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/*
* parsefastaqcommand.cpp
* Mothur
*
* Created by westcott on 9/30/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "parsefastaqcommand.h"
#include "sequence.hpp"
//**********************************************************************************************************************
vector<string> ParseFastaQCommand::setParameters(){
try {
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); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ParseFastaQCommand::getHelpString(){
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, 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 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;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "getHelpString");
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 {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["fastq"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
exit(1);
}
}
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(string option){
try {
abort = false; calledHelp = false;
split = 1;
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string,string>::iterator it;
//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; }
}
//initialize outputTypes
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 (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("fastq");
//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["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; }
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); }
string temp;
temp = validParameter.validFile(parameters, "fasta", false); if(temp == "not found"){ temp = "T"; }
fasta = m->isTrue(temp);
temp = validParameter.validFile(parameters, "qfile", false); if(temp == "not found"){ temp = "T"; }
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 != "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 ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; }
}
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
exit(1);
}
}
//**********************************************************************************************************************
int ParseFastaQCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//open Output Files
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);
//fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
for (int i = -64; i < 65; i++) {
char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
convertTable.push_back(temp);
}
int count = 0;
while (!in.eof()) {
if (m->control_pressed) { break; }
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(); }
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(); outputNames.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
}
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, "ParseFastaQCommand", "execute");
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 -= int('!'); //char '!'
}else {
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) {
m->errorOut(e, "ParseFastaQCommand", "convertQual");
exit(1);
}
}
//**********************************************************************************************************************
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);
}
}
//**********************************************************************************************************************
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