#include "seqerrorcommand.h"
+//**********************************************************************************************************************
+vector<string> SeqErrorCommand::getValidParameters(){
+ try {
+ string Array[] = {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SeqErrorCommand::SeqErrorCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["error"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SeqErrorCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"query","reference"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SeqErrorCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
SeqErrorCommand::SeqErrorCommand(string option) {
string temp;
//valid paramters for this command
- string AlignArray[] = {"query", "reference", "name", "threshold"};
+ string AlignArray[] = {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
//need to implement name file option
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["error"] = tempOutNames;
+ outputTypes["count"] = 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 = ""; }
it = parameters.find("query");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["query"] = inputDir + it->second; }
}
it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["reference"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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; }
}
outputDir = validParameter.validFile(parameters, "outputdir", false);
if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(queryFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(queryFileName); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "1.00"; }
convert(temp, threshold);
- errorFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".errors";
- openOutputFile(errorFileName, errorFile);
+ 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();
+
}
}
catch(exception& e) {
//***************************************************************************************************************
-SeqErrorCommand::~SeqErrorCommand(){ errorFile.close(); }
+SeqErrorCommand::~SeqErrorCommand(){
+ errorSummaryFile.close();
+ errorSeqFile.close();
+}
//***************************************************************************************************************
if(namesFileName != ""){ weights = getWeights(); }
ifstream queryFile;
- openInputFile(queryFileName, queryFile);
+ m->openInputFile(queryFileName, queryFile);
int totalBases = 0;
int totalMatches = 0;
int total = 0;
- string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".count";
+ string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
ofstream errorCountFile;
- openOutputFile(errorCountFileName, 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");
try {
ifstream referenceFile;
- openInputFile(referenceFileName, referenceFile);
+ m->openInputFile(referenceFileName, referenceFile);
while(referenceFile){
Sequence currentSeq(referenceFile);
currentSeq.removeAmbigBases();
}
referenceSeqs.push_back(currentSeq);
- gobble(referenceFile);
+ m->gobble(referenceFile);
}
numRefs = referenceSeqs.size();
string q = query.getAligned();
string r = reference.getAligned();
+
int started = 0;
Compare errors;
started = 1;
if(q[i] == 'A'){
- if(r[i] == 'A'){ errors.AA++; errors.matches++; }
- if(r[i] == 'T'){ errors.AT++; }
- if(r[i] == 'G'){ errors.AG++; }
- if(r[i] == 'C'){ errors.AC++; }
- if(r[i] == '-'){ errors.Ai++; }
+ 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++; }
- if(r[i] == 'T'){ errors.TT++; errors.matches++; }
- if(r[i] == 'G'){ errors.TG++; }
- if(r[i] == 'C'){ errors.TC++; }
- if(r[i] == '-'){ errors.Ti++; }
+ 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++; }
- if(r[i] == 'T'){ errors.GT++; }
- if(r[i] == 'G'){ errors.GG++; errors.matches++; }
- if(r[i] == 'C'){ errors.GC++; }
- if(r[i] == '-'){ errors.Gi++; }
+ 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++; }
- if(r[i] == 'T'){ errors.CT++; }
- if(r[i] == 'G'){ errors.CG++; }
- if(r[i] == 'C'){ errors.CC++; errors.matches++; }
- if(r[i] == '-'){ errors.Ci++; }
+ 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++; }
- if(r[i] == 'T'){ errors.NT++; }
- if(r[i] == 'G'){ errors.NG++; }
- if(r[i] == 'C'){ errors.NC++; }
- if(r[i] == '-'){ errors.Ni++; }
+ 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++; }
- if(r[i] == 'T'){ errors.dT++; }
- if(r[i] == 'G'){ errors.dG++; }
- if(r[i] == 'C'){ errors.dC++; }
+ 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++;
map<string, int> SeqErrorCommand::getWeights(){
ifstream nameFile;
- openInputFile(namesFileName, nameFile);
+ m->openInputFile(namesFileName, nameFile);
string seqName;
string redundantSeqs;
while(nameFile){
nameFile >> seqName >> redundantSeqs;
- nameCountMap[seqName] = getNumNames(redundantSeqs);
- gobble(nameFile);
+ nameCountMap[seqName] = m->getNumNames(redundantSeqs);
+ m->gobble(nameFile);
}
return nameCountMap;
}
void SeqErrorCommand::printErrorHeader(){
try {
- errorFile << "query\treference\tweight\t";
- errorFile << "AA\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\t";
- errorFile << "insertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\n";
+ errorSummaryFile << "query\treference\tweight\t";
+ errorSummaryFile << "AA\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\t";
+ errorSummaryFile << "insertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\n";
- errorFile << setprecision(6);
- errorFile.setf(ios::fixed);
+ errorSummaryFile << setprecision(6);
+ errorSummaryFile.setf(ios::fixed);
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "printErrorHeader");
void SeqErrorCommand::printErrorData(Compare error){
try {
- errorFile << error.queryName << '\t' << error.refName << '\t' << error.weight << '\t';
- errorFile << error.AA << '\t' << error.AT << '\t' << error.AG << '\t' << error.AC << '\t';
- errorFile << error.TA << '\t' << error.TT << '\t' << error.TG << '\t' << error.TC << '\t';
- errorFile << error.GA << '\t' << error.GT << '\t' << error.GG << '\t' << error.GC << '\t';
- errorFile << error.CA << '\t' << error.CT << '\t' << error.CG << '\t' << error.CC << '\t';
- errorFile << error.NA << '\t' << error.NT << '\t' << error.NG << '\t' << error.NC << '\t';
- errorFile << error.Ai << '\t' << error.Ti << '\t' << error.Gi << '\t' << error.Ci << '\t' << error.Ni << '\t' ;
- errorFile << error.dA << '\t' << error.dT << '\t' << error.dG << '\t' << error.dC << '\t';
+ errorSummaryFile << error.queryName << '\t' << error.refName << '\t' << error.weight << '\t';
+ errorSummaryFile << error.AA << '\t' << error.AT << '\t' << error.AG << '\t' << error.AC << '\t';
+ errorSummaryFile << error.TA << '\t' << error.TT << '\t' << error.TG << '\t' << error.TC << '\t';
+ errorSummaryFile << error.GA << '\t' << error.GT << '\t' << error.GG << '\t' << error.GC << '\t';
+ errorSummaryFile << error.CA << '\t' << error.CT << '\t' << error.CG << '\t' << error.CC << '\t';
+ errorSummaryFile << error.NA << '\t' << error.NT << '\t' << error.NG << '\t' << error.NC << '\t';
+ errorSummaryFile << error.Ai << '\t' << error.Ti << '\t' << error.Gi << '\t' << error.Ci << '\t' << error.Ni << '\t' ;
+ errorSummaryFile << error.dA << '\t' << error.dT << '\t' << error.dG << '\t' << error.dC << '\t';
- errorFile << error.Ai + error.Ti + error.Gi + error.Ci << '\t'; //insertions
- errorFile << error.dA + error.dT + error.dG + error.dC << '\t'; //deletions
- errorFile << 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
- errorFile << error.NA + error.NT + error.NG + error.NC + error.Ni << '\t'; //ambiguities
- errorFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << endl;
+ errorSummaryFile << error.Ai + error.Ti + error.Gi + error.Ci << '\t'; //insertions
+ errorSummaryFile << error.dA + error.dT + error.dG + error.dC << '\t'; //deletions
+ errorSummaryFile << 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
+ errorSummaryFile << error.NA + error.NT + error.NG + error.NC + error.Ni << '\t'; //ambiguities
+ errorSummaryFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << endl;
+ errorSeqFile << '>' << error.queryName << "\tref:" << error.refName << '\n' << error.sequence << endl;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "printErrorData");
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