closestRefIndex];
reference.setAligned(chimeraTest.getClosestRefAlignment());
query.setAligned(chimeraTest.getQueryAlignment());
if(numParentSeqs > 1 && ignoreChimeras == 1) { ignoreSeq = 1; }
else { ignoreSeq = 0; }
Compare minCompare = getErrors(query, reference, m);
if(hasNameMap){
it = weights.find(query.getName());
minCompare.weight = it->second;
}
else{ minCompare.weight = 1; }
printErrorData(minCompare, numParentSeqs, out, outError, substitutionMatrix, ignoreChimeras);
if(!ignoreSeq){
int numRs = 0;
for(int i=0;i<minCompare.sequence.length();i++){
char letter = minCompare.sequence[i];
if(letter != 'r'){
errorForward[letter][i] += minCompare.weight;
int errorReverseLocation = minCompare.total-(i-numRs)-1;
if (errorReverseLocation < 0) { errorReverseLocation = 0; m->mothurOut("[WARNING]: negative value for errorReverse " + query.getName() + "\n"); }
errorReverse[letter][minCompare.total-(i-numRs)-1] += minCompare.weight;
}else { numRs++; }
}
}
if(aligned && qFileName != "" && rFileName != ""){
report.read(reportFile);
int startBase = report.getQueryStart();
int endBase = report.getQueryEnd();
quality.read(qualFile);
if(!ignoreSeq){
quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
}
}
else if(!aligned && qFileName != ""){
quality.read(qualFile);
int qualityLength = quality.getLength();
if(qualityLength != query.getNumBases()){ m->mothurOut("[WARNING]: - quality and fasta sequence files do not match at " + query.getName() + '\t' + toString(qualityLength) + '\t' + toString(query.getNumBases()) +'\n'); }
int startBase = 1;
int endBase = qualityLength;
if(!ignoreSeq){
quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
}
}
if(minCompare.errorRate <= threshold && !ignoreSeq){
totalBases += (minCompare.total * minCompare.weight);
totalMatches += minCompare.matches * minCompare.weight;
if(minCompare.mismatches > maxMismatch){
maxMismatch = minCompare.mismatches;
misMatchCounts.resize(maxMismatch + 1, 0);
}
misMatchCounts[minCompare.mismatches] += minCompare.weight;
megaAlignVector[closestRefIndex] += query.getInlineSeq() + '\n';
}
index++;
if (queryFile.eof()) { break; }
if(index % 100 == 0){ m->mothurOutJustToScreen(toString(index)+"\n"); }
}
queryFile.close();
if(qFileName != "" && rFileName != "") { reportFile.close(); qualFile.close(); }
else if(qFileName != "" && aligned == false){ qualFile.close(); }
//report progress
m->mothurOutJustToScreen(toString(index)+"\n");
return index;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "process");
exit(1);
}
}
//***************************************************************************************************************
vector<Sequence> SeqErrorCommand::getReferences(string refFileName){
try {
int numAmbigSeqs = 0;
int maxStartPos = 0;
int minEndPos = 100000;
ifstream referenceFile;
util.openInputFile(refFileName, referenceFile);
vector<Sequence> referenceSeqs;
while(!referenceFile.eof()){
if (m->getControl_pressed()) { break; }
Sequence currentSeq(referenceFile); gobble(referenceFile);
int numAmbigs = currentSeq.getAmbigBases();
if(numAmbigs > 0){ numAmbigSeqs++; }
int startPos = currentSeq.getStartPos();
if(startPos > maxStartPos) { maxStartPos = startPos; }
int endPos = currentSeq.getEndPos();
if(endPos < minEndPos) { minEndPos = endPos; }
if (currentSeq.getNumBases() == 0) { m->mothurOut("[WARNING]: " + currentSeq.getName() + " is blank, ignoring.\n"); }
else { referenceSeqs.push_back(currentSeq); }
}
referenceFile.close();
numRefs = referenceSeqs.size();
for(int i=0;i<numRefs;i++){
referenceSeqs[i].padToPos(maxStartPos);
referenceSeqs[i].padFromPos(minEndPos);
}
if(numAmbigSeqs != 0){ m->mothurOut("[WARNING]: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored.\n"); }
return referenceSeqs;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "getReferences");
exit(1);
}
}
//***************************************************************************************************************
void SeqErrorCommand::printSubMatrix(vector<vector<int> >& substitutionMatrix){
try {
string fileNameRoot = outputdir + util.getRootName(util.getSimpleName(queryFileName));
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
string subMatrixFileName = getOutputFileName("errormatrix",variables);
ofstream subMatrixFile;
util.openOutputFile(subMatrixFileName, subMatrixFile);
outputNames.push_back(subMatrixFileName); outputTypes["errormatrix"].push_back(subMatrixFileName);
vector<string> bases(6);
bases[0] = "A";
bases[1] = "T";
bases[2] = "G";
bases[3] = "C";
bases[4] = "Gap";
bases[5] = "N";
vector<int> refSums(5,1);
for(int i=0;i<5;i++){
subMatrixFile << "\tr" << bases[i];
for(int j=0;j<6;j++){
refSums[i] += substitutionMatrix[i][j];
}
}
subMatrixFile << endl;
for(int i=0;i<6;i++){
subMatrixFile << 'q' << bases[i];
for(int j=0;j<5;j++){
subMatrixFile << '\t' << substitutionMatrix[j][i];
}
subMatrixFile << endl;
}
subMatrixFile << "total";
for(int i=0;i<5;i++){
subMatrixFile << '\t' << refSums[i];
}
subMatrixFile << endl;
subMatrixFile.close();
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "printSubMatrix");
exit(1);
}
}
//***************************************************************************************************************
void SeqErrorCommand::printErrorFRFile(map<char, vector<int> >& errorForward, map<char, vector<int> >& errorReverse){
try{
string fileNameRoot = outputdir + util.getRootName(util.getSimpleName(queryFileName));
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
string errorForwardFileName = getOutputFileName("errorforward",variables);
ofstream errorForwardFile;
util.openOutputFile(errorForwardFileName, errorForwardFile);
outputNames.push_back(errorForwardFileName); outputTypes["errorforward"].push_back(errorForwardFileName);
errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
for(int i=0;i<maxLength;i++){
float match = (float)errorForward['m'][i];
float subst = (float)errorForward['s'][i];
float insert = (float)errorForward['i'][i];
float del = (float)errorForward['d'][i];
float amb = (float)errorForward['a'][i];
float total = match + subst + insert + del + amb;
if(util.isEqual(total, 0)){ break; }
errorForwardFile << i+1 << '\t' << total << '\t' << match/total << '\t' << subst/total << '\t' << insert/total << '\t' << del/total << '\t' << amb/total << endl;
}
errorForwardFile.close();
string errorReverseFileName = getOutputFileName("errorreverse",variables);
ofstream errorReverseFile;
util.openOutputFile(errorReverseFileName, errorReverseFile);
outputNames.push_back(errorReverseFileName); outputTypes["errorreverse"].push_back(errorReverseFileName);
errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
for(int i=0;i<maxLength;i++){
float match = (float)errorReverse['m'][i];
float subst = (float)errorReverse['s'][i];
float insert = (float)errorReverse['i'][i];
float del = (float)errorReverse['d'][i];
float amb = (float)errorReverse['a'][i];
float total = match + subst + insert + del + amb;
if(util.isEqual(total, 0)){ break; }
errorReverseFile << i+1 << '\t' << total << '\t' << match/total << '\t' << subst/total << '\t' << insert/total << '\t' << del/total << '\t' << amb/total << endl;
}
errorReverseFile.close();
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
exit(1);
}
}
//***************************************************************************************************************
void SeqErrorCommand::printErrorQuality(map<char, vector<int> >& qScoreErrorMap){
try{
string fileNameRoot = outputdir + util.getRootName(util.getSimpleName(queryFileName));
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
string errorQualityFileName = getOutputFileName("errorquality",variables);
ofstream errorQualityFile;
util.openOutputFile(errorQualityFileName, errorQualityFile);
outputNames.push_back(errorQualityFileName); outputTypes["errorquality"].push_back(errorQualityFileName);
errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
for(int i=0;i<101;i++){
errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
}
errorQualityFile.close();
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "printErrorQuality");
exit(1);
}
}
//***************************************************************************************************************
void SeqErrorCommand::printQualityFR(vector<vector<int> >& qualForwardMap, vector<vector<int> >& qualReverseMap){
try{
int numRows = 0;
int numColumns = qualForwardMap[0].size();
for(int i=0;i<qualForwardMap.size();i++){
for(int j=0;j<numColumns;j++){
if(qualForwardMap[i][j] != 0){
if(numRows < i) { numRows = i+20; }
}
}
}
string fileNameRoot = outputdir + util.getRootName(util.getSimpleName(queryFileName));
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
string qualityForwardFileName = getOutputFileName("errorqualforward",variables);
ofstream qualityForwardFile;
util.openOutputFile(qualityForwardFileName, qualityForwardFile);
outputNames.push_back(qualityForwardFileName); outputTypes["errorqualforward"].push_back(qualityForwardFileName);
for(int i=0;i<numColumns;i++){ qualityForwardFile << '\t' << i; } qualityForwardFile << endl;
for(int i=0;i<numRows;i++){
qualityForwardFile << i+1;
for(int j=0;j<numColumns;j++){
qualityForwardFile << '\t' << qualForwardMap[i][j];
}
qualityForwardFile << endl;
}
qualityForwardFile.close();
string qualityReverseFileName = getOutputFileName("errorqualreverse",variables);
ofstream qualityReverseFile;
util.openOutputFile(qualityReverseFileName, qualityReverseFile);
outputNames.push_back(qualityReverseFileName); outputTypes["errorqualreverse"].push_back(qualityReverseFileName);
for(int i=0;i<numColumns;i++){ qualityReverseFile << '\t' << i; } qualityReverseFile << endl;
for(int i=0;i<numRows;i++){
qualityReverseFile << i+1;
for(int j=0;j<numColumns;j++){
qualityReverseFile << '\t' << qualReverseMap[i][j];
}
qualityReverseFile << endl;
}
qualityReverseFile.close();
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "printQualityFR");
exit(1);
}
}
//***************************************************************************************************************
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