*/
#include "deconvolutecommand.h"
+#include "sequence.hpp"
//**********************************************************************************************************************
vector<string> DeconvoluteCommand::setParameters(){
string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
- FastaMap fastamap;
-
- if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); }
- else { fastamap.readFastaFile(inFastaName, oldNameMapFName); }
+ map<string, string> nameMap;
+ map<string, string>::iterator itNames;
+ if (oldNameMapFName != "") { m->readNames(oldNameMapFName, nameMap); }
if (m->control_pressed) { return 0; }
- fastamap.printCondensedFasta(outFastaFile);
- fastamap.printNamesFile(outNameFile);
+ ifstream in;
+ m->openInputFile(inFastaName, in);
+
+ ofstream outFasta;
+ m->openOutputFile(outFastaFile, outFasta);
+
+ map<string, string> sequenceStrings; //sequenceString -> list of names. "atgc...." -> seq1,seq2,seq3.
+ map<string, string>::iterator itStrings;
+ set<string> nameInFastaFile; //for sanity checking
+ set<string>::iterator itname;
+ int count = 0;
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); outFasta.close(); remove(outFastaFile.c_str()); return 0; }
+
+ Sequence seq(in);
+
+ if (seq.getName() != "") {
+
+ //sanity checks
+ itname = nameInFastaFile.find(seq.getName());
+ if (itname == nameInFastaFile.end()) { nameInFastaFile.insert(seq.getName()); }
+ else { m->mothurOut("[ERROR]: You already have a sequence named " + seq.getName() + " in your fasta file, sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
+ itStrings = sequenceStrings.find(seq.getAligned());
+
+ if (itStrings == sequenceStrings.end()) { //this is a new unique sequence
+ //output to unique fasta file
+ seq.printSequence(outFasta);
+
+ if (oldNameMapFName != "") {
+ itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) { //namefile and fastafile do not match
+ m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
+ }else {
+ sequenceStrings[seq.getAligned()] = itNames->second;
+ }
+ }else { sequenceStrings[seq.getAligned()] = seq.getName(); }
+ }else { //this is a dup
+ if (oldNameMapFName != "") {
+ itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) { //namefile and fastafile do not match
+ m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
+ }else {
+ sequenceStrings[seq.getAligned()] += "," + itNames->second;
+ }
+ }else { sequenceStrings[seq.getAligned()] += "," + seq.getName(); }
+ }
+
+ count++;
+ }
+
+ m->gobble(in);
+
+ if(count % 1000 == 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
+ }
+
+ if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
+
+ in.close();
+ outFasta.close();
+
+ if (m->control_pressed) { remove(outFastaFile.c_str()); return 0; }
+
+ //print new names file
+ ofstream outNames;
+ m->openOutputFile(outNameFile, outNames);
+
+ for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
+ if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); outNames.close(); remove(outNameFile.c_str()); return 0; }
+
+ //get rep name
+ int pos = (itStrings->second).find_first_of(',');
+
+ if (pos == string::npos) { // only reps itself
+ outNames << itStrings->second << '\t' << itStrings->second << endl;
+ }else {
+ outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
+ }
+ }
+ outNames.close();
if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
int numSeqs = alignDB.getNumSeqs();
cutoff += 0.005;
+ if (!alignDB.sameLength()) { m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
+
string outputFile;
if (output == "lt") { //does the user want lower triangle phylip formatted file
if (taxons[0] == '\'') { taxons = taxons.substr(1); }
if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
}
-
+ m->splitAtChar(taxons, listOfTaxons, '-');
if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
}
string name, tax;
//bool wroteSomething = false;
-
- bool taxonsHasConfidence = false;
- vector< map<string, float> > searchTaxons;
- string noConfidenceTaxons = taxons;
- int hasConPos = taxons.find_first_of('(');
- if (hasConPos != string::npos) {
- taxonsHasConfidence = true;
- searchTaxons = getTaxons(taxons);
- noConfidenceTaxons = removeConfidences(taxons);
+ vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
+ vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
+ vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
+
+ for (int i = 0; i < listOfTaxons.size(); i++) {
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ int hasConPos = listOfTaxons[i].find_first_of('(');
+ if (hasConPos != string::npos) {
+ taxonsHasConfidence[i] = true;
+ searchTaxons[i] = getTaxons(listOfTaxons[i]);
+ noConfidenceTaxons[i] = removeConfidences(listOfTaxons[i]);
+ }
}
in >> name; //read from first column
in >> tax; //read from second column
- string newtax = tax;
-
+ for (int j = 0; j < listOfTaxons.size(); j++) {
+
+ string newtax = tax;
- //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
- if (!taxonsHasConfidence) {
- int hasConfidences = tax.find_first_of('(');
- if (hasConfidences != string::npos) {
- newtax = removeConfidences(tax);
- }
-
- int pos = newtax.find(taxons);
+ //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
+ if (!taxonsHasConfidence[j]) {
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ newtax = removeConfidences(tax);
+ }
- if (pos != string::npos) { //this sequence contains the taxon the user wants
- names.insert(name);
- out << name << '\t' << tax << endl;
- }
+ int pos = newtax.find(noConfidenceTaxons[j]);
- }else{//if taxons has them and you don't them remove taxons
- int hasConfidences = tax.find_first_of('(');
- if (hasConfidences == string::npos) {
-
- int pos = newtax.find(noConfidenceTaxons);
-
if (pos != string::npos) { //this sequence contains the taxon the user wants
- names.insert(name);
+ names.insert(name);
out << name << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
}
- }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
- //first remove confidences from both and see if the taxonomy exists
-
- string noNewTax = tax;
+ }else{//if listOfTaxons[i] has them and you don't them remove taxons
int hasConfidences = tax.find_first_of('(');
- if (hasConfidences != string::npos) {
- noNewTax = removeConfidences(tax);
- }
+ if (hasConfidences == string::npos) {
- int pos = noNewTax.find(noConfidenceTaxons);
+ int pos = newtax.find(noConfidenceTaxons[j]);
- if (pos != string::npos) { //if yes, then are the confidences okay
+ if (pos != string::npos) { //this sequence contains the taxon the user wants
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ //since you belong to at least one of the taxons we want you are included so no need to search for other
+ break;
+ }
+ }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
+ //first remove confidences from both and see if the taxonomy exists
+
+ string noNewTax = tax;
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ noNewTax = removeConfidences(tax);
+ }
+
+ int pos = noNewTax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //if yes, then are the confidences okay
- bool good = true;
- vector< map<string, float> > usersTaxon = getTaxons(newtax);
+ bool good = true;
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
- //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
- //we want to "line them up", so we will find the the index where the searchstring starts
- int index = 0;
- for (int i = 0; i < usersTaxon.size(); i++) {
+ //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
+ //we want to "line them up", so we will find the the index where the searchstring starts
+ int index = 0;
+ for (int i = 0; i < usersTaxon.size(); i++) {
- if (usersTaxon[i].begin()->first == searchTaxons[0].begin()->first) {
- index = i;
- int spot = 0;
- bool goodspot = true;
- //is this really the start, or are we dealing with a taxon of the same name?
- while ((spot < searchTaxons.size()) && ((i+spot) < usersTaxon.size())) {
- if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; }
- else { spot++; }
- }
+ if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
+ index = i;
+ int spot = 0;
+ bool goodspot = true;
+ //is this really the start, or are we dealing with a taxon of the same name?
+ while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
+ if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
+ else { spot++; }
+ }
- if (goodspot) { break; }
+ if (goodspot) { break; }
+ }
}
- }
- for (int i = 0; i < searchTaxons.size(); i++) {
+ for (int i = 0; i < searchTaxons[j].size(); i++) {
- if ((i+index) < usersTaxon.size()) { //just in case, should never be false
- if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons
+ if ((i+index) < usersTaxon.size()) { //just in case, should never be false
+ if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
+ good = false;
+ break;
+ }
+ }else {
good = false;
break;
}
- }else {
- good = false;
- break;
}
- }
- //passed the test so add you
- if (good) {
- names.insert(name);
- out << name << '\t' << tax << endl;
+ //passed the test so add you
+ if (good) {
+ names.insert(name);
+ out << name << '\t' << tax << endl;
+ break;
+ }
}
}
}
- }
-
+ }
m->gobble(in);
}
private:
set<string> names;
- vector<string> outputNames;
+ vector<string> outputNames, listOfTaxons;
string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
bool abort, dups;
CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
+ CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
+
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
if (qualfile == "not open") { abort = true; }
else if (qualfile == "not found") { qualfile = ""; }
+ accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
+ if (accnosfile2 == "not open") { abort = true; }
+ else if (accnosfile2 == "not found") { accnosfile2 = ""; }
+
+
string usedDups = "true";
string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "true"; usedDups = ""; }
dups = m->isTrue(temp);
in >> name;
if (namesAccnos.count(name) == 0){ //name unique to accnos2
- namesAccnos2.insert(name);
+ int pos = name.find_last_of('_');
+ string tempName = name;
+ if (pos != string::npos) { tempName = tempName.substr(pos+1); cout << tempName << endl; }
+ if (namesAccnos.count(tempName) == 0){
+ namesAccnos2.insert(name);
+ }else { //you are in both so erase
+ namesAccnos.erase(name);
+ namesDups.insert(name);
+ }
}else { //you are in both so erase
namesAccnos.erase(name);
namesDups.insert(name);
setGroups(); //set the groups to be analyzed and sorts them
-
+
+ if (numGroups < 2) { m->mothurOut("[ERROR]: libshuff requires at least 2 groups, you only have " + toString(numGroups) + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+
/********************************************************************************************/
//this is needed because when we read the matrix we sort it into groups in alphabetical order
//the rest of the command and the classes used in this command assume specific order
for (int i = 0; i < processors; i++) {
lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
- cout << i << '\t' << lines[i].start << '\t' << lines[i].end << endl;
}
if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
void help() { m->mothurOut(getHelpString()); }
private:
- void printSims(ostream&);
+ struct linePair {
+ int start;
+ int end;
+ };
+ vector<linePair> lines;
+
+ void printSims(ostream&, vector< vector<float> >&);
int process(vector<SharedRAbundVector*>);
vector<Calculator*> matrixCalculators;
- vector< vector<float> > simMatrix;
+ //vector< vector<float> > simMatrix;
InputData* input;
vector<SharedRAbundVector*> lookup;
string exportFileName, output, sharedfile;
- int numGroups;
+ int numGroups, processors;
ofstream out;
bool abort, allLines;
set<string> labels; //holds labels to be used
string outputFile, calc, groups, label, outputDir;
vector<string> Estimators, Groups, outputNames; //holds estimators to be used
+ int process(vector<SharedRAbundVector*>, string, string);
+ int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
+
};
}
}
/*********************************************************************************************/
+void MothurOut::mothurOut(string output, ofstream& outputFile) {
+ try {
+
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+#endif
+
+ cout << output;
+ out << output;
+ outputFile << output;
+
+#ifdef USE_MPI
+ }
+#endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOut");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine(ofstream& outputFile) {
+ try {
+#ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+#endif
+
+ cout << endl;
+ out << endl;
+ outputFile << endl;
+
+#ifdef USE_MPI
+ }
+#endif
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "MothurOutEndLine");
+ exit(1);
+ }
+}
+/*********************************************************************************************/
void MothurOut::mothurOutJustToLog(string output) {
try {
#ifdef USE_MPI
static MothurOut* getInstance();
void setFileName(string);
- void mothurOut(string);
- void mothurOutEndLine();
+ void mothurOut(string); //writes to cout and the logfile
+ void mothurOutEndLine(); //writes to cout and the logfile
+ void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
+ void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
void mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
//***************************************************************************************************************
-RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, string chimeraReportFileName){
+RefChimeraTest::RefChimeraTest(vector<Sequence>& refs){
m = MothurOut::getInstance();
- m->openOutputFile(chimeraReportFileName, chimeraReportFile);
numRefSeqs = refs.size();
referenceSeqs.resize(numRefSeqs);
alignLength = referenceSeqs[0].length();
- chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
-// chimeraReportFile << "leftParentTri,middleParentTri,rightParentTri\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
}
+//***************************************************************************************************************
+int RefChimeraTest::printHeader(ofstream& chimeraReportFile){
+ try {
+ chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
+ return 0;
+ }catch(exception& e) {
+ m->errorOut(e, "RefChimeraTest", "execute");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
+int RefChimeraTest::analyzeQuery(string queryName, string querySeq, ofstream& chimeraReportFile){
vector<vector<int> > left(numRefSeqs);
vector<int> singleLeft, bestLeft;
class RefChimeraTest {
public:
- RefChimeraTest(vector<Sequence>&, string);
- int analyzeQuery(string, string);
+ RefChimeraTest(vector<Sequence>&);
+ int printHeader(ofstream&);
+ int analyzeQuery(string, string, ofstream&);
int getClosestRefIndex();
private:
int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
int numRefSeqs;
int alignLength;
int bestMatch;
- ofstream chimeraReportFile;
+ //ofstream chimeraReportFile;
MothurOut* m;
};
if (taxons[0] == '\'') { taxons = taxons.substr(1); }
if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
}
-
+ m->splitAtChar(taxons, listOfTaxons, '-');
if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
bool wroteSomething = false;
- bool taxonsHasConfidence = false;
- vector< map<string, float> > searchTaxons;
- string noConfidenceTaxons = taxons;
- int hasConPos = taxons.find_first_of('(');
- if (hasConPos != string::npos) {
- taxonsHasConfidence = true;
- searchTaxons = getTaxons(taxons);
- noConfidenceTaxons = removeConfidences(taxons);
+ vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
+ vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
+ vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
+
+ for (int i = 0; i < listOfTaxons.size(); i++) {
+ noConfidenceTaxons[i] = listOfTaxons[i];
+ int hasConPos = listOfTaxons[i].find_first_of('(');
+ if (hasConPos != string::npos) {
+ taxonsHasConfidence[i] = true;
+ searchTaxons[i] = getTaxons(listOfTaxons[i]);
+ noConfidenceTaxons[i] = removeConfidences(listOfTaxons[i]);
+ }
}
in >> name; //read from first column
in >> tax; //read from second column
- string newtax = tax;
+ bool remove = false;
- //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
- if (!taxonsHasConfidence) {
-
- int hasConfidences = tax.find_first_of('(');
- if (hasConfidences != string::npos) {
- newtax = removeConfidences(tax);
- }
-
- int pos = newtax.find(taxons);
+ for (int j = 0; j < listOfTaxons.size(); j++) {
+ string newtax = tax;
- if (pos == string::npos) {
- wroteSomething = true;
- out << name << '\t' << tax << endl;
- }else{ //this sequence contains the taxon the user wants to remove
- names.insert(name);
- }
-
- }else{//if taxons has them and you don't them remove taxons
- int hasConfidences = tax.find_first_of('(');
- if (hasConfidences == string::npos) {
-
- int pos = newtax.find(noConfidenceTaxons);
+ //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
+ if (!taxonsHasConfidence[j]) {
- if (pos == string::npos) {
- wroteSomething = true;
- out << name << '\t' << tax << endl;
- }else{ //this sequence contains the taxon the user wants to remove
- names.insert(name);
- }
- }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
- //first remove confidences from both and see if the taxonomy exists
-
- string noNewTax = tax;
int hasConfidences = tax.find_first_of('(');
if (hasConfidences != string::npos) {
- noNewTax = removeConfidences(tax);
+ newtax = removeConfidences(tax);
}
- int pos = noNewTax.find(noConfidenceTaxons);
+ int pos = newtax.find(noConfidenceTaxons[j]);
- if (pos != string::npos) { //if yes, then are the confidences okay
+ if (pos == string::npos) {
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
+ }else{ //this sequence contains the taxon the user wants to remove
+ names.insert(name);
+ remove=true; break;
+ }
+
+ }else{//if taxons has them and you don't them remove taxons
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences == string::npos) {
- bool remove = false;
- vector< map<string, float> > usersTaxon = getTaxons(newtax);
+ int pos = newtax.find(noConfidenceTaxons[j]);
- //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
- //we want to "line them up", so we will find the the index where the searchstring starts
- int index = 0;
- for (int i = 0; i < usersTaxon.size(); i++) {
+ if (pos == string::npos) {
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
+ }else{ //this sequence contains the taxon the user wants to remove
+ names.insert(name);
+ remove=true; break;
+ }
+ }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
+ //first remove confidences from both and see if the taxonomy exists
+
+ string noNewTax = tax;
+ int hasConfidences = tax.find_first_of('(');
+ if (hasConfidences != string::npos) {
+ noNewTax = removeConfidences(tax);
+ }
+
+ int pos = noNewTax.find(noConfidenceTaxons[j]);
+
+ if (pos != string::npos) { //if yes, then are the confidences okay
- if (usersTaxon[i].begin()->first == searchTaxons[0].begin()->first) {
- index = i;
- int spot = 0;
- bool goodspot = true;
- //is this really the start, or are we dealing with a taxon of the same name?
- while ((spot < searchTaxons.size()) && ((i+spot) < usersTaxon.size())) {
- if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; }
- else { spot++; }
- }
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
+
+ //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
+ //we want to "line them up", so we will find the the index where the searchstring starts
+ int index = 0;
+ for (int i = 0; i < usersTaxon.size(); i++) {
- if (goodspot) { break; }
+ if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
+ index = i;
+ int spot = 0;
+ bool goodspot = true;
+ //is this really the start, or are we dealing with a taxon of the same name?
+ while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
+ if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
+ else { spot++; }
+ }
+
+ if (goodspot) { break; }
+ }
}
- }
-
- for (int i = 0; i < searchTaxons.size(); i++) {
- if ((i+index) < usersTaxon.size()) { //just in case, should never be false
- if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons
+ for (int i = 0; i < searchTaxons[j].size(); i++) {
+
+ if ((i+index) < usersTaxon.size()) { //just in case, should never be false
+ if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
+ remove = true;
+ break;
+ }
+ }else {
remove = true;
break;
}
+ }
+
+ //passed the test so remove you
+ if (remove) {
+ names.insert(name);
+ remove=true; break;
}else {
- remove = true;
- break;
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
}
- }
-
- //passed the test so remove you
- if (remove) {
- names.insert(name);
}else {
- wroteSomething = true;
- out << name << '\t' << tax << endl;
+ //wroteSomething = true;
+ //out << name << '\t' << tax << endl;
}
- }else {
- wroteSomething = true;
- out << name << '\t' << tax << endl;
}
}
+
}
-
-
-
+ if (!remove) { wroteSomething = true; out << name << '\t' << tax << endl; }
m->gobble(in);
}
in.close();
private:
set<string> names;
- vector<string> outputNames;
+ vector<string> outputNames, listOfTaxons;
string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
bool abort, dups;
#include "reportfile.h"
#include "qualityscores.h"
#include "refchimeratest.h"
+#include "filterseqscommand.h"
//**********************************************************************************************************************
vector<string> SeqErrorCommand::setParameters(){
CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pfilter("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfilter);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "1.00"; }
convert(temp, threshold);
- temp = validParameter.validFile(parameters, "ignorechimeras", false); if (temp == "not found") { temp = "1"; }
- convert(temp, ignoreChimeras);
+ temp = validParameter.validFile(parameters, "ignorechimeras", false); if (temp == "not found") { temp = "T"; }
+ ignoreChimeras = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "T"; }
+ filter = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
int SeqErrorCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+
+ int start = time(NULL);
maxLength = 2000;
+ totalBases = 0;
+ totalMatches = 0;
+
+ //run vertical filter on query and reference files.
+ if (filter) {
+ string inputString = "fasta=" + queryFileName + "-" + referenceFileName;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: filter.seqs(" + inputString + ") to improve processing time."); m->mothurOutEndLine();
+
+ Command* filterCommand = new FilterSeqsCommand(inputString);
+ filterCommand->execute();
+
+ map<string, vector<string> > filenames = filterCommand->getOutputFiles();
+
+ delete filterCommand;
+
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ queryFileName = filenames["fasta"][0];
+ referenceFileName = filenames["fasta"][1];
+ }
string 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();
-
+
string errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
- m->openOutputFile(errorSeqFileName, errorSeqFile);
outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
-
+
+ string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
+ outputNames.push_back(errorChimeraFileName); outputTypes["error.chimera"].push_back(errorChimeraFileName);
+
getReferences(); //read in reference sequences - make sure there's no ambiguous bases
- map<string, int> weights;
if(namesFileName != ""){ weights = getWeights(); }
- ifstream queryFile;
- m->openInputFile(queryFileName, queryFile);
+ vector<unsigned long int> fastaFilePos;
+ vector<unsigned long int> qFilePos;
+ vector<unsigned long int> reportFilePos;
- ifstream reportFile;
- ifstream qualFile;
+ setLines(queryFileName, qualFileName, reportFileName, fastaFilePos, qFilePos, reportFilePos);
+
+ if (m->control_pressed) { return 0; }
+
+ for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+ lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
+ if (qualFileName != "") { qLines.push_back(linePair(qFilePos[i], qFilePos[(i+1)])); }
+ if (reportFileName != "") { rLines.push_back(linePair(reportFilePos[i], reportFilePos[(i+1)])); }
+ }
+ if(qualFileName == "") { qLines = lines; rLines = lines; } //fills with duds
+
+ int numSeqs = 0;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
+ }else{
+ numSeqs = createProcesses(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName);
+ }
+#else
+ numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
+#endif
+
+ if(qualFileName != "" && reportFileName != ""){
+ printErrorQuality(qScoreErrorMap);
+ printQualityFR(qualForwardMap, qualReverseMap);
+ }
+
+ printErrorFRFile(errorForward, errorReverse);
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- ReportFile report;
- QualityScores quality;
- vector<vector<int> > qualForwardMap;
- vector<vector<int> > qualReverseMap;
+ 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");
+ 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->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ printSubMatrix();
+
+ string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.ref-query";
+ ofstream megAlignmentFile;
+ m->openOutputFile(megAlignmentFileName, megAlignmentFile);
+ outputNames.push_back(megAlignmentFileName); outputTypes["error.ref-query"].push_back(megAlignmentFileName);
+
+ for(int i=0;i<numRefs;i++){
+ megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
+ megAlignmentFile << megaAlignVector[i] << endl;
+ }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
+ m->mothurOutEndLine();
+
+ 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, "SeqErrorCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SeqErrorCommand::createProcesses(string filename, string qFileName, string rFileName, string summaryFileName, string errorOutputFileName, string chimeraOutputFileName) {
+ try {
+ int process = 1;
+ processIDS.clear();
+ map<char, vector<int> >::iterator it;
+ int num = 0;
- if(qualFileName != "" && reportFileName != ""){
- m->openInputFile(qualFileName, qualFile);
- report = ReportFile(reportFile, reportFileName);
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
- qualForwardMap.resize(maxLength);
- qualReverseMap.resize(maxLength);
- for(int i=0;i<maxLength;i++){
- qualForwardMap[i].assign(41,0);
- qualReverseMap[i].assign(41,0);
- }
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+
+ num = driver(filename, qFileName, rFileName, summaryFileName + toString(getpid()) + ".temp", errorOutputFileName+ toString(getpid()) + ".temp", chimeraOutputFileName + toString(getpid()) + ".temp", lines[process], qLines[process], rLines[process]);
+
+ //pass groupCounts to parent
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".info.temp";
+ m->openOutputFile(tempFile, out);
+
+ //output totalBases and totalMatches
+ out << num << '\t' << totalBases << '\t' << totalMatches << endl << endl;
+
+ //output substitutionMatrix
+ for(int i = 0; i < substitutionMatrix.size(); i++) {
+ for (int j = 0; j < substitutionMatrix[i].size(); j++) {
+ out << substitutionMatrix[i][j] << '\t';
+ }
+ out << endl;
+ }
+ out << endl;
+
+ //output qScoreErrorMap
+ for (it = qScoreErrorMap.begin(); it != qScoreErrorMap.end(); it++) {
+ vector<int> thisScoreErrorMap = it->second;
+ out << it->first << '\t';
+ for (int i = 0; i < thisScoreErrorMap.size(); i++) {
+ out << thisScoreErrorMap[i] << '\t';
+ }
+ out << endl;
+ }
+ out << endl;
+
+ //output qualForwardMap
+ for(int i = 0; i < qualForwardMap.size(); i++) {
+ for (int j = 0; j < qualForwardMap[i].size(); j++) {
+ out << qualForwardMap[i][j] << '\t';
+ }
+ out << endl;
+ }
+ out << endl;
+
+ //output qualReverseMap
+ for(int i = 0; i < qualReverseMap.size(); i++) {
+ for (int j = 0; j < qualReverseMap[i].size(); j++) {
+ out << qualReverseMap[i][j] << '\t';
+ }
+ out << endl;
+ }
+ out << endl;
+
+
+ //output errorForward
+ for (it = errorForward.begin(); it != errorForward.end(); it++) {
+ vector<int> thisErrorForward = it->second;
+ out << it->first << '\t';
+ for (int i = 0; i < thisErrorForward.size(); i++) {
+ out << thisErrorForward[i] << '\t';
+ }
+ out << endl;
+ }
+ out << endl;
+
+ //output errorReverse
+ for (it = errorReverse.begin(); it != errorReverse.end(); it++) {
+ vector<int> thisErrorReverse = it->second;
+ out << it->first << '\t';
+ for (int i = 0; i < thisErrorReverse.size(); i++) {
+ out << thisErrorReverse[i] << '\t';
+ }
+ out << endl;
+ }
+ out << endl;
+
+ //output misMatchCounts
+ out << misMatchCounts.size() << endl;
+ for (int j = 0; j < misMatchCounts.size(); j++) {
+ out << misMatchCounts[j] << '\t';
+ }
+ out << endl;
+
+
+ //output megaAlignVector
+ for (int j = 0; j < megaAlignVector.size(); j++) {
+ out << megaAlignVector[j] << endl;
+ }
+ out << endl;
+
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ num = driver(filename, qFileName, rFileName, summaryFileName, errorOutputFileName, chimeraOutputFileName, lines[0], qLines[0], rLines[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
}
- int totalBases = 0;
- int totalMatches = 0;
+ //append files
+ for(int i=0;i<processIDS.size();i++){
+
+ m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
+
+ m->appendFiles((summaryFileName + toString(processIDS[i]) + ".temp"), summaryFileName);
+ remove((summaryFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->appendFiles((errorOutputFileName + toString(processIDS[i]) + ".temp"), errorOutputFileName);
+ remove((errorOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->appendFiles((chimeraOutputFileName + toString(processIDS[i]) + ".temp"), chimeraOutputFileName);
+ remove((chimeraOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+
+ ifstream in;
+ string tempFile = filename + toString(processIDS[i]) + ".info.temp";
+ m->openInputFile(tempFile, in);
+
+ //input totalBases and totalMatches
+ int tempBases, tempMatches, tempNumSeqs;
+ in >> tempNumSeqs >> tempBases >> tempMatches; m->gobble(in);
+ totalBases += tempBases; totalMatches += tempMatches; num += tempNumSeqs;
+
+ //input substitutionMatrix
+ int tempNum;
+ for(int i = 0; i < substitutionMatrix.size(); i++) {
+ for (int j = 0; j < substitutionMatrix[i].size(); j++) {
+ in >> tempNum; substitutionMatrix[i][j] += tempNum;
+ }
+ m->gobble(in);
+ }
+ m->gobble(in);
+
+ //input qScoreErrorMap
+ char first;
+ for (int i = 0; i < qScoreErrorMap.size(); i++) {
+ in >> first;
+ vector<int> thisScoreErrorMap = qScoreErrorMap[first];
+
+ for (int i = 0; i < thisScoreErrorMap.size(); i++) {
+ in >> tempNum; thisScoreErrorMap[i] += tempNum;
+ }
+ qScoreErrorMap[first] = thisScoreErrorMap;
+ m->gobble(in);
+ }
+ m->gobble(in);
+
+ //input qualForwardMap
+ for(int i = 0; i < qualForwardMap.size(); i++) {
+ for (int j = 0; j < qualForwardMap[i].size(); j++) {
+ in >> tempNum; qualForwardMap[i][j] += tempNum;
+ }
+ m->gobble(in);
+ }
+ m->gobble(in);
+
+ //input qualReverseMap
+ for(int i = 0; i < qualReverseMap.size(); i++) {
+ for (int j = 0; j < qualReverseMap[i].size(); j++) {
+ in >> tempNum; qualReverseMap[i][j] += tempNum;
+ }
+ m->gobble(in);
+ }
+ m->gobble(in);
+
+ //input errorForward
+ for (int i = 0; i < errorForward.size(); i++) {
+ in >> first;
+ vector<int> thisErrorForward = errorForward[first];
+
+ for (int i = 0; i < thisErrorForward.size(); i++) {
+ in >> tempNum; thisErrorForward[i] += tempNum;
+ }
+ errorForward[first] = thisErrorForward;
+ m->gobble(in);
+ }
+ m->gobble(in);
+
+ //input errorReverse
+ for (int i = 0; i < errorReverse.size(); i++) {
+ in >> first;
+ vector<int> thisErrorReverse = errorReverse[first];
+
+ for (int i = 0; i < thisErrorReverse.size(); i++) {
+ in >> tempNum; thisErrorReverse[i] += tempNum;
+ }
+ errorReverse[first] = thisErrorReverse;
+ m->gobble(in);
+ }
+ m->gobble(in);
+
+ //input misMatchCounts
+ int misMatchSize;
+ in >> misMatchSize; m->gobble(in);
+ if (misMatchSize > misMatchCounts.size()) { misMatchCounts.resize(misMatchSize, 0); }
+ for (int j = 0; j < misMatchCounts.size(); j++) {
+ in >> tempNum; misMatchCounts[j] += tempNum;
+ }
+ m->gobble(in);
+
+ //input megaAlignVector
+ string thisLine;
+ for (int j = 0; j < megaAlignVector.size(); j++) {
+ thisLine = m->getline(in); m->gobble(in); megaAlignVector[j] += thisLine + '\n';
+ }
+ m->gobble(in);
+
+ in.close(); remove(tempFile.c_str());
+
+ }
+
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SeqErrorCommand::driver(string filename, string qFileName, string rFileName, string summaryFileName, string errorOutputFileName, string chimeraOutputFileName, linePair line, linePair qline, linePair rline) {
+
+ try {
+ ReportFile report;
+ QualityScores quality;
- vector<int> misMatchCounts(11, 0);
+ misMatchCounts.resize(11, 0);
int maxMismatch = 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(maxLength,0);
errorForward['s'].assign(maxLength,0);
errorForward['i'].assign(maxLength,0);
errorForward['d'].assign(maxLength,0);
errorForward['a'].assign(maxLength,0);
- map<char, vector<int> > errorReverse;
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);
-
- string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
- RefChimeraTest chimeraTest(referenceSeqs, errorChimeraFileName);
- outputNames.push_back(errorChimeraFileName); outputTypes["error.chimera"].push_back(errorChimeraFileName);
+ //open inputfiles and go to beginning place for this processor
+ ifstream queryFile;
+ m->openInputFile(filename, queryFile);
+ queryFile.seekg(line.start);
+
+ ifstream reportFile;
+ ifstream qualFile;
+ if(qFileName != "" && rFileName != ""){
+ m->openInputFile(qFileName, qualFile);
+ qualFile.seekg(qline.start);
+
+ //gobble headers
+ if (rline.start == 0) { report = ReportFile(reportFile, rFileName); }
+ else{
+ m->openInputFile(rFileName, reportFile);
+ reportFile.seekg(rline.start);
+ }
+
+ qualForwardMap.resize(maxLength);
+ qualReverseMap.resize(maxLength);
+ for(int i=0;i<maxLength;i++){
+ qualForwardMap[i].assign(41,0);
+ qualReverseMap[i].assign(41,0);
+ }
+ }
+
+ ofstream outChimeraReport;
+ m->openOutputFile(chimeraOutputFileName, outChimeraReport);
+ RefChimeraTest chimeraTest(referenceSeqs);
+ if (line.start == 0) { chimeraTest.printHeader(outChimeraReport); }
+
+ ofstream errorSummaryFile;
+ m->openOutputFile(summaryFileName, errorSummaryFile);
+ if (line.start == 0) { printErrorHeader(errorSummaryFile); }
+
+ ofstream errorSeqFile;
+ m->openOutputFile(errorOutputFileName, errorSeqFile);
+
+ megaAlignVector.resize(numRefs, "");
- vector<string> megaAlignVector(numRefs, "");
-
int index = 0;
bool ignoreSeq = 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; }
-
+ bool moreSeqs = 1;
+ while (moreSeqs) {
+
+ if (m->control_pressed) { queryFile.close(); if(qFileName != "" && rFileName != ""){ reportFile.close(); qualFile.close(); } outChimeraReport.close(); errorSummaryFile.close();errorSeqFile.close(); return 0; }
+
Sequence query(queryFile);
- int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
+ int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned(), outChimeraReport);
int closestRefIndex = chimeraTest.getClosestRefIndex();
-
+
if(numParentSeqs > 1 && ignoreChimeras == 1) { ignoreSeq = 1; }
else { ignoreSeq = 0; }
-
+
Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
if(namesFileName != ""){
minCompare.weight = it->second;
}
else{ minCompare.weight = 1; }
-
- printErrorData(minCompare, numParentSeqs);
-
+
+ printErrorData(minCompare, numParentSeqs, errorSummaryFile, errorSeqFile);
+
if(!ignoreSeq){
-
+
for(int i=0;i<minCompare.sequence.length();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 origLength = report.getQueryLength();
int startBase = report.getQueryStart();
int endBase = report.getQueryEnd();
-
+
quality = QualityScores(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);
}
}
-
+
if(minCompare.errorRate < threshold && !ignoreSeq){
totalBases += (minCompare.total * minCompare.weight);
totalMatches += minCompare.matches * minCompare.weight;
megaAlignVector[closestRefIndex] += query.getInlineSeq() + '\n';
}
-
+
index++;
- if(index % 1000 == 0){ m->mothurOut(toString(index) + '\n'); }
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long int pos = queryFile.tellg();
+ if ((pos == -1) || (pos >= line.end)) { break; }
+ #else
+ if (queryFile.eof()) { break; }
+ #endif
+
+ if(index % 100 == 0){ m->mothurOut(toString(index) + '\n'); }
}
queryFile.close();
+ if(qFileName != "" && rFileName != ""){ reportFile.close(); qualFile.close(); }
errorSummaryFile.close();
errorSeqFile.close();
-
- if(qualFileName != "" && reportFileName != ""){
- printErrorQuality(qScoreErrorMap);
- printQualityFR(qualForwardMap, qualReverseMap);
- }
-
- printErrorFRFile(errorForward, errorReverse);
-
- if (m->control_pressed) { 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");
- 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->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
-
- printSubMatrix();
-
- string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.ref-query";
- ofstream megAlignmentFile;
- m->openOutputFile(megAlignmentFileName, megAlignmentFile);
- outputNames.push_back(megAlignmentFileName); outputTypes["error.ref-query"].push_back(megAlignmentFileName);
-
- for(int i=0;i<numRefs;i++){
- megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
- megAlignmentFile << megaAlignVector[i] << endl;
- }
+ //report progress
+ if(index % 100 != 0){ m->mothurOut(toString(index) + '\n'); }
- 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;
+ return index;
}
catch(exception& e) {
- m->errorOut(e, "SeqErrorCommand", "execute");
+ m->errorOut(e, "SeqErrorCommand", "driver");
exit(1);
}
}
-
//***************************************************************************************************************
void SeqErrorCommand::getReferences(){
//***************************************************************************************************************
-void SeqErrorCommand::printErrorHeader(){
+void SeqErrorCommand::printErrorHeader(ofstream& errorSummaryFile){
try {
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";
//***************************************************************************************************************
-void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs){
+void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs, ofstream& errorSummaryFile, ofstream& errorSeqFile){
try {
errorSummaryFile << error.queryName << '\t' << error.refName << '\t' << error.weight << '\t';
}
}
+/**************************************************************************************************/
+int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos, vector<unsigned long int>& rfileFilePos) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //set file positions for fasta file
+ fastaFilePos = m->divideFile(filename, processors);
+
+ if (qfilename == "") { return processors; }
+
+ //get name of first sequence in each chunk
+ map<string, int> firstSeqNames;
+ for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+ ifstream in;
+ m->openInputFile(filename, in);
+ in.seekg(fastaFilePos[i]);
+
+ Sequence temp(in);
+ firstSeqNames[temp.getName()] = i;
+
+ in.close();
+ }
+
+ //make copy to use below
+ map<string, int> firstSeqNamesReport = firstSeqNames;
+
+ //seach for filePos of each first name in the qfile and save in qfileFilePos
+ ifstream inQual;
+ m->openInputFile(qfilename, inQual);
+
+ string input;
+ while(!inQual.eof()){
+ input = m->getline(inQual);
+
+ if (input.length() != 0) {
+ if(input[0] == '>'){ //this is a sequence name line
+ istringstream nameStream(input);
+
+ string sname = ""; nameStream >> sname;
+ sname = sname.substr(1);
+
+ map<string, int>::iterator it = firstSeqNames.find(sname);
+
+ if(it != firstSeqNames.end()) { //this is the start of a new chunk
+ unsigned long int pos = inQual.tellg();
+ qfileFilePos.push_back(pos - input.length() - 1);
+ firstSeqNames.erase(it);
+ }
+ }
+ }
+
+ if (firstSeqNames.size() == 0) { break; }
+ }
+ inQual.close();
+
+ if (firstSeqNames.size() != 0) {
+ for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
+ m->mothurOut(it->first + " is in your fasta file and not in your quality file, aborting."); m->mothurOutEndLine();
+ }
+ m->control_pressed = true;
+ return processors;
+ }
+
+ //get last file position of qfile
+ FILE * pFile;
+ unsigned long int size;
+
+ //get num bytes in file
+ pFile = fopen (qfilename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+
+ qfileFilePos.push_back(size);
+
+ //seach for filePos of each first name in the rfile and save in rfileFilePos
+ string junk;
+ ifstream inR;
+ m->openInputFile(rfilename, inR);
+
+ //read column headers
+ for (int i = 0; i < 16; i++) {
+ if (!inR.eof()) { inR >> junk; }
+ else { break; }
+ }
+
+ while(!inR.eof()){
+
+ if (m->control_pressed) { inR.close(); return processors; }
+
+ input = m->getline(inR);
+
+ if (input.length() != 0) {
+
+ istringstream nameStream(input);
+ string sname = ""; nameStream >> sname;
+
+ map<string, int>::iterator it = firstSeqNamesReport.find(sname);
+
+ if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk
+ unsigned long int pos = inR.tellg();
+ rfileFilePos.push_back(pos - input.length() - 1);
+ firstSeqNamesReport.erase(it);
+ }
+ }
+
+ if (firstSeqNamesReport.size() == 0) { break; }
+ m->gobble(inR);
+ }
+ inR.close();
+
+ if (firstSeqNamesReport.size() != 0) {
+ for (map<string, int>::iterator it = firstSeqNamesReport.begin(); it != firstSeqNamesReport.end(); it++) {
+ m->mothurOut(it->first + " is in your fasta file and not in your report file, aborting."); m->mothurOutEndLine();
+ }
+ m->control_pressed = true;
+ return processors;
+ }
+
+ //get last file position of qfile
+ FILE * rFile;
+ unsigned long int sizeR;
+
+ //get num bytes in file
+ rFile = fopen (rfilename.c_str(),"rb");
+ if (rFile==NULL) perror ("Error opening file");
+ else{
+ fseek (rFile, 0, SEEK_END);
+ sizeR=ftell (rFile);
+ fclose (rFile);
+ }
+
+ rfileFilePos.push_back(sizeR);
+
+ return processors;
+
+#else
+
+ fastaFilePos.push_back(0); qfileFilePos.push_back(0);
+ //get last file position of fastafile
+ FILE * pFile;
+ unsigned long int size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+ fastaFilePos.push_back(size);
+
+ //get last file position of fastafile
+ FILE * qFile;
+
+ //get num bytes in file
+ qFile = fopen (qfilename.c_str(),"rb");
+ if (qFile==NULL) perror ("Error opening file");
+ else{
+ fseek (qFile, 0, SEEK_END);
+ size=ftell (qFile);
+ fclose (qFile);
+ }
+ qfileFilePos.push_back(size);
+
+ return 1;
+
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "setLines");
+ exit(1);
+ }
+}
//***************************************************************************************************************
private:
bool abort;
+
+ struct linePair {
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ };
+
+ vector<int> processIDS; //processid
+ vector<linePair> lines;
+ vector<linePair> qLines;
+ vector<linePair> rLines;
void getReferences();
map<string,int> getWeights();
Compare getErrors(Sequence, Sequence);
- void printErrorHeader();
- void printErrorData(Compare, int);
+ void printErrorHeader(ofstream&);
+ void printErrorData(Compare, int, ofstream&, ofstream&);
void printSubMatrix();
void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
void printErrorQuality(map<char, vector<int> >);
void printQualityFR(vector<vector<int> >, vector<vector<int> >);
+
+ int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long int>&);
+ int driver(string, string, string, string, string, string, linePair, linePair, linePair);
+ int createProcesses(string, string, string, string, string, string);
string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
double threshold;
- bool ignoreChimeras;
+ bool ignoreChimeras, filter;
int numRefs, processors;
- int maxLength;
- ofstream errorSummaryFile, errorSeqFile;
+ int maxLength, totalBases, totalMatches;
+ //ofstream errorSummaryFile, errorSeqFile;
vector<string> outputNames;
vector<Sequence> referenceSeqs;
vector<vector<int> > substitutionMatrix;
+ vector<vector<int> > qualForwardMap;
+ vector<vector<int> > qualReverseMap;
+ vector<int> misMatchCounts;
+ map<char, vector<int> > qScoreErrorMap;
+ map<char, vector<int> > errorForward;
+ map<char, vector<int> > errorReverse;
+ map<string, int> weights;
+ vector<string> megaAlignVector;
+
};
#endif
/***********************************************************************/
-SequenceDB::SequenceDB() { m = MothurOut::getInstance(); }
+SequenceDB::SequenceDB() { m = MothurOut::getInstance(); length = 0; samelength = true; }
/***********************************************************************/
//the clear function free's the memory
SequenceDB::~SequenceDB() { clear(); }
SequenceDB::SequenceDB(int newSize) {
data.resize(newSize, Sequence());
+ length = 0; samelength = true;
}
/***********************************************************************/
SequenceDB::SequenceDB(ifstream& filehandle) {
try{
+ length = 0; samelength = true;
//read through file
while (!filehandle.eof()) {
//input sequence info into sequencedb
Sequence newSequence(filehandle);
- if (newSequence.getName() != "") { data.push_back(newSequence); }
+ if (newSequence.getName() != "") {
+ if (length == 0) { length = newSequence.getAligned().length(); }
+ if (length != newSequence.getAligned().length()) { samelength = false; }
+ data.push_back(newSequence);
+ }
//takes care of white space
m->gobble(filehandle);
break;
}else { sequence += line; }
}
-
+
+ if (length == 0) { length = sequence.length(); }
+ if (length != sequence.length()) { samelength = false; }
+
return sequence;
}
catch(exception& e) {
void SequenceDB::set(int index, string newUnaligned) {
try {
+ if (length == 0) { length = newUnaligned.length(); }
+ if (length != newUnaligned.length()) { samelength = false; }
+
data[index] = Sequence(data[index].getName(), newUnaligned);
}
catch(exception& e) {
void SequenceDB::set(int index, Sequence newSeq) {
try {
+ if (length == 0) { length = newSeq.getAligned().length(); }
+ if (length != newSeq.getAligned().length()) { samelength = false; }
+
data[index] = newSeq;
}
catch(exception& e) {
void SequenceDB::push_back(Sequence newSequence) {
try {
+ if (length == 0) { length = newSequence.getAligned().length(); }
+ if (length != newSequence.getAligned().length()) { samelength = false; }
+
data.push_back(newSequence);
}
catch(exception& e) {
void clear(); //clears data - remeber to loop through and delete the sequences inside or you will have a memory leak
int size(); //returns datas size
void print(ostream&); //loops through data using sequence class print
+ bool sameLength() { return samelength; }
private:
vector<Sequence> data;
string readName(ifstream&);
string readSequence(ifstream&);
MothurOut* m;
+ bool samelength;
+ int length;
};
ifstream intemp;
m->openInputFile(tempdistFileName, intemp);
- for (int i = 0; i < calcDists.size(); i++) {
+ for (int k = 0; k < calcDists.size(); k++) {
int size = 0;
intemp >> size; m->gobble(intemp);
intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
seqDist tempDist(seq1, seq2, dist);
- calcDists[i].push_back(tempDist);
+ calcDists[k].push_back(tempDist);
}
}
intemp.close();
temp = validParameter.validFile(parameters, "name", true);
if (temp == "not found") { nameFile = ""; }
- else if(temp == "not open") { abort = true; }
+ else if(temp == "not open") { nameFile = ""; abort = true; }
else { nameFile = temp; }
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
ofstream temp;
m->openOutputFile(trimFASTAFileName, temp); temp.close();
m->openOutputFile(scrapFASTAFileName, temp); temp.close();
- m->openOutputFile(trimQualFileName, temp); temp.close();
- m->openOutputFile(scrapQualFileName, temp); temp.close();
- m->openOutputFile(trimNameFileName, temp); temp.close();
- m->openOutputFile(scrapNameFileName, temp); temp.close();
+ if(qFileName != ""){
+ m->openOutputFile(trimQualFileName, temp); temp.close();
+ m->openOutputFile(scrapQualFileName, temp); temp.close();
+ }
+ if (nameFile != "") {
+ m->openOutputFile(trimNameFileName, temp); temp.close();
+ m->openOutputFile(scrapNameFileName, temp); temp.close();
+ }
driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
projects / mothur.git / commitdiff