//***************************************************************************************************************
-TrimSeqsCommand::TrimSeqsCommand(){
+TrimSeqsCommand::TrimSeqsCommand(string option){
try {
- oligos = 0;
- totalBarcodeCount = 0;
- matchBarcodeCount = 0;
+ abort = false;
- globaldata = GlobalData::getInstance();
- if(globaldata->getFastaFile() == ""){
- cout << "you need to at least enter a fasta file name" << endl;
- }
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", "qthreshold", "qaverage", "allfiles"};
+
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ 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; }
+
+
+ //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"){ flip = 0; }
+ else if(isTrue(temp)) { flip = 1; }
- if(isTrue(globaldata->getFlip())) { flip = 1; }
- if(globaldata->getOligosFile() != "") { oligos = 1; }
- if(!flip && !oligos) { cout << "huh?" << endl; }
+ 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"; }
+ convert(temp, maxHomoP);
+
+ 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, "qfile", true);
+ if (temp == "not found") { qFileName = ""; }
+ else if(temp == "not open") { abort = 0; }
+ else { qFileName = temp; }
+
+ 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);
+
+ if(allFiles && oligoFile == ""){
+ cout << "You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request." << endl;
+ }
+
+ if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
+ cout << "You didn't set any options... quiting command." << endl;
+ abort = true;
+ }
+
+ }
}
catch(exception& e) {
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";
+
+ }
+ 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";
+ 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);
+ }
+}
+
//***************************************************************************************************************
int TrimSeqsCommand::execute(){
try{
- getOligos();
-
+
+ if (abort == true) { return 0; }
+
+ vector<ofstream*> groupFileNames;
+ vector<ofstream*> fastaFileNames;
+ if(oligoFile != "") { getOligos(fastaFileNames, groupFileNames); }
+
ifstream inFASTA;
- openInputFile(globaldata->getFastaFile(), inFASTA);
+ openInputFile(fastaFile, inFASTA);
ofstream outFASTA;
- string trimSeqFile = getRootName(globaldata->getFastaFile()) + "trim.fasta";
+ string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
openOutputFile(trimSeqFile, outFASTA);
ofstream outGroups;
- string groupFile = getRootName(globaldata->getFastaFile()) + "groups";
+ string groupFile = getRootName(fastaFile) + "groups";
openOutputFile(groupFile, outGroups);
-
+
ofstream scrapFASTA;
- string scrapSeqFile = getRootName(globaldata->getFastaFile()) + "scrap.fasta";
+ string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
openOutputFile(scrapSeqFile, scrapFASTA);
-
+
+ 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'; }
success = stripReverse(currSeq);
if(!success){ trashCode += 'r'; }
}
+ if(minLength > 0 || maxLength > 0){
+ success = cullLength(currSeq);
+ if(!success){ trashCode += 'l'; }
+ }
+ if(maxHomoP > 0){
+ success = cullHomoP(currSeq);
+ if(!success){ trashCode += 'h'; }
+ }
+ if(maxAmbig != -1){
+ success = cullAmbigs(currSeq);
+ if(!success){ trashCode += 'n'; }
+ }
+
if(flip){ currSeq.reverseComplement(); } // should go last
-
+
if(trashCode.length() == 0){
currSeq.printSequence(outFASTA);
- outGroups << currSeq.getName() << '\t' << group << endl;
+ if(barcodes.size() != 0){
+ outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
+
+ if(allFiles){
+ *groupFileNames[group] << currSeq.getName() << '\t' << groupVector[group] << endl;
+ currSeq.printSequence(*fastaFileNames[group]);
+ }
+ }
}
else{
currSeq.setName(currSeq.getName() + '|' + trashCode);
currSeq.setUnaligned(origSeq);
currSeq.printSequence(scrapFASTA);
}
-
gobble(inFASTA);
}
inFASTA.close();
scrapFASTA.close();
outGroups.close();
+ for(int i=0;i<groupFileNames.size();i++){
+ groupFileNames[i]->close();
+ delete groupFileNames[i];
+
+ fastaFileNames[i]->close();
+ delete fastaFileNames[i];
+ }
+
return 0;
}
catch(exception& e) {
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(){
-
+void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec, vector<ofstream*>& outGroupsVec){
+
ifstream inOligos;
- openInputFile(globaldata->getOligosFile(), inOligos);
+ openInputFile(oligoFile, inOligos);
+ ofstream test;
+
string type, oligo, group;
+ int index=0;
while(!inOligos.eof()){
inOligos >> type;
- if(type == "forward"){
- inOligos >> oligo;
- forPrimer.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 == "reverse"){
+ else{
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
+
+ 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));
+ outGroupsVec.push_back(new ofstream((getRootName(fastaFile) + group + ".groups").c_str(), ios::ate));
+ }
+ }
}
-
- gobble(inOligos);
}
-
+
numFPrimers = forPrimer.size();
numRPrimers = revPrimer.size();
}
//***************************************************************************************************************
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, string& group){
+bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
string rawSequence = seq.getUnaligned();
bool success = 0; //guilty until proven innocent
-
- for(map<string,string>::iterator it=barcodes.begin();it!=barcodes.end();it++){
+
+ 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 (rawSequence.compare(0,oligo.length(),oligo) == 0){
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
group = it->second;
seq.setUnaligned(rawSequence.substr(oligo.length()));
- matchBarcodeCount++;
success = 1;
break;
}
}
- totalBarcodeCount++;
return success;
}
for(int i=0;i<numFPrimers;i++){
string oligo = forPrimer[i];
-
+
if(rawSequence.length() < oligo.length()){
success = 0;
break;
}
-
- if (rawSequence.compare(0,oligo.length(),oligo) == 0){
+
+ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
seq.setUnaligned(rawSequence.substr(oligo.length()));
- matchFPrimerCount++;
success = 1;
break;
}
}
- totalFPrimerCount++;
return success;
}
break;
}
- if(rawSequence.compare(rawSequence.length()-oligo.length(),oligo.length(),oligo) == 0){
+ if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
- matchRPrimerCount++;
success = 1;
break;
}
}
+ return success;
+
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::cullLength(Sequence& seq){
+
+ 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; }
- totalRPrimerCount++;
return success;
}
//***************************************************************************************************************
+
+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;
+
+}
+
+//***************************************************************************************************************
+
+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;
+
+}
+
+//***************************************************************************************************************
+
+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; }
+
+ if(success == 0) { break; }
+ }
+ else{
+ success = 1;
+ }
+ }
+
+ return success;
+}
+
+//***************************************************************************************************************
+
+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()) { cout << "sequence name mismatch btwn fasta and qual file" << endl; }
+ 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;
+}
+
+//***************************************************************************************************************
+
+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()) { cout << "sequence name mismatch btwn fasta and qual file" << endl; }
+ 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;
+}
+
+//***************************************************************************************************************
+
+
projects / mothur.git / blobdiff