*/
#include "seqerrorcommand.h"
+#include "reportfile.h"
+#include "qualityscores.h"
//**********************************************************************************************************************
vector<string> SeqErrorCommand::getValidParameters(){
try {
- string Array[] = {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
+ string Array[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
string temp;
//valid paramters for this command
- string AlignArray[] = {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
-
-//need to implement name file option
+ string AlignArray[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
}
it = parameters.find("name");
- //user has given a template file
+ //user has given a names 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("qfile");
+ //user has given a quality score 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["qfile"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("report");
+ //user has given a alignment report 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["report"] = inputDir + it->second; }
+ }
}
//check for required parameters
if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
else if (referenceFileName == "not open") { abort = true; }
- //if the user changes the output directory command factory will send this info to us in the output parameter
+
+ //check for optional parameters
namesFileName = validParameter.validFile(parameters, "name", true);
if(namesFileName == "not found"){ namesFileName = ""; }
- cout << namesFileName << endl;
+
+ qualFileName = validParameter.validFile(parameters, "qfile", true);
+ if(qualFileName == "not found"){ qualFileName = ""; }
+
+ reportFileName = validParameter.validFile(parameters, "report", true);
+ if(reportFileName == "not found"){ reportFileName = ""; }
+
+ 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;
+ }
outputDir = validParameter.validFile(parameters, "outputdir", false);
if (outputDir == "not found"){
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) {
SeqErrorCommand::~SeqErrorCommand(){
errorSummaryFile.close();
- errorSeqFile.close();
+ errorSeqFile.close();
}
//***************************************************************************************************************
ifstream queryFile;
m->openInputFile(queryFileName, queryFile);
-
+
+ ifstream reportFile;
+ ifstream qualFile;
+
+ 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;
int totalMatches = 0;
int numSeqs = 0;
map<string, int>::iterator it;
+ map<char, vector<int> > qScoreErrorMap;
+ qScoreErrorMap['m'].assign(41, 0);
+ qScoreErrorMap['s'].assign(41, 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){
Compare minCompare;
-
Sequence query(queryFile);
for(int i=0;i<numRefs;i++){
if(currCompare.errorRate < minCompare.errorRate){
minCompare = currCompare;
}
-
}
if(namesFileName != ""){
it = weights.find(query.getName());
minCompare.weight = it->second;
}
- else {
- minCompare.weight = 1;
- }
+ else { minCompare.weight = 1; }
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);
+
+ int origLength = report.getQueryLength();
+ int startBase = report.getQueryStart();
+ int endBase = report.getQueryEnd();
+
+ 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){
totalBases += (minCompare.total * minCompare.weight);
totalMatches += minCompare.matches * minCompare.weight;
numSeqs++;
}
+
}
queryFile.close();
int total = 0;
+ if(qualFileName != "" && reportFileName != ""){
+ string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality";
+ ofstream errorQualityFile;
+ m->openOutputFile(errorQualityFileName, errorQualityFile);
+ outputNames.push_back(errorQualityFileName); outputTypes["error.quality"].push_back(errorQualityFileName);
+
+ errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
+ 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++){
+ 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++){
+ qualityReverseFile << i+1;
+ for(int j=0;j<lastColumn;j++){
+ qualityReverseFile << '\t' << qualReverseMap[i][j];
+ }
+ qualityReverseFile << endl;
+ }
+
+ }
+
+
+ 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();
+
+
+ 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();
+
+
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();
+
+
+
+
+
+ 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();
+
+
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