if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
if(!success) { trashCode += 'q'; }
- qFile.close();
}
if(barcodes.size() != 0){
success = stripBarcode(currSeq, group);
outFASTA.close();
scrapFASTA.close();
outGroups.close();
+ if(qFileName != "") { qFile.close(); }
for(int i=0;i<fastaFileNames.size();i++){
fastaFileNames[i]->close();
//***************************************************************************************************************
void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
-
- ifstream inOligos;
- openInputFile(oligoFile, inOligos);
-
- 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'; }
- }
+ try {
+ ifstream inOligos;
+ openInputFile(oligoFile, inOligos);
+
+ ofstream test;
+
+ string type, oligo, group;
+ int index=0;
+
+ while(!inOligos.eof()){
+ inOligos >> type;
- if(type == "forward"){
- forPrimer.push_back(oligo);
- }
- else if(type == "reverse"){
- revPrimer.push_back(oligo);
+ 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 if(type == "barcode"){
- inOligos >> group;
- barcodes[oligo]=index++;
- groupVector.push_back(group);
+ 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));
+ if(allFiles){
+ outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
+ }
}
}
}
+
+ inOligos.close();
+
+ numFPrimers = forPrimer.size();
+ numRPrimers = revPrimer.size();
+
}
-
- inOligos.close();
-
- numFPrimers = forPrimer.size();
- numRPrimers = revPrimer.size();
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "getOligos");
+ exit(1);
+ }
+
}
//***************************************************************************************************************
bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
-
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- 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;
- }
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- success = 1;
- 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;
+
}
- 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];
+ try {
+ string rawSequence = seq.getUnaligned();
+ bool success = 0; //guilty until proven innocent
- 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;
+ 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(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
- 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){
-
- int numNs = seq.getAmbigBases();
- bool success = 0; //guilty until proven innocent
-
- if(numNs <= maxAmbig) { success = 1; }
- else { success = 0; }
-
- return success;
+ 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);
+ }
}
//***************************************************************************************************************
bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
-
- 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; }
+ try {
+ bool success = 1;
+ int length = oligo.length();
+
+ for(int i=0;i<length;i++){
- if(success == 0) { break; }
- }
- else{
- success = 1;
+ 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;
}
-
- return success;
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+ exit(1);
+ }
+
}
//***************************************************************************************************************
bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
-
- string rawSequence = seq.getUnaligned();
- int seqLength = rawSequence.length();
- string name;
-
- qFile >> name;
- 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;
+ 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;
}
- for(int i=end+1;i<seqLength;i++){
- qFile >> score;
+ catch(exception& e) {
+ errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
+ exit(1);
}
-
- seq.setUnaligned(rawSequence.substr(0,end));
-
- return 1;
}
//***************************************************************************************************************
bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
-
- string rawSequence = seq.getUnaligned();
- int seqLength = seq.getNumBases();
- bool success = 0; //guilty until proven innocent
- string name;
-
- qFile >> name;
- 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; } }
-
- float score;
- float average = 0;
-
- for(int i=0;i<seqLength;i++){
- qFile >> score;
- average += score;
+ 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);
}
- average /= seqLength;
-
- if(average >= qAverage) { success = 1; }
- else { success = 0; }
-
- return success;
}
//***************************************************************************************************************
-
-
projects / mothur.git / blobdiff