abort = true;
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["error"] = tempOutNames;
- outputTypes["count"] = tempOutNames;
+ outputTypes["error.summary"] = tempOutNames;
+ outputTypes["error.seq"] = tempOutNames;
+ outputTypes["error.quality"] = tempOutNames;
+ outputTypes["error.qual.forward"] = tempOutNames;
+ outputTypes["error.qual.reverse"] = tempOutNames;
+ outputTypes["error.forward"] = tempOutNames;
+ outputTypes["error.reverse"] = tempOutNames;
+ outputTypes["error.count"] = tempOutNames;
+ outputTypes["error.matrix"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
//valid paramters for this command
string AlignArray[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"};
-//need to implement name file option
-
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["error"] = tempOutNames;
- outputTypes["count"] = tempOutNames;
+ outputTypes["error.summary"] = tempOutNames;
+ outputTypes["error.seq"] = tempOutNames;
+ outputTypes["error.quality"] = tempOutNames;
+ outputTypes["error.qual.forward"] = tempOutNames;
+ outputTypes["error.qual.reverse"] = tempOutNames;
+ outputTypes["error.forward"] = tempOutNames;
+ outputTypes["error.reverse"] = tempOutNames;
+ outputTypes["error.count"] = tempOutNames;
+ outputTypes["error.matrix"] = 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);
abort = true;
}
-
-
outputDir = validParameter.validFile(parameters, "outputdir", false);
if (outputDir == "not found"){
outputDir = "";
// ...at some point should added some additional type checking...
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "1.00"; }
convert(temp, threshold);
-
- errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
- m->openOutputFile(errorSummaryFileName, errorSummaryFile);
- outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
- printErrorHeader();
-
- errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
- m->openOutputFile(errorSeqFileName, errorSeqFile);
- outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
- printErrorHeader();
+ substitutionMatrix.resize(6);
+ for(int i=0;i<6;i++){ substitutionMatrix[i].assign(6,0); }
}
}
catch(exception& e) {
void SeqErrorCommand::help(){
try {
m->mothurOut("The seq.error command reads a query alignment file and a reference alignment file and creates .....\n");
-
-
-
m->mothurOut("Example seq.error(...).\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n\n");
//***************************************************************************************************************
SeqErrorCommand::~SeqErrorCommand(){
- errorSummaryFile.close();
- errorSeqFile.close();
+
}
//***************************************************************************************************************
int SeqErrorCommand::execute(){
try{
if (abort == true) { return 0; }
+
+ errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
+ m->openOutputFile(errorSummaryFileName, errorSummaryFile);
+ outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
+ printErrorHeader();
+
+ errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
+ m->openOutputFile(errorSeqFileName, errorSeqFile);
+ outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
+ printErrorHeader();
getReferences(); //read in reference sequences - make sure there's no ambiguous bases
ReportFile report;
QualityScores quality;
-
+ vector<vector<int> > qualForwardMap;
+ vector<vector<int> > qualReverseMap;
+
if(qualFileName != "" && reportFileName != ""){
m->openInputFile(qualFileName, qualFile);
report = ReportFile(reportFile, reportFileName);
+
+ qualForwardMap.resize(1000);
+ qualReverseMap.resize(1000);
+ for(int i=0;i<1000;i++){
+ qualForwardMap[i].assign(100,0);
+ qualReverseMap[i].assign(100,0);
+ }
}
int totalBases = 0;
qScoreErrorMap['i'].assign(41, 0);
qScoreErrorMap['a'].assign(41, 0);
+
+
+ map<char, vector<int> > errorForward;
+ errorForward['m'].assign(1000,0);
+ errorForward['s'].assign(1000,0);
+ errorForward['i'].assign(1000,0);
+ errorForward['d'].assign(1000,0);
+ errorForward['a'].assign(1000,0);
+
+ map<char, vector<int> > errorReverse;
+ errorReverse['m'].assign(1000,0);
+ errorReverse['s'].assign(1000,0);
+ errorReverse['i'].assign(1000,0);
+ errorReverse['d'].assign(1000,0);
+ errorReverse['a'].assign(1000,0);
+
+
+
while(queryFile){
+
+ if (m->control_pressed) { errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
Compare minCompare;
Sequence query(queryFile);
printErrorData(minCompare);
+ for(int i=0;i<minCompare.total;i++){
+ char letter = minCompare.sequence[i];
+ errorForward[letter][i] += minCompare.weight;
+ errorReverse[letter][minCompare.total-i-1] += minCompare.weight;
+ }
+
if(qualFileName != "" && reportFileName != ""){
report = ReportFile(reportFile);
quality = QualityScores(qualFile, origLength);
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){
}
queryFile.close();
-
- int total = 0;
-
+
if(qualFileName != "" && reportFileName != ""){
string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality";
ofstream errorQualityFile;
for(int i=0;i<41;i++){
errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
}
+ errorQualityFile.close();
+
+
+
+ int lastRow = 0;
+ int lastColumn = 0;
+
+ for(int i=0;i<qualForwardMap.size();i++){
+ for(int j=0;j<qualForwardMap[i].size();j++){
+ if(qualForwardMap[i][j] != 0){
+ if(lastRow < i) { lastRow = i+2; }
+ if(lastColumn < j) { lastColumn = j+2; }
+ }
+
+ }
+ }
+
+
+ string qualityForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.forward";
+ ofstream qualityForwardFile;
+ m->openOutputFile(qualityForwardFileName, qualityForwardFile);
+ outputNames.push_back(errorQualityFileName); outputTypes["error.qual.forward"].push_back(qualityForwardFileName);
+
+ for(int i=0;i<lastColumn;i++){ qualityForwardFile << '\t' << i; } qualityForwardFile << endl;
+ for(int i=0;i<lastRow;i++){
+
+ if (m->control_pressed) { qualityForwardFile.close(); errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ qualityForwardFile << i+1;
+ for(int j=0;j<lastColumn;j++){
+ qualityForwardFile << '\t' << qualForwardMap[i][j];
+ }
+ qualityForwardFile << endl;
+ }
+ qualityForwardFile.close();
+
+
+ string qualityReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.reverse";
+ ofstream qualityReverseFile;
+ m->openOutputFile(qualityReverseFileName, qualityReverseFile);
+ outputNames.push_back(errorQualityFileName); outputTypes["error.qual.reverse"].push_back(qualityReverseFileName);
+
+ for(int i=0;i<lastColumn;i++){ qualityReverseFile << '\t' << i; } qualityReverseFile << endl;
+ for(int i=0;i<lastRow;i++){
+
+ if (m->control_pressed) { qualityReverseFile.close(); errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ qualityReverseFile << i+1;
+ for(int j=0;j<lastColumn;j++){
+ qualityReverseFile << '\t' << qualReverseMap[i][j];
+ }
+ qualityReverseFile << endl;
+ }
+ qualityReverseFile.close();
+ }
+
+
+ string errorForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.forward";
+ ofstream errorForwardFile;
+ m->openOutputFile(errorForwardFileName, errorForwardFile);
+ outputNames.push_back(errorForwardFileName); outputTypes["error.forward"].push_back(errorForwardFileName);
+
+ errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
+ for(int i=0;i<1000;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(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();
+
+ if (m->control_pressed) { errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ string errorReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.reverse";
+ ofstream errorReverseFile;
+ m->openOutputFile(errorReverseFileName, errorReverseFile);
+ outputNames.push_back(errorReverseFileName); outputTypes["error.reverse"].push_back(errorReverseFileName);
+
+ errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
+ for(int i=0;i<1000;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(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();
+ if (m->control_pressed) { errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
ofstream errorCountFile;
m->openOutputFile(errorCountFileName, errorCountFile);
outputNames.push_back(errorCountFileName); outputTypes["error.count"].push_back(errorCountFileName);
-
m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n\n");
m->mothurOut("Errors\tSequences\n");
-
- errorCountFile << "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->control_pressed) { errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ string subMatrixFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.matrix";
+ ofstream subMatrixFile;
+ m->openOutputFile(subMatrixFileName, subMatrixFile);
+ outputNames.push_back(subMatrixFileName); outputTypes["error.matrix"].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();
+
+ errorSummaryFile.close();
+ errorSeqFile.close();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ 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;
}
string q = query.getAligned();
string r = reference.getAligned();
-
int started = 0;
Compare errors;
errorSummaryFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << endl;
errorSeqFile << '>' << error.queryName << "\tref:" << error.refName << '\n' << error.sequence << endl;
+
+
+ int a=0; int t=1; int g=2; int c=3;
+ int gap=4; int n=5;
+
+ 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;
+
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "printErrorData");
projects / mothur.git / blobdiff