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|
/*
* parsefastaqcommand.cpp
* Mothur
*
* Created by westcott on 9/30/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "fastaqinfocommand.h"
#include "sequence.hpp"
#include "counttable.h"
//**********************************************************************************************************************
vector<string> ParseFastaQCommand::setParameters(){
try {
CommandParameter pfile("file", "InputTypes", "", "", "fastqFile", "fastqFile", "none","",false,false,true); parameters.push_back(pfile);
CommandParameter pfastq("fastq", "InputTypes", "", "", "fastqFile", "fastqFile", "none","",false,false,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 preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
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+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false; fileOption = 0; createFileGroup = false; hasIndex = false;
split = 1;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["fastq"] = tempOutNames;
outputTypes["count"] = tempOutNames;
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 or can be used to parse fastq files by sample.\n";
helpString += "The fastq.info command parameters are file, fastq, fasta, qfile, oligos, group and format; file or 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 checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. If found the sequence is flipped. The default is false.\n";
helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=illumina1.8+.\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";
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-[filename],[sample],[tag],fasta-[filename],[sample],fasta"; }
else if (type == "count") { pattern = "[filename],count_table"; }
else if (type == "qfile") { pattern = "[filename],qual-[filename],[sample],[tag],qual-[filename],[sample],qual"; }
else if (type == "fastq") { pattern = "[filename],[sample],fastq-[filename],[sample],[tag],fastq"; } //make.sra assumes the [filename],[sample],[tag],fastq format for the 4 column file option. If this changes, may have to modify fixMap function.
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(string option) : Command(){
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
fastaQFile = validParameter.validFile(parameters, "fastq");
if (fastaQFile == "not found") { fastaQFile= ""; }
else if (fastaQFile == "not open") { fastaQFile = ""; abort = true; }
else { inputfile = fastaQFile; }
file = validParameter.validFile(parameters, "file");
if (file == "not found") { file = ""; }
else if (file == "not open") { file = ""; abort = true; }
else { inputfile = file; fileOption = true; }
if ((file == "") && (fastaQFile == "")) { m->mothurOut("You must provide a file or fastq option.\n"); abort = true; }
oligosfile = validParameter.validFile(parameters, "oligos");
if (oligosfile == "not found") { oligosfile = ""; }
else if (oligosfile == "not open") { oligosfile = ""; abort = true; }
else { current->setOligosFile(oligosfile); split = 2; }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not found") { groupfile = ""; }
else if (groupfile == "not open") { groupfile = ""; abort = true; }
else { current->setGroupFile(groupfile); split = 2; }
if ((groupfile != "") && (oligosfile != "")) { m->mothurOut("You must enter ONLY ONE of the following: oligos or group.\n"); abort = true; }
if (outputdir == ""){ outputdir = util.hasPath(inputfile); }
string temp;
temp = validParameter.valid(parameters, "fasta"); if(temp == "not found"){ temp = "T"; }
fasta = util.isTrue(temp);
temp = validParameter.valid(parameters, "qfile"); if(temp == "not found"){ temp = "T"; }
qual = util.isTrue(temp);
temp = validParameter.valid(parameters, "pacbio"); if(temp == "not found"){ temp = "F"; }
pacbio = util.isTrue(temp);
temp = validParameter.valid(parameters, "bdiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, bdiffs);
temp = validParameter.valid(parameters, "pdiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, pdiffs);
temp = validParameter.valid(parameters, "ldiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, ldiffs);
temp = validParameter.valid(parameters, "sdiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, sdiffs);
temp = validParameter.valid(parameters, "tdiffs"); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
util.mothurConvert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
format = validParameter.valid(parameters, "format"); if (format == "not found"){ format = "illumina1.8+"; }
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) && (file == "") && (fastaQFile == "") && (oligosfile == "")) { m->mothurOut("[ERROR]: no outputs selected. Aborting.\n"); abort=true; }
temp = validParameter.valid(parameters, "checkorient"); if (temp == "not found") { temp = "F"; }
reorient = util.isTrue(temp);
}
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
exit(1);
}
}
//**********************************************************************************************************************
int ParseFastaQCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
vector< vector<string> > files;
if (file != "") { files = readFile(); }
if (m->getControl_pressed()) { return 0; }
TrimOligos* trimOligos = nullptr; TrimOligos* rtrimOligos = nullptr;
pairedOligos = false; numBarcodes = 0; numPrimers= 0; numLinkers= 0; numSpacers = 0; numRPrimers = 0;
if (oligosfile != "") {
readOligos(oligosfile);
//find group read belongs to
if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getPairedPrimers(), oligos.getPairedBarcodes(), hasIndex); numBarcodes = oligos.getPairedBarcodes().size(); numPrimers = oligos.getPairedPrimers().size(); }
else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, oligos.getPrimers(), oligos.getBarcodes(), oligos.getReversePrimers(), oligos.getLinkers(), oligos.getSpacers()); numPrimers = oligos.getPrimers().size(); numBarcodes = oligos.getBarcodes().size(); }
if (reorient) {
rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getReorientedPairedPrimers(), oligos.getReorientedPairedBarcodes(), hasIndex);
numBarcodes = oligos.getReorientedPairedBarcodes().size();
numPrimers = oligos.getReorientedPairedPrimers().size();
}
}else if (groupfile != "") { readGroup(groupfile); }
string inputFile = "";
if (file != "") {
inputFile = file;
if (m->getControl_pressed()) {
if (groupfile != "") { delete groupMap; }
if (oligosfile != "") { delete trimOligos; if (reorient) { delete rtrimOligos; } }
return 0;
}
//groupfile name for pacbio with option 2
map<string, string> variables;
variables["[filename]"] = util.getRootName(file);
string pacbioFastaFileName = getOutputFileName("fasta", variables);
string pacbioQualFileName = getOutputFileName("qfile", variables);
if ((fileOption == 2) && pacbio) {
seqGroups.clear();
if (fasta) {
ofstream temppbf; util.openOutputFile(pacbioFastaFileName, temppbf);
temppbf.close();
outputNames.push_back(pacbioFastaFileName); outputTypes["fasta"].push_back(pacbioFastaFileName);
}
if (qual) {
ofstream temppbq; util.openOutputFile(pacbioQualFileName, temppbq);
temppbq.close();
outputNames.push_back(pacbioQualFileName); outputTypes["qfile"].push_back(pacbioQualFileName);
}
} //clear old file for append
for (int i = 0; i < files.size(); i++) { //process each pair
if (m->getControl_pressed()) { break; }
if (((fileOption == 2) || (fileOption == 4)) && !pacbio) { //2 column and 4 column format file file
processFile(files[i], trimOligos, rtrimOligos);
}else if ((fileOption == 2) && pacbio) { //pacbio with group filename option
split = 1;
if (current->getMothurCalling()) {
//add group names to fastq files and make copies - for sra command parse
ofstream temp;
map<string, string> variables;
variables["[filename]"] = util.getRootName(files[i][0]);
variables["[sample]"] = file2Group[i];
variables["[tag]"] = "";
string newfqFile = getOutputFileName("fastq", variables);
util.openOutputFile(newfqFile, temp); temp.close();
util.appendFiles(files[i][0], newfqFile);
outputNames.push_back(newfqFile); outputTypes["fastq"].push_back(newfqFile);
}
inputFile = files[i][0];
//process each file to create fasta and qual files
set<string> seqNames;
if (fasta || qual) { seqNames = processFile(inputFile, trimOligos, rtrimOligos); } //split = 1, so no parsing by group will be done.
if (seqNames.size() != 0) {
string pacbioGroup = file2Group[i];
for (set<string>::iterator it = seqNames.begin(); it != seqNames.end(); it++) {
seqGroups[*it] = pacbioGroup;
}
groupCounts[pacbioGroup] = seqNames.size();
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputFile));
string fastaFile = getOutputFileName("fasta",variables);
string qualFile = getOutputFileName("qfile",variables);
if (fasta) { util.appendFiles(fastaFile, pacbioFastaFileName); }
if (qual) { util.appendFiles(qualFile, pacbioQualFileName); }
}
}else if (fileOption == 3) { //3 column file option with sample names
if (current->getMothurCalling()) {
//add group names to fastq files and make copies - for sra command parse
ofstream temp, temp2;
map<string, string> variables;
variables["[filename]"] = util.getRootName(files[i][0]);
variables["[sample]"] = file2Group[i];
variables["[tag]"] = "forward";
string newffqFile = getOutputFileName("fastq", variables);
util.openOutputFile(newffqFile, temp); temp.close();
util.appendFiles(files[i][0], newffqFile);
outputNames.push_back(newffqFile); outputTypes["fastq"].push_back(newffqFile);
variables["[filename]"] = util.getRootName(files[i][1]);
variables["[sample]"] = file2Group[i];
variables["[tag]"] = "reverse";
string newfrqFile = getOutputFileName("fastq", variables);
util.openOutputFile(newfrqFile, temp2); temp2.close();
util.appendFiles(files[i][1], newfrqFile);
outputNames.push_back(newfrqFile); outputTypes["fastq"].push_back(newfrqFile);
}
//if requested, make fasta and qual
if (fasta || qual) { processFile(files[i], trimOligos, rtrimOligos); } //split = 1, so no parsing by group will be done.
}
}
}else {
inputFile = fastaQFile;
processFile(fastaQFile, trimOligos, rtrimOligos);
vector<string> filesFakeOut; filesFakeOut.push_back(fastaQFile);
files.push_back(filesFakeOut);
}
if ((fileOption == 2) && pacbio) {
map<string, string> variables;
variables["[filename]"] = util.getRootName(file);
string pacbioGroupFileName = getOutputFileName("count", variables);
outputNames.push_back(pacbioGroupFileName); outputTypes["count"].push_back(pacbioGroupFileName);
CountTable ct; ct.createTable(seqGroups);
ct.printCompressedTable(pacbioGroupFileName);
}
if (split > 1) {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir = util.hasPath(inputFile); }
map<string, string> vars;
vars["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(inputFile));
string outputGroupFileName = getOutputFileName("count",vars);
if (seqGroups.size() != 0) { //Create count file
outputNames.push_back(outputGroupFileName); outputTypes["count"].push_back(outputGroupFileName);
CountTable ct; ct.createTable(seqGroups);
ct.printCompressedTable(outputGroupFileName);
}
for (int i = 0; i < files.size(); i++) { //process each pair
for (int j = 0; j < files[i].size(); j++) {
if (files[i][j] != "") {
map<string, vector<string> > filenames = splitFastqFile(outputGroupFileName, files[i][j]);
map<string, vector<string> >::iterator it = filenames.find("fastq");
if (it != filenames.end()) { //fastq files were produced
for (int k = 0; k < it->second.size(); k++) { outputNames.push_back(it->second[k]); outputTypes["fastq"].push_back(it->second[k]); }
}
}
}
}
//ffqnoMatchFile, rfqnoMatchFile, ffnoMatchFile, rfnoMatchFile, fqnoMatchFile, rqnoMatchFile
if(util.isBlank(ffqnoMatchFile)){ util.mothurRemove(ffqnoMatchFile); }
else { outputNames.push_back(ffqnoMatchFile); outputTypes["fastq"].push_back(ffqnoMatchFile); }
if(fasta){
if(util.isBlank(ffnoMatchFile)){ util.mothurRemove(ffnoMatchFile); }
else { outputNames.push_back(ffnoMatchFile); outputTypes["fasta"].push_back(ffnoMatchFile); }
}
if(qual){
if(util.isBlank(fqnoMatchFile)){ util.mothurRemove(fqnoMatchFile); }
else { outputNames.push_back(fqnoMatchFile); outputTypes["qfile"].push_back(fqnoMatchFile); }
}
if (pairedOligos) {
if (fileOption > 0) {
if(util.isBlank(rfqnoMatchFile)){ util.mothurRemove(rfqnoMatchFile); }
else { outputNames.push_back(rfqnoMatchFile); outputTypes["fastq"].push_back(rfqnoMatchFile); }
if(fasta){
if(util.isBlank(rfnoMatchFile)){ util.mothurRemove(rfnoMatchFile); }
else { outputNames.push_back(rfnoMatchFile); outputTypes["fasta"].push_back(rfnoMatchFile); }
}
if(qual){
if(util.isBlank(rqnoMatchFile)){ util.mothurRemove(rqnoMatchFile); }
else { outputNames.push_back(rqnoMatchFile); outputTypes["qfile"].push_back(rqnoMatchFile); }
}
}
}
}
//output group counts
int total = 0;
if (groupCounts.size() != 0) { m->mothurOut("\nGroup count: \n"); }
for (map<string, long long>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) { total += it->second; m->mothurOut(it->first + "\t" + toString(it->second) + "\n"); }
if (total != 0) { m->mothurOut("\nTotal of all groups is " + toString(total) + "\n"); }
if (groupfile != "") { delete groupMap; }
if (oligosfile != "") { delete trimOligos; if (reorient) { delete rtrimOligos; } }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.clear(); outputNames.clear(); return 0; }
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setQualFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "execute");
exit(1);
}
}
/**************************************************************************************************/
map<string, vector<string> > ParseFastaQCommand::splitFastqFile(string outputGroupFile, string resultFastqfile) {
try {
//run split.groups command
//use unique.seqs to create new name and fastafile
string inputString = "fastq=" + resultFastqfile + ", count=" + outputGroupFile;
m->mothurOut("/******************************************/\n");
m->mothurOut("Generating parsed files... Running command: split.groups(" + inputString + ")\n");
current->setMothurCalling(true);
Command* splitCommand = new SplitGroupCommand(inputString);
splitCommand->execute();
map<string, vector<string> > filenames = splitCommand->getOutputFiles();
delete splitCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
if (fasta || qual) { //do we need to create a fasta and qual file for these split fastq files
string fastaBool = "false"; string qualBool = "false";
if (fasta) { fastaBool = "true"; }
if (qual) { qualBool = "true"; }
map<string, vector<string> >::iterator it = filenames.find("fastq");
if (it != filenames.end()) { //fastq files were produced
for (int k = 0; k < it->second.size(); k++) {
string inputString = "fastq=" + it->second[k] + ", fasta=" + fastaBool + ", qfile=" + qualBool;
m->mothurOut("/******************************************/\n");
m->mothurOut("Generating parsed fasta and qual files... Running command: fastq.info(" + inputString + ")\n");
current->setMothurCalling(true);
Command* fastqCommand = new ParseFastaQCommand(inputString);
fastqCommand->execute();
map<string, vector<string> > fnames = fastqCommand->getOutputFiles();
delete fastqCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
if (fasta) {
map<string, vector<string> >::iterator itFastaName = fnames.find("fasta");
if (itFastaName != fnames.end()) {
string fName = itFastaName->second[0];
outputNames.push_back(fName); outputTypes["fasta"].push_back(fName);
}
}
if (qual) {
map<string, vector<string> >::iterator itQualName = fnames.find("qfile");
if (itQualName != fnames.end()) {
string qName = itQualName->second[0];
outputNames.push_back(qName); outputTypes["qfile"].push_back(qName);
}
}
}
}
}
return filenames;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "splitFastqFile");
exit(1);
}
}
//**********************************************************************************************************************
//assumes file option was used.
//Adds reads to seqGroup and groupCounts for use with split.groups command later.
//Outputs fasta and qual files for file pair if desired
//Appends scrap files if needed
int ParseFastaQCommand::processFile(vector<string> files, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos){
try {
string inputfile = files[0]; string inputReverse = files[1];
//open Output Files
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputfile));
string ffastaFile = getOutputFileName("fasta",variables);
string fqualFile = getOutputFileName("qfile",variables);
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputReverse));
string rfastaFile = getOutputFileName("fasta",variables);
string rqualFile = getOutputFileName("qfile",variables);
ofstream outfFasta, outfQual, outrFasta, outrQual;
if (fasta) { util.openOutputFile(ffastaFile, outfFasta); outputNames.push_back(ffastaFile); outputTypes["fasta"].push_back(ffastaFile); util.openOutputFile(rfastaFile, outrFasta); outputNames.push_back(rfastaFile); outputTypes["fasta"].push_back(rfastaFile);}
if (qual) { util.openOutputFile(fqualFile, outfQual); outputNames.push_back(fqualFile); outputTypes["qfile"].push_back(fqualFile); util.openOutputFile(rqualFile, outrQual); outputNames.push_back(rqualFile); outputTypes["qfile"].push_back(rqualFile); }
ifstream inf; util.openInputFile(inputfile, inf);
ifstream inr; util.openInputFile(inputReverse, inr);
ifstream inFIndex, inRIndex;
if (files[2] != "") { util.openInputFile(files[2], inFIndex); }
if (files[3] != "") { util.openInputFile(files[3], inRIndex); }
int count = 0;
while (!inf.eof() && !inr.eof()) {
if (m->getControl_pressed()) { break; }
bool ignoref, ignorer;
FastqRead thisfRead(inf, ignoref, format);
FastqRead thisrRead(inr, ignorer, format);
if (!ignoref && ! ignorer) {
if (qual) {
thisfRead.getQuality().printQScores(outfQual);
thisrRead.getQuality().printQScores(outrQual);
}
if (pacbio) { //change sequence bases with 0 quality scores to N
vector<int> fqual = thisfRead.getScores();
vector<int> rqual = thisrRead.getScores();
string fseq = thisfRead.getSeq();
string rseq = thisrRead.getSeq();
for (int i = 0; i < fqual.size(); i++) { if (fqual[i] == 0){ fseq[i] = 'N'; } }
thisfRead.setSeq(fseq);
for (int i = 0; i < rqual.size(); i++) { if (rqual[i] == 0){ rseq[i] = 'N'; } }
thisrRead.setSeq(rseq);
}
FastqRead copyForward = thisfRead;
FastqRead copyReverse = thisrRead;
//print sequence info to files
if (fasta) {
thisfRead.getSequence().printSequence(outfFasta);
thisrRead.getSequence().printSequence(outrFasta);
}
if (m->getControl_pressed()) { break; }
if (split > 1) {
Sequence findexBarcode("findex", "NONE"); Sequence rindexBarcode("rindex", "NONE");
if (fileOption == 4) {
bool ignorefi, ignoreri;
if (files[2] != "") {
FastqRead thisfiRead(inFIndex, ignorefi, format);
if (!ignorefi) { findexBarcode.setAligned(thisfiRead.getSequence().getAligned()); }
}
if (files[3] != "") {
FastqRead thisriRead(inRIndex, ignoreri, format);
if (!ignoreri) { rindexBarcode.setAligned(thisriRead.getSequence().getAligned()); }
}
}
int trashCodeLength; string thisGroup = "ignore";
if (oligosfile != "") {
QualityScores tempF = thisfRead.getQuality();
QualityScores tempR = thisrRead.getQuality();
if ((files[2] != "") || (files[3] != "")) { //has index files
//barcode already removed so no need to reset sequence to trimmed version
trashCodeLength = findGroup(findexBarcode, tempF, rindexBarcode, tempR, thisGroup, trimOligos, rtrimOligos, numBarcodes, numPrimers);
}else {
Sequence tempSeqF = thisfRead.getSequence();
Sequence tempSeqR = thisrRead.getSequence();
trashCodeLength = findGroup(tempSeqF, tempF, tempSeqR, tempR, thisGroup, trimOligos, rtrimOligos, numBarcodes, numPrimers);
thisfRead.setSeq(tempSeqF.getUnaligned());
thisrRead.setSeq(tempSeqR.getUnaligned());
}
thisfRead.setScores(tempF.getScores()); //set to trimmed scores
thisrRead.setScores(tempR.getScores());
}else if (groupfile != "") { trashCodeLength = findGroup(thisfRead.getSequence(), thisGroup, "groupMode"); }
else { m->mothurOut("[ERROR]: uh oh, we shouldn't be here...\n"); }
bool addToScrap = false;
if(trashCodeLength == 0){
int pos = thisGroup.find("ignore");
if (pos == string::npos) {
if (thisGroup != "") {
seqGroups[copyForward.getName()] = thisGroup;
map<string, long long>::iterator it = groupCounts.find(thisGroup);
if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
else { groupCounts[it->first]++; }
}
}else { addToScrap = true; }
}else{ addToScrap = true; }
if (addToScrap) {
//print no match fastq
ofstream out, out2;
util.openOutputFileAppend(ffqnoMatchFile, out);
copyForward.printFastq(out);
out.close();
util.openOutputFileAppend(rfqnoMatchFile, out2);
copyReverse.printFastq(out2);
out2.close();
//print no match fasta, if wanted
if (fasta) {
ofstream outf, outr;
util.openOutputFileAppend(ffnoMatchFile, outf);
thisfRead.getSequence().printSequence(outf);
outf.close();
util.openOutputFileAppend(rfnoMatchFile, outr);
thisrRead.getSequence().printSequence(outr);
outr.close();
}
//print no match quality parse, if wanted
if (qual) {
ofstream outq, outq2;
util.openOutputFileAppend(fqnoMatchFile, outq);
thisfRead.getQuality().printQScores(outq);
outq.close();
util.openOutputFileAppend(rqnoMatchFile, outq2);
thisrRead.getQuality().printQScores(outq2);
outq2.close();
}
}
}
//report progress
if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
count++;
}
}
inf.close(); inr.close();
if (files[2] != "") { inFIndex.close(); }
if (files[3] != "") { inRIndex.close(); }
if (fasta) { outfFasta.close(); outrFasta.close(); }
if (qual) { outfQual.close(); outrQual.close(); }
//report progress
if (!m->getControl_pressed()) { if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
return 0;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "processFile");
exit(1);
}
}
//**********************************************************************************************************************
set<string> ParseFastaQCommand::processFile(string inputfile, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos){
try {
//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);
}
//open Output Files
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputfile));
string fastaFile = getOutputFileName("fasta",variables);
string qualFile = getOutputFileName("qfile",variables);
ofstream outFasta, outQual;
//fasta and quality files for whole input file
if (fasta) { util.openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); }
if (qual) { util.openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile); }
ifstream in; util.openInputFile(inputfile, in);
int count = 0;
set<string> names;
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
bool ignore;
FastqRead thisRead(in, ignore, format);
if (!ignore) {
if (qual) { thisRead.getQuality().printQScores(outQual); }
if (pacbio) {
vector<int> qual = thisRead.getScores();
string seq = thisRead.getSeq();
for (int i = 0; i < qual.size(); i++) { if (qual[i] == 0){ seq[i] = 'N'; } }
thisRead.setSeq(seq);
names.insert(thisRead.getName());
}
FastqRead copy = thisRead;
//print sequence info to files
if (fasta) { thisRead.getSequence().printSequence(outFasta); }
if (m->getControl_pressed()) { break; }
if (split > 1) {
int trashCodeLength = 0; string thisGroup = "ignore";
if (oligosfile != "") {
Sequence tempSeq = thisRead.getSequence();
QualityScores tempQual = thisRead.getQuality();
trashCodeLength = findGroup(tempSeq, tempQual, thisGroup, trimOligos, rtrimOligos, numBarcodes, numPrimers);
thisRead.setSeq(tempSeq.getUnaligned());
thisRead.setScores(tempQual.getScores());
}
else if (groupfile != "") { trashCodeLength = findGroup(thisRead.getSequence(), thisGroup, "groupMode"); }
else { m->mothurOut("[ERROR]: uh oh, we shouldn't be here...\n"); }
bool addToScrap = false;
if(trashCodeLength == 0){
int pos = thisGroup.find("ignore");
if (pos == string::npos) {
if (thisGroup != "") {
seqGroups[copy.getName()] = thisGroup;
map<string, long long>::iterator it = groupCounts.find(thisGroup);
if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
else { groupCounts[it->first]++; }
}
}else { addToScrap = true; }
}else{ addToScrap = true; }
if (addToScrap) {
//print no match fastq
ofstream out;
util.openOutputFileAppend(ffqnoMatchFile, out);
copy.printFastq(out);
out.close();
//print no match fasta, if wanted
if (fasta) {
ofstream outf;
util.openOutputFileAppend(ffnoMatchFile, outf);
thisRead.getSequence().printSequence(outf);
outf.close();
}
//print no match quality parse, if wanted
if (qual) {
ofstream outq;
util.openOutputFileAppend(fqnoMatchFile, outq);
thisRead.getQuality().printQScores(outq);
outq.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->getControl_pressed()){ if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
return names;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "processFile");
exit(1);
}
}
//**********************************************************************************************************************
int ParseFastaQCommand::findGroup(Sequence& currSeq, QualityScores& currQual, string& thisGroup, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos, int numBarcodes, int numPrimers) {
try {
int success = 1; int barcode, primer;
string trashCode = "";
int currentSeqsDiffs = 0;
//for reorient
Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
QualityScores savedQual(currQual.getName(), currQual.getScores());
if(numLinkers != 0){
success = trimOligos->stripLinker(currSeq, currQual);
if(success > ldiffs) { trashCode += 'k'; }
else{ currentSeqsDiffs += success; }
}
if(numBarcodes != 0){
vector<int> results = trimOligos->stripBarcode(currSeq, currQual, barcode);
if (pairedOligos) { success = results[0] + results[2]; }
else { success = results[0]; }
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(numSpacers != 0){
success = trimOligos->stripSpacer(currSeq, currQual);
if(success > sdiffs) { trashCode += 's'; }
else{ currentSeqsDiffs += success; }
}
if(numPrimers != 0){
vector<int> results = trimOligos->stripForward(currSeq, currQual, primer, true);
if (pairedOligos) { success = results[0] + results[2]; }
else { success = results[0]; }
if(success > pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
if(numRPrimers != 0){
vector<int> results = trimOligos->stripReverse(currSeq, currQual);
success = results[0];
if(success > pdiffs) { trashCode += 'r'; }
else{ currentSeqsDiffs += success; }
}
if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
int thisSuccess = 0;
string thisTrashCode = "";
int thisCurrentSeqsDiffs = 0;
int thisBarcodeIndex = 0;
int thisPrimerIndex = 0;
if(numBarcodes != 0){
vector<int> results = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
if (pairedOligos) { thisSuccess = results[0] + results[2]; }
else { thisSuccess = results[0]; }
if(thisSuccess > bdiffs) { thisTrashCode += "b"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if(numPrimers != 0){
vector<int> results = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, true);
if (pairedOligos) { thisSuccess = results[0] + results[2]; }
else { thisSuccess = results[0]; }
if(thisSuccess > pdiffs) { thisTrashCode += "f"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
if (thisTrashCode == "") {
trashCode = thisTrashCode;
success = thisSuccess;
currentSeqsDiffs = thisCurrentSeqsDiffs;
barcode = thisBarcodeIndex;
primer = thisPrimerIndex;
}else { trashCode += "(" + thisTrashCode + ")"; }
}
if (trashCode.length() == 0) { //is this sequence in the ignore group
thisGroup = oligos.getGroupName(barcode, primer);
int pos = thisGroup.find("ignore");
if (pos != string::npos) { trashCode += "i"; }
}
return trashCode.length();
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "findGroup");
exit(1);
}
}
//**********************************************************************************************************************
int ParseFastaQCommand::findGroup(Sequence seq, string& group, string groupMode) {
try {
string trashCode = "";
group = groupMap->getGroup(seq.getName());
if (group == "not found") { trashCode += "g"; } //scrap for group
return trashCode.length();
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "findGroup");
exit(1);
}
}
//**********************************************************************************************************************
int ParseFastaQCommand::findGroup(Sequence& fcurrSeq, QualityScores& fcurrQual, Sequence& rcurrSeq, QualityScores& rcurrQual, string& thisGroup, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos, int numBarcodes, int numPrimers) {
try {
int success = 1; int barcode, primer;
string trashCode = "";
int currentSeqsDiffs = 0;
//for reorient
Sequence fsavedSeq(fcurrSeq.getName(), fcurrSeq.getAligned());
QualityScores fsavedQual(fcurrQual.getName(), fcurrQual.getScores());
Sequence rsavedSeq(rcurrSeq.getName(), rcurrSeq.getAligned());
QualityScores rsavedQual(rcurrQual.getName(), rcurrQual.getScores());
if(numBarcodes != 0){
vector<int> results = trimOligos->stripBarcode(fcurrSeq, rcurrSeq, fcurrQual, rcurrQual, barcode);
if (pairedOligos) { success = results[0] + results[2]; }
else { success = results[0]; }
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(numPrimers != 0){
vector<int> results = trimOligos->stripForward(fcurrSeq, rcurrSeq, fcurrQual, rcurrQual, primer);
if (pairedOligos) { success = results[0] + results[2]; }
else { success = results[0]; }
if(success > pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
int thisSuccess = 0;
string thisTrashCode = "";
int thisCurrentSeqsDiffs = 0;
int thisBarcodeIndex = 0;
int thisPrimerIndex = 0;
if(numBarcodes != 0){
vector<int> results = rtrimOligos->stripBarcode(fsavedSeq, rsavedSeq, fsavedQual, rsavedQual, thisBarcodeIndex);
if (pairedOligos) { thisSuccess = results[0] + results[2]; }
else { thisSuccess = results[0]; }
if(thisSuccess > bdiffs) { thisTrashCode += 'b'; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if(numPrimers != 0){
vector<int> results = rtrimOligos->stripForward(fsavedSeq, rsavedSeq, fsavedQual, rsavedQual, thisPrimerIndex);
if (pairedOligos) { thisSuccess = results[0] + results[2]; }
else { thisSuccess = results[0]; }
if(thisSuccess > pdiffs) { thisTrashCode += 'f'; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
if (thisTrashCode == "") {
trashCode = thisTrashCode;
success = thisSuccess;
currentSeqsDiffs = thisCurrentSeqsDiffs;
barcode = thisBarcodeIndex;
primer = thisPrimerIndex;
}else { trashCode += "(" + thisTrashCode + ")"; }
}
if (trashCode.length() == 0) { //is this sequence in the ignore group
thisGroup = oligos.getGroupName(barcode, primer);
int pos = thisGroup.find("ignore");
if (pos != string::npos) { trashCode += "i"; }
}
return trashCode.length();
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "findGroup");
exit(1);
}
}
//**********************************************************************************************************************
/*
file option 1
ffastqfile1 rfastqfile1
ffastqfile2 rfastqfile2
...
file option 2
group ffastqfile rfastqfile
group ffastqfile rfastqfile
group ffastqfile rfastqfile
...
file option 3
My.forward.fastq My.reverse.fastq none My.rindex.fastq //none is an option is no forward or reverse index file
*/
//lines can be 2, 3, or 4 columns
// forward.fastq reverse.fastq -> 2 column
// groupName forward.fastq reverse.fastq -> 3 column
// forward.fastq reverse.fastq forward.index.fastq reverse.index.fastq -> 4 column
// forward.fastq reverse.fastq none reverse.index.fastq -> 4 column
// forward.fastq reverse.fastq forward.index.fastq none -> 4 column
vector< vector<string> > ParseFastaQCommand::readFile(){
try {
string mode = "parseFastq";
if (pacbio) { mode = "parsefastqpacbio"; } //reads 2 column option as group filename
FileFile dataFile(inputfile, mode);
vector< vector<string> > files = dataFile.getFiles(); //if pacbio 2 columns, files[x][0] = filename, files[x][1] = "", files[x][2] = "", files[x][3] = "",
file2Group = dataFile.getGroupNames();
createFileGroup = dataFile.isColumnWithGroupNames();
hasIndex = dataFile.containsIndexFiles();
int dataFileFormat = dataFile.getFileFormat();
if (hasIndex && (oligosfile == "")) { m->mothurOut("[ERROR]: You need to provide an oligos file if you are going to use an index file.\n"); m->setControl_pressed(true); }
if ((oligosfile != "") && (dataFileFormat == 2)) { m->mothurOut("[ERROR]: You cannot have an oligosfile and 3 column file option at the same time. Aborting. \n"); m->setControl_pressed(true); }
if ((oligosfile != "") && (dataFileFormat == 1) && pacbio) { m->mothurOut("[ERROR]: You cannot have an oligosfile and 2 column pacbio file option at the same time. Aborting. \n"); m->setControl_pressed(true); }
if ((groupfile != "") && (dataFileFormat == 2)){ m->mothurOut("[ERROR]: You cannot have an groupfile and 3 column file option at the same time. Aborting. \n"); m->setControl_pressed(true); }
for (int i = 0; i < files.size(); i++) {
string group = "";
string forward, reverse, findex, rindex;
forward = files[i][0]; reverse = files[i][1]; findex = files[i][2]; rindex = files[i][3];
if (dataFileFormat == 1) { //2 column
fileOption = 2;
}else if (dataFileFormat == 2) { //3 column
fileOption = 3;
}else if (dataFileFormat == 3) { //4 column
fileOption = 4;
if ((findex == "none") || (findex == "NONE")){ files[i][2] = ""; }
if ((rindex == "none") || (rindex == "NONE")){ files[i][3] = ""; }
}
}
if (files.size() == 0) { m->setControl_pressed(true); }
return files;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "readFileNames");
exit(1);
}
}
//***************************************************************************************************************
bool ParseFastaQCommand::readOligos(string oligoFile){
try {
bool allBlank = false;
if (fileOption > 0) { oligos.read(oligosfile, false); } // like make.contigs
else { oligos.read(oligosfile); }
if (m->getControl_pressed()) { return false; } //error in reading oligos
if (oligos.hasPairedPrimers() || oligos.hasPairedBarcodes()) {
pairedOligos = true;
numPrimers = oligos.getPairedPrimers().size();
numBarcodes = oligos.getPairedBarcodes().size();
}else {
pairedOligos = false;
numPrimers = oligos.getPrimers().size();
numBarcodes = oligos.getBarcodes().size();
}
numLinkers = oligos.getLinkers().size();
numSpacers = oligos.getSpacers().size();
numRPrimers = oligos.getReversePrimers().size();
vector<string> groupNames = oligos.getSRAGroupNames();
if (groupNames.size() == 0) { allBlank = true; }
if (allBlank) { m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile.\n"); return false; }
//make blank files for scrap matches
ofstream temp, tempff, tempfq, rtemp, temprf, temprq;
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputfile));
variables["[sample]"] = "scrap";
if (fileOption > 0) { variables["[tag]"] = "forward"; }
ffqnoMatchFile = getOutputFileName("fastq", variables);
util.openOutputFile(ffqnoMatchFile, temp); temp.close();
if (fileOption > 0) {
variables["[tag]"] = "reverse";
rfqnoMatchFile = getOutputFileName("fastq", variables);
util.openOutputFile(rfqnoMatchFile, rtemp); rtemp.close();
}
if (fasta) {
if (fileOption > 0) { variables["[tag]"] = "forward"; }
ffnoMatchFile = getOutputFileName("fasta", variables);
util.openOutputFile(ffnoMatchFile, tempff); tempff.close();
if (fileOption > 0) {
variables["[tag]"] = "reverse";
rfnoMatchFile = getOutputFileName("fasta", variables);
util.openOutputFile(rfnoMatchFile, temprf); temprf.close();
}
}
if (qual) {
if (fileOption > 0) { variables["[tag]"] = "forward"; }
fqnoMatchFile = getOutputFileName("qfile", variables);
util.openOutputFile(fqnoMatchFile, tempfq); tempfq.close();
if (fileOption > 0) {
variables["[tag]"] = "reverse";
rqnoMatchFile = getOutputFileName("qfile", variables);
util.openOutputFile(rqnoMatchFile, temprq); temprq.close();
}
}
return true;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "getOligos");
exit(1);
}
}
//***************************************************************************************************************
bool ParseFastaQCommand::readGroup(string groupfile){
try {
groupMap = new GroupMap();
groupMap->readMap(groupfile);
vector<string> groups = groupMap->getNamesOfGroups();
return true;
}
catch(exception& e) {
m->errorOut(e, "ParseFastaQCommand", "readGroup");
exit(1);
}
}
//**********************************************************************************************************************
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