TrimSeqsCommand::TrimSeqsCommand(string option){
try {
- globaldata = GlobalData::getInstance();
abort = false;
//allow user to run help
else {
//valid paramters for this command
- string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength"};
+ string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", "qthreshold", "qaverage", "allfiles"};
+
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
- ValidParameters* validParameter = new ValidParameters();
-
//check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//check for required parameters
- fastafile = validParameter->validFile(parameters, "fasta", true);
- if (fastafile == "not found") { cout << "fasta is a required parameter for the screen.seqs command." << endl; abort = true; }
- else if (fastafile == "not open") { abort = true; }
- else { globaldata->setFastaFile(fastafile); }
+ fastaFile = validParameter.validFile(parameters, "fasta", true);
+ if (fastaFile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
+ else if (fastaFile == "not open") { abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
- temp = validParameter->validFile(parameters, "flip", false); if (temp == "not found") { temp = "0"; }
- if(isTrue(temp)) { flip = 1; }
+ temp = validParameter.validFile(parameters, "flip", false);
+ if (temp == "not found"){ flip = 0; }
+ else if(isTrue(temp)) { flip = 1; }
- temp = validParameter->validFile(parameters, "oligos", false); if (temp == "not found") { temp = ""; }
- if(temp != "") { oligos = 1; }
- else { oligos = 0; }
-
- temp = validParameter->validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
+ temp = validParameter.validFile(parameters, "oligos", true);
+ if (temp == "not found"){ oligoFile = ""; }
+ else if(temp == "not open"){ abort = true; }
+ else { oligoFile = temp; }
+
+ temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
convert(temp, maxAmbig);
- temp = validParameter->validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; }
+ temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; }
convert(temp, maxHomoP);
- temp = validParameter->validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
+ temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
convert(temp, minLength);
- temp = validParameter->validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
- convert(temp, maxLength);
+ temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, maxLength);
+
+ temp = validParameter.validFile(parameters, "qfile", true);
+ if (temp == "not found") { qFileName = ""; }
+ else if(temp == "not open") { abort = 0; }
+ else { qFileName = temp; }
- if(!flip && !oligos && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP ){ cout << "huh?" << endl; }
+ temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qThreshold);
+
+ temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qAverage);
+
+ temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
+ allFiles = isTrue(temp);
- delete validParameter;
+ if(allFiles && oligoFile == ""){
+ mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); mothurOutEndLine();
+ }
+ if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
+ mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); mothurOutEndLine();
+ qAverage=0;
+ qThreshold=0;
+ }
+ if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
+ mothurOut("You didn't set any options... quiting command."); mothurOutEndLine();
+ abort = true;
+ }
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TrimSeqsCommand class function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void TrimSeqsCommand::help(){
try {
- cout << "The trim.seqs command reads a fastafile and creates ....." << "\n";
- cout << "The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength." << "\n";
- cout << "The fasta parameter is required." << "\n";
- cout << "The flip parameter .... The default is 0." << "\n";
- cout << "The oligos parameter .... The default is ""." << "\n";
- cout << "The maxambig parameter .... The default is -1." << "\n";
- cout << "The maxhomop parameter .... The default is 0." << "\n";
- cout << "The minlength parameter .... The default is 0." << "\n";
- cout << "The maxlength parameter .... The default is 0." << "\n";
- cout << "The trim.seqs command should be in the following format: " << "\n";
- cout << "trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, " << "\n";
- cout << "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) " << "\n";
- cout << "Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...)." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+ mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
+ mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength.\n");
+ mothurOut("The fasta parameter is required.\n");
+ mothurOut("The flip parameter .... The default is 0.\n");
+ mothurOut("The oligos parameter .... The default is "".\n");
+ mothurOut("The maxambig parameter .... The default is -1.\n");
+ mothurOut("The maxhomop parameter .... The default is 0.\n");
+ mothurOut("The minlength parameter .... The default is 0.\n");
+ mothurOut("The maxlength parameter .... The default is 0.\n");
+ mothurOut("The trim.seqs command should be in the following format: \n");
+ mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n");
+ mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
+ mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TrimSeqsCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TrimSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
try{
if (abort == true) { return 0; }
-
- getOligos();
-
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ ifstream inFASTA;
+ openInputFile(fastaFile, inFASTA);
+
ofstream outFASTA;
- string trimSeqFile = getRootName(fastafile) + "trim.fasta";
+ string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
openOutputFile(trimSeqFile, outFASTA);
ofstream outGroups;
- string groupFile = getRootName(fastafile) + "groups";
- openOutputFile(groupFile, outGroups);
-
+ vector<ofstream*> fastaFileNames;
+ if(oligoFile != ""){
+ string groupFile = getRootName(fastaFile) + "groups";
+ openOutputFile(groupFile, outGroups);
+ getOligos(fastaFileNames);
+ }
+
ofstream scrapFASTA;
- string scrapSeqFile = getRootName(fastafile) + "scrap.fasta";
+ string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
openOutputFile(scrapSeqFile, scrapFASTA);
-
- bool success;
+ ifstream qFile;
+ if(qFileName != "") { openInputFile(qFileName, qFile); }
+
+ bool success;
+
while(!inFASTA.eof()){
Sequence currSeq(inFASTA);
string origSeq = currSeq.getUnaligned();
- string group;
+ int group;
string trashCode = "";
-
+
+ if(qFileName != ""){
+ if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
+ else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
+ if(!success) { trashCode += 'q'; }
+ }
if(barcodes.size() != 0){
+
success = stripBarcode(currSeq, group);
if(!success){ trashCode += 'b'; }
}
}
if(minLength > 0 || maxLength > 0){
success = cullLength(currSeq);
- if(!success){ trashCode += 'l'; }
+ if ((currSeq.getUnaligned().length() > 300) && (success)) { cout << "too long " << currSeq.getUnaligned().length() << endl; }
+ if(!success){ trashCode += 'l'; }
}
if(maxHomoP > 0){
success = cullHomoP(currSeq);
}
if(flip){ currSeq.reverseComplement(); } // should go last
-
+
if(trashCode.length() == 0){
+ currSeq.setAligned(currSeq.getUnaligned()); //this is because of a modification we made to the sequence class to fix a bug. all seqs have an aligned version, which is the version that gets printed.
currSeq.printSequence(outFASTA);
- outGroups << currSeq.getName() << '\t' << group << endl;
+ if(barcodes.size() != 0){
+ outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
+
+ if(allFiles){
+ currSeq.printSequence(*fastaFileNames[group]);
+ }
+ }
}
else{
currSeq.setName(currSeq.getName() + '|' + trashCode);
currSeq.setUnaligned(origSeq);
currSeq.printSequence(scrapFASTA);
}
-
gobble(inFASTA);
}
inFASTA.close();
outFASTA.close();
scrapFASTA.close();
outGroups.close();
+ if(qFileName != "") { qFile.close(); }
+
+ for(int i=0;i<fastaFileNames.size();i++){
+ fastaFileNames[i]->close();
+ delete fastaFileNames[i];
+ }
+
+ for(int i=0;i<fastaFileNames.size();i++){
+ string seqName;
+ openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
+ ofstream outGroups;
+ openOutputFile(getRootName(fastaFile) + groupVector[i] + ".groups", outGroups);
+
+ while(!inFASTA.eof()){
+ if(inFASTA.get() == '>'){
+ inFASTA >> seqName;
+ outGroups << seqName << '\t' << groupVector[i] << endl;
+ }
+ while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+ }
+ outGroups.close();
+ inFASTA.close();
+ }
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the TrimSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TrimSeqsCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(){
-
- ifstream inOligos;
- //openInputFile(globaldata->getOligosFile(), inOligos);
-
- string type, oligo, group;
-
- while(!inOligos.eof()){
- inOligos >> type;
+void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
+ try {
+ ifstream inOligos;
+ openInputFile(oligoFile, inOligos);
- if(type == "forward"){
- inOligos >> oligo;
- forPrimer.push_back(oligo);
- }
- else if(type == "reverse"){
- inOligos >> oligo;
- revPrimer.push_back(oligo);
- }
- else if(type == "barcode"){
- inOligos >> oligo >> group;
- barcodes[oligo]=group;
- }
- else if(type[0] == '#'){
- char c;
- while ((c = inOligos.get()) != EOF) { if (c == 10){ break; } } // get rest of line
+ ofstream test;
+
+ string type, oligo, group;
+ int index=0;
+
+ while(!inOligos.eof()){
+ inOligos >> type;
+
+ if(type[0] == '#'){
+ while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ }
+ else{
+ inOligos >> oligo;
+
+ for(int i=0;i<oligo.length();i++){
+ oligo[i] = toupper(oligo[i]);
+ if(oligo[i] == 'U') { oligo[i] = 'T'; }
+ }
+
+ if(type == "forward"){
+ forPrimer.push_back(oligo);
+ }
+ else if(type == "reverse"){
+ revPrimer.push_back(oligo);
+ }
+ else if(type == "barcode"){
+ inOligos >> group;
+ barcodes[oligo]=index++;
+ groupVector.push_back(group);
+
+ if(allFiles){
+ outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
+ }
+ }
+ }
}
- gobble(inOligos);
+ inOligos.close();
+
+ numFPrimers = forPrimer.size();
+ numRPrimers = revPrimer.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "getOligos");
+ exit(1);
}
- numFPrimers = forPrimer.size();
- numRPrimers = revPrimer.size();
}
//***************************************************************************************************************
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, string& group){
-
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- for(map<string,string>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
+bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
- if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
- success = 0;
- break;
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+ string oligo = it->first;
+ if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
+ success = 0;
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+ group = it->second;
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
+ success = 1;
+ break;
+ }
}
+ return success;
- if (rawSequence.compare(0,oligo.length(),oligo) == 0){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- success = 1;
- break;
- }
}
- return success;
-
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "stripBarcode");
+ exit(1);
+ }
+
}
//***************************************************************************************************************
bool TrimSeqsCommand::stripForward(Sequence& seq){
-
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- for(int i=0;i<numFPrimers;i++){
- string oligo = forPrimer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
- }
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
- if (rawSequence.compare(0,oligo.length(),oligo) == 0){
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- success = 1;
- break;
+ for(int i=0;i<numFPrimers;i++){
+ string oligo = forPrimer[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = 0;
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
+ seq.setUnaligned(rawSequence.substr(oligo.length()));
+ success = 1;
+ break;
+ }
}
+
+ return success;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "stripForward");
+ exit(1);
}
-
- return success;
-
}
//***************************************************************************************************************
bool TrimSeqsCommand::stripReverse(Sequence& seq){
-
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- for(int i=0;i<numRPrimers;i++){
- string oligo = revPrimer[i];
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
- }
+ for(int i=0;i<numRPrimers;i++){
+ string oligo = revPrimer[i];
+
+ if(rawSequence.length() < oligo.length()){
+ success = 0;
+ break;
+ }
+
+ if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
+ seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
+ success = 1;
+ break;
+ }
+ }
+ return success;
- if(rawSequence.compare(rawSequence.length()-oligo.length(),oligo.length(),oligo) == 0){
- seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
- success = 1;
- break;
- }
- }
- return success;
-
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "stripReverse");
+ exit(1);
+ }
}
//***************************************************************************************************************
bool TrimSeqsCommand::cullLength(Sequence& seq){
+ try {
- int length = seq.getNumBases();
- bool success = 0; //guilty until proven innocent
-
- if(length >= minLength && maxLength == 0) { success = 1; }
- else if(length >= minLength && length <= maxLength) { success = 1; }
- else { success = 0; }
+ int length = seq.getNumBases();
+ bool success = 0; //guilty until proven innocent
+
+ if(length >= minLength && maxLength == 0) { success = 1; }
+ else if(length >= minLength && length <= maxLength) { success = 1; }
+ else { success = 0; }
+
+ return success;
- return success;
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "cullLength");
+ exit(1);
+ }
}
//***************************************************************************************************************
bool TrimSeqsCommand::cullHomoP(Sequence& seq){
-
- int longHomoP = seq.getLongHomoPolymer();
- bool success = 0; //guilty until proven innocent
-
- if(longHomoP <= maxHomoP){ success = 1; }
- else { success = 0; }
-
- return success;
+ try {
+ int longHomoP = seq.getLongHomoPolymer();
+ bool success = 0; //guilty until proven innocent
+
+ if(longHomoP <= maxHomoP){ success = 1; }
+ else { success = 0; }
+
+ return success;
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "cullHomoP");
+ exit(1);
+ }
}
//***************************************************************************************************************
bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
+ try {
+ int numNs = seq.getAmbigBases();
+ bool success = 0; //guilty until proven innocent
+
+ if(numNs <= maxAmbig) { success = 1; }
+ else { success = 0; }
+
+ return success;
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "cullAmbigs");
+ exit(1);
+ }
- int numNs = seq.getAmbigBases();
- bool success = 0; //guilty until proven innocent
-
- if(numNs <= maxAmbig){ success = 1; }
- else { success = 0; }
-
- return success;
-
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
+ try {
+ bool success = 1;
+ int length = oligo.length();
+
+ for(int i=0;i<length;i++){
+
+ if(oligo[i] != seq[i]){
+ if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
+ else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
+ else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
+ else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
+ else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
+ else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
+ else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
+ else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
+
+ if(success == 0) { break; }
+ }
+ else{
+ success = 1;
+ }
+ }
+
+ return success;
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+ exit(1);
+ }
+
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
+ try {
+ string rawSequence = seq.getUnaligned();
+ int seqLength = rawSequence.length();
+ string name;
+
+ qFile >> name;
+ if (name.length() != 0) { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine(); } }
+ while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
+
+ int score;
+ int end = seqLength;
+
+ for(int i=0;i<seqLength;i++){
+ qFile >> score;
+
+ if(score <= qThreshold){
+ end = i;
+ break;
+ }
+ }
+ for(int i=end+1;i<seqLength;i++){
+ qFile >> score;
+ }
+
+ seq.setUnaligned(rawSequence.substr(0,end));
+
+ return 1;
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
+ try {
+ string rawSequence = seq.getUnaligned();
+ int seqLength = seq.getNumBases();
+ bool success = 0; //guilty until proven innocent
+ string name;
+
+ qFile >> name;
+ if (name[0] == '>') { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine(); } }
+
+ while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
+
+ float score;
+ float average = 0;
+
+ for(int i=0;i<seqLength;i++){
+ qFile >> score;
+ average += score;
+ }
+ average /= seqLength;
+
+ if(average >= qAverage) { success = 1; }
+ else { success = 0; }
+
+ return success;
+ }
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+ exit(1);
+ }
}
//***************************************************************************************************************
projects / mothur.git / blobdiff