//**********************************************************************************************************************
vector<string> ParseFastaQCommand::setParameters(){
try {
- CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
- CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
- CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqual);
- CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa", "sanger", "", "", "",false,false); parameters.push_back(pformat);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pfastq);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter pgroup("group", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqual);
+ CommandParameter ppacbio("pacbio", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppacbio);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "sanger", "", "", "","",false,false,true); parameters.push_back(pformat);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
try {
string helpString = "";
helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
- helpString += "The fastq.info command parameters are fastq, fasta, qfile and format; fastq is required.\n";
+ helpString += "The fastq.info command parameters are fastq, fasta, qfile, oligos, group and format; fastq is required.\n";
helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
- helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa or illumina, default=sanger.\n";
+ helpString += "The oligos parameter allows you to provide an oligos file to split your fastq file into separate fastq files by barcode and primers. \n";
+ helpString += "The group parameter allows you to provide a group file to split your fastq file into separate fastq files by group. \n";
+ helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the reads. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
+ helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
+ helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
+ helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
+ helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
+ helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=sanger.\n";
helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
+ helpString += "The pacbio parameter allows you to indicate .... When set to true, quality scores of 0 will results in a corresponding base of N. Default=F.\n";
helpString += "Example fastq.info(fastaq=test.fastaq).\n";
helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
return helpString;
}
}
//**********************************************************************************************************************
-string ParseFastaQCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
-
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "qfile") { outputFileName = "qual"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ParseFastaQCommand", "getOutputFileNameTag");
- exit(1);
- }
+string ParseFastaQCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],fasta"; }
+ else if (type == "qfile") { pattern = "[filename],qual"; }
+ else if (type == "fastq") { pattern = "[filename],[group],fastq"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(){
try {
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["fastq"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(string option){
try {
- abort = false; calledHelp = false;
+ abort = false; calledHelp = false;
+ split = 1;
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["fastq"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fastq"] = inputDir + it->second; }
}
+
+ it = parameters.find("oligos");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["oligos"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
}
//check for required parameters
fastaQFile = validParameter.validFile(parameters, "fastq", true);
if (fastaQFile == "not found") { m->mothurOut("fastq is a required parameter for the fastq.info command."); m->mothurOutEndLine(); abort = true; }
- else if (fastaQFile == "not open") { fastaQFile = ""; abort = true; }
+ else if (fastaQFile == "not open") { fastaQFile = ""; abort = true; }
+
+ oligosfile = validParameter.validFile(parameters, "oligos", true);
+ if (oligosfile == "not found") { oligosfile = ""; }
+ else if (oligosfile == "not open") { oligosfile = ""; abort = true; }
+ else { m->setOligosFile(oligosfile); split = 2; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not found") { groupfile = ""; }
+ else if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else { m->setGroupFile(groupfile); split = 2; }
+
+ if ((groupfile != "") && (oligosfile != "")) { m->mothurOut("You must enter ONLY ONE of the following: oligos or group."); m->mothurOutEndLine(); abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastaQFile); }
fasta = m->isTrue(temp);
temp = validParameter.validFile(parameters, "qfile", false); if(temp == "not found"){ temp = "T"; }
- qual = m->isTrue(temp);
+ qual = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "pacbio", false); if(temp == "not found"){ temp = "F"; }
+ pacbio = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
+
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
+
format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; }
- if ((format != "sanger") && (format != "illumina") && (format != "solexa")) {
- m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa and illumina, aborting." ); m->mothurOutEndLine();
+ if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
abort=true;
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//open Output Files
- string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("fasta");
- string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("qfile");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ string fastaFile = getOutputFileName("fasta",variables);
+ string qualFile = getOutputFileName("qfile",variables);
ofstream outFasta, outQual;
if (fasta) { m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); }
if (qual) { m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile); }
+
+ TrimOligos* trimOligos = NULL;
+ int numBarcodes, numPrimers; numBarcodes = 0; numPrimers = 0;
+ if (oligosfile != "") {
+ readOligos(oligosfile);
+ numPrimers = primers.size(); numBarcodes = barcodes.size();
+ //find group read belongs to
+ if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, pairedPrimers, pairedBarcodes); numBarcodes = pairedBarcodes.size(); numPrimers = pairedPrimers.size(); }
+ else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer); }
+
+ }
+ else if (groupfile != "") { readGroup(groupfile); }
ifstream in;
m->openInputFile(fastaQFile, in);
convertTable.push_back(temp);
}
+
+ int count = 0;
while (!in.eof()) {
if (m->control_pressed) { break; }
-
- //read sequence name
- string name = m->getline(in); m->gobble(in);
- if (name == "") { m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
- else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
- else { name = name.substr(1); }
-
- //read sequence
- string sequence = m->getline(in); m->gobble(in);
- if (sequence == "") { m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; break; }
-
- //read sequence name
- string name2 = m->getline(in); m->gobble(in);
- if (name2 == "") { m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
- else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
- else { name2 = name2.substr(1); }
-
- //read quality scores
- string quality = m->getline(in); m->gobble(in);
- if (quality == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
-
- //sanity check sequence length and number of quality scores match
- if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
- if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
-
- //print sequence info to files
- if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
-
- if (qual) {
- vector<int> qualScores = convertQual(quality);
- outQual << ">" << name << endl;
- for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
- outQual << endl;
+
+ bool ignore;
+ fastqRead2 thisRead = readFastq(in, ignore);
+
+ if (!ignore) {
+ vector<int> qualScores;
+ if (qual) {
+ qualScores = convertQual(thisRead.quality);
+ outQual << ">" << thisRead.seq.getName() << endl;
+ for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
+ outQual << endl;
+ }
+
+ if (m->control_pressed) { break; }
+
+ if (pacbio) {
+ if (!qual) { qualScores = convertQual(thisRead.quality); } //convert if not done
+ string sequence = thisRead.seq.getAligned();
+ for (int i = 0; i < qualScores.size(); i++) {
+ if (qualScores[i] == 0){ sequence[i] = 'N'; }
+ }
+ thisRead.seq.setAligned(sequence);
+ }
+
+ //print sequence info to files
+ if (fasta) { thisRead.seq.printSequence(outFasta); }
+
+ if (split > 1) {
+ int barcodeIndex, primerIndex, trashCodeLength;
+ if (oligosfile != "") { trashCodeLength = findGroup(thisRead, barcodeIndex, primerIndex, trimOligos, numBarcodes, numPrimers); }
+ else if (groupfile != "") { trashCodeLength = findGroup(thisRead, barcodeIndex, primerIndex, "groupMode"); }
+ else { m->mothurOut("[ERROR]: uh oh, we shouldn't be here...\n"); }
+
+ if(trashCodeLength == 0){
+ ofstream out;
+ m->openOutputFileAppend(fastqFileNames[barcodeIndex][primerIndex], out);
+ out << thisRead.wholeRead;
+ out.close();
+ }else{
+ ofstream out;
+ m->openOutputFileAppend(noMatchFile, out);
+ out << thisRead.wholeRead;
+ out.close();
+ }
+ }
+ //report progress
+ if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
+ if(count > 100000){ break; }
+ count++;
}
}
in.close();
if (fasta) { outFasta.close(); }
if (qual) { outQual.close(); }
+
+ //report progress
+ if (!m->control_pressed) { if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
+
+ if (split > 1) {
+
+ if (groupfile != "") { delete groupMap; }
+ else if (oligosfile != "") { delete trimOligos; }
+
+ map<string, string>::iterator it;
+ set<string> namesToRemove;
+ for(int i=0;i<fastqFileNames.size();i++){
+ for(int j=0;j<fastqFileNames[0].size();j++){
+ if (fastqFileNames[i][j] != "") {
+ if (namesToRemove.count(fastqFileNames[i][j]) == 0) {
+ if(m->isBlank(fastqFileNames[i][j])){
+ m->mothurRemove(fastqFileNames[i][j]);
+ namesToRemove.insert(fastqFileNames[i][j]);
+ }
+ }
+ }
+ }
+ }
+
+ //remove names for outputFileNames, just cleans up the output
+ for(int i = 0; i < outputNames.size(); i++) {
+ if (namesToRemove.count(outputNames[i]) != 0) {
+ outputNames.erase(outputNames.begin()+i);
+ i--;
+ }
+ }
+ if(m->isBlank(noMatchFile)){ m->mothurRemove(noMatchFile); }
+ else { outputNames.push_back(noMatchFile); outputTypes["fastq"].push_back(noMatchFile); }
+ }
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); outputNames.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
//set fasta file as new current fastafile
string current = "";
exit(1);
}
}
+//**********************************************************************************************************************
+fastqRead2 ParseFastaQCommand::readFastq(ifstream& in, bool& ignore){
+ try {
+ ignore = false;
+ string wholeRead = "";
+
+ //read sequence name
+ string line = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += line + "\n"; }
+ vector<string> pieces = m->splitWhiteSpace(line);
+ string name = ""; if (pieces.size() != 0) { name = pieces[0]; }
+ if (name == "") { m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true; }
+ else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; }
+ else { name = name.substr(1); }
+
+ //read sequence
+ string sequence = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += sequence + "\n"; }
+ if (sequence == "") { m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; }
+
+ //read sequence name
+ line = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += line + "\n"; }
+ pieces = m->splitWhiteSpace(line);
+ string name2 = ""; if (pieces.size() != 0) { name2 = pieces[0]; }
+ if (name2 == "") { m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; }
+ else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; }
+ else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } }
+
+
+ //read quality scores
+ string quality = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += quality + "\n"; }
+ if (quality == "") { m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; }
+
+ //sanity check sequence length and number of quality scores match
+ if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
+ if (quality.length() != sequence.length()) { m->mothurOut("[WARNING]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores, ignoring read."); ignore=true; }
+
+ m->checkName(name);
+ Sequence seq(name, sequence);
+ fastqRead2 read(seq, quality, wholeRead);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + read.seq.getName() + " " + read.seq.getAligned() + " " + quality + "\n"); }
+
+ return read;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "readFastq");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
vector<int> ParseFastaQCommand::convertQual(string qual) {
try {
vector<int> qualScores;
+ bool negativeScores = false;
+
for (int i = 0; i < qual.length(); i++) {
int temp = 0;
temp = int(qual[i]);
if (format == "illumina") {
temp -= 64; //char '@'
+ }else if (format == "illumina1.8+") {
+ temp -= int('!'); //char '!'
}else if (format == "solexa") {
temp = int(convertTable[temp]); //convert to sanger
- temp -= 33; //char '!'
+ temp -= int('!'); //char '!'
}else {
- temp -= 33; //char '!'
+ temp -= int('!'); //char '!'
}
+ if (temp < -5) { negativeScores = true; }
qualScores.push_back(temp);
}
+ if (negativeScores) { m->mothurOut("[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding \n"); m->control_pressed = true; }
+
return qualScores;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
+int ParseFastaQCommand::findGroup(fastqRead2 thisRead, int& barcode, int& primer, TrimOligos*& trimOligos, int numBarcodes, int numPrimers) {
+ try {
+ int success = 1;
+ string trashCode = "";
+ int currentSeqsDiffs = 0;
+
+ Sequence currSeq(thisRead.seq.getName(), thisRead.seq.getAligned());
+ QualityScores currQual; currQual.setScores(convertQual(thisRead.quality));
+
+ if(linker.size() != 0){
+ success = trimOligos->stripLinker(currSeq, currQual);
+ if(success > ldiffs) { trashCode += 'k'; }
+ else{ currentSeqsDiffs += success; }
+
+ }
+
+ if(numBarcodes != 0){
+ success = trimOligos->stripBarcode(currSeq, currQual, barcode);
+ if(success > bdiffs) { trashCode += 'b'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if(spacer.size() != 0){
+ success = trimOligos->stripSpacer(currSeq, currQual);
+ if(success > sdiffs) { trashCode += 's'; }
+ else{ currentSeqsDiffs += success; }
+
+ }
+
+ if(numPrimers != 0){
+ success = trimOligos->stripForward(currSeq, currQual, primer, true);
+ if(success > pdiffs) { trashCode += 'f'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
+
+ if(revPrimer.size() != 0){
+ success = trimOligos->stripReverse(currSeq, currQual);
+ if(!success) { trashCode += 'r'; }
+ }
+
+
+ return trashCode.length();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "findGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ParseFastaQCommand::findGroup(fastqRead2 thisRead, int& barcode, int& primer, string groupMode) {
+ try {
+ string trashCode = "";
+ primer = 0;
+
+ string group = groupMap->getGroup(thisRead.seq.getName());
+ if (group == "not found") { trashCode += "g"; } //scrap for group
+ else { //find file group
+ map<string, int>::iterator it = barcodes.find(group);
+ if (it != barcodes.end()) {
+ barcode = it->second;
+ }else { trashCode += "g"; }
+ }
+
+ return trashCode.length();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "findGroup");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+bool ParseFastaQCommand::readOligos(string oligoFile){
+ try {
+ ifstream inOligos;
+ m->openInputFile(oligoFile, inOligos);
+
+ string type, oligo, roligo, group;
+ bool hasPrimer = false; bool hasPairedBarcodes = false; pairedOligos = false;
+
+ int indexPrimer = 0;
+ int indexBarcode = 0;
+ int indexPairedPrimer = 0;
+ int indexPairedBarcode = 0;
+ set<string> uniquePrimers;
+ set<string> uniqueBarcodes;
+
+ while(!inOligos.eof()){
+
+ inOligos >> type;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
+
+ 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
+ m->gobble(inOligos);
+ }
+ else{
+ m->gobble(inOligos);
+ //make type case insensitive
+ for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
+
+ inOligos >> oligo;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
+
+ for(int i=0;i<oligo.length();i++){
+ oligo[i] = toupper(oligo[i]);
+ if(oligo[i] == 'U') { oligo[i] = 'T'; }
+ }
+
+ if(type == "FORWARD"){
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ //check for repeat barcodes
+ map<string, int>::iterator itPrime = primers.find(oligo);
+ if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); } }
+
+ primers[oligo]=indexPrimer; indexPrimer++;
+ primerNameVector.push_back(group);
+ }
+ else if (type == "PRIMER"){
+ m->gobble(inOligos);
+
+ inOligos >> roligo;
+
+ for(int i=0;i<roligo.length();i++){
+ roligo[i] = toupper(roligo[i]);
+ if(roligo[i] == 'U') { roligo[i] = 'T'; }
+ }
+ roligo = reverseOligo(roligo);
+
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ oligosPair newPrimer(oligo, roligo);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
+
+ //check for repeat barcodes
+ string tempPair = oligo+roligo;
+ if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine(); }
+ else { uniquePrimers.insert(tempPair); }
+
+ if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
+
+ pairedPrimers[indexPairedPrimer]=newPrimer; indexPairedPrimer++;
+ primerNameVector.push_back(group);
+ hasPrimer = true;
+ }
+ else if(type == "REVERSE"){
+ //Sequence oligoRC("reverse", oligo);
+ //oligoRC.reverseComplement();
+ string oligoRC = reverseOligo(oligo);
+ revPrimer.push_back(oligoRC);
+ }
+ else if(type == "BARCODE"){
+ inOligos >> group;
+
+ //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
+ //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
+
+ string temp = "";
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { temp += c; }
+ }
+
+ //then this is illumina data with 4 columns
+ if (temp != "") {
+ hasPairedBarcodes = true;
+ string reverseBarcode = group; //reverseOligo(group); //reverse barcode
+ group = temp;
+
+ for(int i=0;i<reverseBarcode.length();i++){
+ reverseBarcode[i] = toupper(reverseBarcode[i]);
+ if(reverseBarcode[i] == 'U') { reverseBarcode[i] = 'T'; }
+ }
+
+ reverseBarcode = reverseOligo(reverseBarcode);
+ oligosPair newPair(oligo, reverseBarcode);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
+ //check for repeat barcodes
+ string tempPair = oligo+reverseBarcode;
+ if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding."); m->mothurOutEndLine(); }
+ else { uniqueBarcodes.insert(tempPair); }
+
+ pairedBarcodes[indexPairedBarcode]=newPair; indexPairedBarcode++;
+ barcodeNameVector.push_back(group);
+ }else {
+ //check for repeat barcodes
+ map<string, int>::iterator itBar = barcodes.find(oligo);
+ if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ barcodes[oligo]=indexBarcode; indexBarcode++;
+ barcodeNameVector.push_back(group);
+ }
+ }else if(type == "LINKER"){
+ linker.push_back(oligo);
+ }else if(type == "SPACER"){
+ spacer.push_back(oligo);
+ }
+ else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
+ }
+ m->gobble(inOligos);
+ }
+ inOligos.close();
+
+ if (hasPairedBarcodes || hasPrimer) {
+ pairedOligos = true;
+ if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true; m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine(); return 0; }
+ }
+
+ //add in potential combos
+ if(barcodeNameVector.size() == 0){
+ barcodes[""] = 0;
+ barcodeNameVector.push_back("");
+ }
+
+ if(primerNameVector.size() == 0){
+ primers[""] = 0;
+ primerNameVector.push_back("");
+ }
+
+ fastqFileNames.resize(barcodeNameVector.size());
+ for(int i=0;i<fastqFileNames.size();i++){
+ fastqFileNames[i].assign(primerNameVector.size(), "");
+ }
+
+
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ if (pairedOligos) {
+ for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
+
+ string primerName = primerNameVector[itPrimer->first];
+ string barcodeName = barcodeNameVector[itBar->first];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastqFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->first];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->first];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ }
+ }
+
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ variables["[group]"] = comboGroupName;
+ fastqFileName = getOutputFileName("fastq", variables);
+ if (uniqueNames.count(fastqFileName) == 0) {
+ outputNames.push_back(fastqFileName);
+ outputTypes["fastq"].push_back(fastqFileName);
+ uniqueNames.insert(fastqFileName);
+ }
+
+ fastqFileNames[itBar->first][itPrimer->first] = fastqFileName;
+ m->openOutputFile(fastqFileName, temp); temp.close();
+
+ }
+ }
+ }
+ }else {
+ for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = primerNameVector[itPrimer->second];
+ string barcodeName = barcodeNameVector[itBar->second];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastqFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ }
+
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ variables["[group]"] = comboGroupName;
+ fastqFileName = getOutputFileName("fastq", variables);
+ if (uniqueNames.count(fastqFileName) == 0) {
+ outputNames.push_back(fastqFileName);
+ outputTypes["fastq"].push_back(fastqFileName);
+ uniqueNames.insert(fastqFileName);
+ }
+
+ fastqFileNames[itBar->second][itPrimer->second] = fastqFileName;
+ m->openOutputFile(fastqFileName, temp); temp.close();
+
+ }
+ }
+ }
+ }
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ variables["[group]"] = "scrap";
+ noMatchFile = getOutputFileName("fastq", variables);
+ m->openOutputFile(noMatchFile, temp); temp.close();
+
+ return true;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getOligos");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+bool ParseFastaQCommand::readGroup(string groupfile){
+ try {
+ fastqFileNames.clear();
+
+ groupMap = new GroupMap();
+ groupMap->readMap(groupfile);
+
+ //like barcodeNameVector - no primer names
+ vector<string> groups = groupMap->getNamesOfGroups();
+
+ fastqFileNames.resize(groups.size());
+ for (int i = 0; i < fastqFileNames.size(); i++) {
+ for (int j = 0; j < 1; j++) {
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ variables["[group]"] = groups[i];
+ string thisFilename = getOutputFileName("fastq",variables);
+ outputNames.push_back(thisFilename);
+ outputTypes["fastq"].push_back(thisFilename);
+
+ ofstream temp;
+ m->openOutputFileBinary(thisFilename, temp); temp.close();
+ fastqFileNames[i].push_back(thisFilename);
+ barcodes[groups[i]] = i;
+ }
+ }
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ variables["[group]"] = "scrap";
+ noMatchFile = getOutputFileName("fastq",variables);
+ m->mothurRemove(noMatchFile);
+
+ return true;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "readGroup");
+ exit(1);
+ }
+}
+//********************************************************************/
+string ParseFastaQCommand::reverseOligo(string oligo){
+ try {
+ string reverse = "";
+
+ for(int i=oligo.length()-1;i>=0;i--){
+
+ if(oligo[i] == 'A') { reverse += 'T'; }
+ else if(oligo[i] == 'T'){ reverse += 'A'; }
+ else if(oligo[i] == 'U'){ reverse += 'A'; }
+
+ else if(oligo[i] == 'G'){ reverse += 'C'; }
+ else if(oligo[i] == 'C'){ reverse += 'G'; }
+
+ else if(oligo[i] == 'R'){ reverse += 'Y'; }
+ else if(oligo[i] == 'Y'){ reverse += 'R'; }
+
+ else if(oligo[i] == 'M'){ reverse += 'K'; }
+ else if(oligo[i] == 'K'){ reverse += 'M'; }
+
+ else if(oligo[i] == 'W'){ reverse += 'W'; }
+ else if(oligo[i] == 'S'){ reverse += 'S'; }
+
+ else if(oligo[i] == 'B'){ reverse += 'V'; }
+ else if(oligo[i] == 'V'){ reverse += 'B'; }
+
+ else if(oligo[i] == 'D'){ reverse += 'H'; }
+ else if(oligo[i] == 'H'){ reverse += 'D'; }
+
+ else { reverse += 'N'; }
+ }
+
+
+ return reverse;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "reverseOligo");
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
projects / mothur.git / blobdiff