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/*
* chopseqscommand.cpp
* Mothur
*
* Created by westcott on 5/10/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "chopseqscommand.h"
#include "removeseqscommand.h"
//**********************************************************************************************************************
vector<string> ChopSeqsCommand::setParameters(){
try {
CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pfastq);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false,true); parameters.push_back(pqfile);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnumbases);
CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcountgaps);
CommandParameter pshort("short", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshort);
CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "","",false,false); parameters.push_back(pkeep);
CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pkeepn("keepn", "Boolean", "", "f", "", "", "","",false,false); parameters.push_back(pkeepn);
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;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["fastq"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = 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, "ChopSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ChopSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The chop.seqs command reads a fasta or fastq file and outputs a *.chop.* file containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n";
helpString += "The chop.seqs command parameters are fasta, fastq, qfile, name, group, count, numbases, countgaps and keep. fasta or fastq is required unless you have a valid current fasta file. numbases is required.\n";
helpString += "The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n";
helpString += "If you provide a name, group or count file any sequences removed from the fasta file will also be removed from those files.\n";
helpString += "The qfile parameter allows you to provide a quality file associated with the fastafile.\n";
helpString += "The numbases parameter allows you to specify the number of bases you want to keep.\n";
helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
helpString += "The keepn parameter allows you to specify you want to keep ambigous bases, default=false.\n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
;
return helpString;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string ChopSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],chop.fasta"; }
else if (type == "fastq") { pattern = "[filename],chop.fastq"; }
else if (type == "qfile") { pattern = "[filename],chop.qual"; }
else if (type == "name") { pattern = "[filename],chop.names"; }
else if (type == "group") { pattern = "[filename],chop.groups"; }
else if (type == "count") { pattern = "[filename],chop.count_table"; }
else if (type == "accnos") { pattern = "[filename],chop.accnos"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(string option) : Command() {
try {
//allow user to run help
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();
//check for required parameters
ValidParameters validParameter;
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { current->setFastaFile(fastafile); }
fastqfile = validParameter.validFile(parameters, "fastq");
if (fastqfile == "not open") { fastqfile = ""; abort = true; }
else if (fastqfile == "not found") { fastqfile = ""; }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); }
qualfile = validParameter.validFile(parameters, "qfile");
if (qualfile == "not open") { qualfile = ""; abort = true; }
else if (qualfile == "not found") { qualfile = ""; }
else { current->setQualFile(qualfile); }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count.\n"); abort = true;
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count.\n"); abort=true;
}
if ((fastqfile == "") && (fastafile == "")) {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current fastafile and did not provide a fastqfile. The fasta or fastq parameter is required to run the chop.seqs command.\n"); abort = true; }
}
string temp = validParameter.valid(parameters, "numbases"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, numbases);
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
temp = validParameter.valid(parameters, "countgaps"); if (temp == "not found") { temp = "f"; }
countGaps = util.isTrue(temp);
temp = validParameter.valid(parameters, "short"); if (temp == "not found") { temp = "f"; }
Short = util.isTrue(temp);
temp = validParameter.valid(parameters, "keepn"); if (temp == "not found") { if (qualfile!= "") { temp = "t"; }else { temp = "f"; } }
keepN = util.isTrue(temp);
format = validParameter.valid(parameters, "format"); if (format == "not found"){ format = "illumina1.8+"; }
if (((!keepN) && (qualfile != "")) || ((countGaps) && (qualfile != ""))){ m->mothurOut("[ERROR]: You cannot set keepn=false with a quality file, or set countgaps to true.\n"); abort = true; }
keep = validParameter.valid(parameters, "keep"); if (keep == "not found") { keep = "front"; }
if (numbases == 0) { m->mothurOut("You must provide the number of bases you want to keep for the chops.seqs command.\n"); abort = true; }
}
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int ChopSeqsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
bool wroteAccnos = true; string outputFileNameAccnos = "";
if (fastafile != "") { wroteAccnos = runChopFasta(outputFileNameAccnos); }
else { wroteAccnos = runChopFastq(outputFileNameAccnos); }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
if (wroteAccnos) {
map<string, string> variables;
outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos);
//use remove.seqs to create new name, group and count file
if ((countfile != "") || (namefile != "") || (groupfile != "")) {
string inputString = "accnos=" + outputFileNameAccnos;
if (countfile != "") { inputString += ", count=" + countfile; }
else{
if (namefile != "") { inputString += ", name=" + namefile; }
if (groupfile != "") { inputString += ", group=" + groupfile; }
}
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: remove.seqs(" + inputString + ")\n");
current->setMothurCalling(true);
Command* removeCommand = new RemoveSeqsCommand(inputString);
removeCommand->execute();
map<string, vector<string> > filenames = removeCommand->getOutputFiles();
delete removeCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
if (groupfile != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(groupfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(groupfile));
string outGroup = getOutputFileName("group", variables);
util.renameFile(filenames["group"][0], outGroup);
outputNames.push_back(outGroup); outputTypes["group"].push_back(outGroup);
}
if (namefile != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(namefile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(namefile));
string outName = getOutputFileName("name", variables);
util.renameFile(filenames["name"][0], outName);
outputNames.push_back(outName); outputTypes["name"].push_back(outName);
}
if (countfile != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(countfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
string outCount = getOutputFileName("count", variables);
util.renameFile(filenames["count"][0], outCount);
outputNames.push_back(outCount); outputTypes["count"].push_back(outCount);
}
}
}
else { util.mothurRemove(outputFileNameAccnos); }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } 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); }
}
if (wroteAccnos) { //set accnos file as new current accnosfile
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setAccnosFile(currentName); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setNameFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(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, "ChopSeqsCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
bool ChopSeqsCommand::runChopFasta(string& outputFileNameAccnos){
try {
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(fastafile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastafile));
string outputFileName = getOutputFileName("fasta", variables);
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
outputFileNameAccnos = getOutputFileName("accnos", variables);
string fastafileTemp = "";
if (qualfile != "") { fastafileTemp = outputFileName + ".qualFile.Positions.temp"; }
bool wroteAccnos = createProcesses(fastafile, outputFileName, outputFileNameAccnos, fastafileTemp);
if (m->getControl_pressed()) { return wroteAccnos; }
if (qualfile != "") {
thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile));
string outputQualFileName = getOutputFileName("qfile", variables);
outputNames.push_back(outputQualFileName); outputTypes["qfile"].push_back(outputQualFileName);
processQual(outputQualFileName, fastafileTemp);
util.mothurRemove(fastafileTemp);
}
return wroteAccnos;
}catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "runChopFasta");
exit(1);
}
}
//**********************************************************************************************************************
bool ChopSeqsCommand::runChopFastq(string& outputFileNameAccnos){
try {
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(fastqfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastqfile));
string outputFileName = getOutputFileName("fastq", variables);
outputNames.push_back(outputFileName); outputTypes["fastq"].push_back(outputFileName);
outputFileNameAccnos = getOutputFileName("accnos", variables);
ifstream in; util.openInputFile(fastqfile, in);
ofstream out; util.openOutputFile(outputFileName, out);
ofstream outAccnos; util.openOutputFile(outputFileNameAccnos, outAccnos);
bool wroteAccnos = false; long long count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
bool ignore;
FastqRead seq(in, ignore, format); gobble(in);
if (seq.getName() != "") {
bool isGood = getFastqChopped(seq);
//output trimmed sequence
if (isGood) { seq.printFastq(out); }
else{
outAccnos << seq.getName() << endl;
wroteAccnos = true;
}
count++;
}
//report progress
if((count) % 10000 == 0){ m->mothurOut(toString(count)+"\n"); }
}
//report progress
if((count) % 10000 != 0){ m->mothurOut(toString(count)+"\n"); }
in.close(); out.close(); outAccnos.close();
return wroteAccnos;
}catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "runChopFastq");
exit(1);
}
}
//**********************************************************************************************************************
bool ChopSeqsCommand::getFastqChopped(FastqRead& seq) {
try {
string temp = seq.getSeq();
vector<int> scores = seq.getScores();
//if needed trim sequence
if (keep == "front") {//you want to keep the beginning
int tempLength = temp.length();
if (tempLength > numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = 0; i < temp.length(); i++) {
numBasesCounted++;
if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; scores.clear(); }
else {
temp = temp.substr(0, stopSpot+1);
if(scores.size() >= stopSpot+1){
scores.resize((stopSpot+1));
}
}
}else {
if (!Short) { temp = ""; scores.clear(); } //sequence too short
}
}else { //you are keeping the back
int tempLength = temp.length();
if (tempLength > numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = (temp.length()-1); i >= 0; i--) {
numBasesCounted++;
if (numBasesCounted >= numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else {
temp = temp.substr(stopSpot);
if(scores.size() >= stopSpot){
vector<int> scores2;
for (int h = stopSpot; h < scores.size(); h++) { scores2.push_back(scores[h]); }
scores.clear(); scores = scores2;
}
}
}else {
if (!Short) { temp = ""; scores.clear(); } //sequence too short
}
}
seq.setSeq(temp); seq.setScores(scores);
if (temp != "") { return true; }
return false;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "getFastqChopped");
exit(1);
}
}
/**************************************************************************************************/
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct chopData {
string filename, keep, qualValues, qualFileOutput;
int count;
unsigned long long start;
unsigned long long end;
OutputWriter* threadWriterAccnos;
OutputWriter* threadWriterOutput;
MothurOut* m;
Utils util;
int numbases;
bool countGaps, Short, wroteAccnos, keepN;
Sequence thisSeq;
chopData(){}
chopData(string f, unsigned long long st, unsigned long long en, OutputWriter* wo, OutputWriter* wa, string qv) {
m = MothurOut::getInstance();
filename = f;
threadWriterOutput = wo;
threadWriterAccnos = wa;
qualFileOutput = qv;
start = st;
end = en;
count = 0;
qualValues = "";
keep = "front";
countGaps = false;
Short = false;
keepN = false; if (qv!="") { keepN = true; }
wroteAccnos = false;
}
void setVariables(string k, bool cGaps, int nbases, bool S, bool kn) {
keep = k;
countGaps = cGaps;
numbases = nbases;
Short = S;
keepN = kn;
}
void setChopped(Sequence s) { thisSeq = s; }
};
//**********************************************************************************************************************
string getChopped(chopData* params) {
try {
string temp = params->thisSeq.getAligned();
string tempUnaligned = params->thisSeq.getUnaligned();
if (params->countGaps) {
//if needed trim sequence
if (params->keep == "front") {//you want to keep the beginning
int tempLength = temp.length();
if (tempLength > params->numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
if (!params->keepN) { if (toupper(temp[i]) == 'N') { temp[i] = '.'; } }
numBasesCounted++;
if (numBasesCounted >= params->numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(0, stopSpot+1); }
}else {
if (!params->Short) { temp = ""; } //sequence too short
}
}else { //you are keeping the back
int tempLength = temp.length();
if (tempLength > params->numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = (temp.length()-1); i >= 0; i--) {
//eliminate N's
if (!params->keepN) { if (toupper(temp[i]) == 'N') { temp[i] = '.'; } }
numBasesCounted++;
if (numBasesCounted >= params->numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(stopSpot+1); }
}else {
if (!params->Short) { temp = ""; } //sequence too short
}
}
}else{
//if needed trim sequence
if (params->keep == "front") {//you want to keep the beginning
int tempLength = tempUnaligned.length();
if (tempLength > params->numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = 0; i < temp.length(); i++) {
//eliminate N's
if (!params->keepN) {
if (toupper(temp[i]) == 'N') {
temp[i] = '.';
tempLength--;
if (tempLength < params->numbases) { stopSpot = 0; break; }
}
}
if(isalpha(temp[i])) { numBasesCounted++; }
if (numBasesCounted >= params->numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(0, stopSpot+1); }
params->qualValues = params->thisSeq.getName() +'\t' + toString(0) + '\t' + toString(stopSpot+1) + '\n';
}else {
if (!params->Short) { temp = ""; params->qualValues = params->thisSeq.getName() +'\t' + toString(0) + '\t' + toString(0) + '\n'; } //sequence too short
else { params->qualValues = params->thisSeq.getName() +'\t' + toString(0) + '\t' + toString(tempLength) + '\n'; }
}
}else { //you are keeping the back
int tempLength = tempUnaligned.length();
if (tempLength > params->numbases) { //you have enough bases to remove some
int stopSpot = 0;
int numBasesCounted = 0;
for (int i = (temp.length()-1); i >= 0; i--) {
if (!params->keepN) {
//eliminate N's
if (toupper(temp[i]) == 'N') {
temp[i] = '.';
tempLength--;
if (tempLength < params->numbases) { stopSpot = 0; break; }
}
}
if(isalpha(temp[i])) { numBasesCounted++; }
if (numBasesCounted >= params->numbases) { stopSpot = i; break; }
}
if (stopSpot == 0) { temp = ""; }
else { temp = temp.substr(stopSpot); }
params->qualValues = params->thisSeq.getName() +'\t' + toString(stopSpot) + '\t' + toString(temp.length()-1) + '\n';
}else {
if (!params->Short) { temp = ""; params->qualValues = params->thisSeq.getName() +'\t' + toString(0) + '\t' + toString(0) + '\n'; } //sequence too short
else { params->qualValues = params->thisSeq.getName() +'\t' + toString(0) + '\t' + toString(tempLength) + '\n'; }
}
}
}
return temp;
}
catch(exception& e) {
params->m->errorOut(e, "ChopSeqsCommand", "getChopped");
exit(1);
}
}
/**************************************************************************************/
void driverChop(chopData* params) {
try {
ifstream in; params->util.openInputFile(params->filename, in);
in.seekg(params->start);
//adjust
if (params->start == 0) { params->util.zapGremlins(in); gobble(in); }
ofstream outfTemp;
if (params->qualFileOutput != "") { params->util.openOutputFile(params->qualFileOutput, outfTemp); }
bool wroteAccnos = false;
while (!in.eof()) {
if (params->m->getControl_pressed()) { break; }
Sequence seq(in); gobble(in);
if (seq.getName() != "") {
params->qualValues = "";
params->thisSeq = seq;
string newSeqString = getChopped(params);
//output trimmed sequence
if (newSeqString != "") { params->threadWriterOutput->write(">"+seq.getName()+"\n"+newSeqString+"\n"); }
else{
params->threadWriterAccnos->write(seq.getName()+"\n");
wroteAccnos = true;
}
if (params->qualFileOutput != "") { outfTemp << params->qualValues << endl; }
params->count++;
}
#if defined NON_WINDOWS
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= params->end)) { break; }
#else
if (params->count == params->end) { break; }
#endif
//report progress
if((params->count) % 10000 == 0){ params->m->mothurOut(toString(params->count)+"\n"); }
}
//report progress
if((params->count) % 10000 != 0){ params->m->mothurOut(toString(params->count)+"\n"); }
in.close();
if (params->qualFileOutput != "") { outfTemp.close(); }
params->wroteAccnos = wroteAccnos;
}
catch(exception& e) {
params->m->errorOut(e, "ChopSeqsCommand", "driver");
exit(1);
}
}
/**************************************************************************************************/
bool ChopSeqsCommand::createProcesses(string filename, string outFasta, string outAccnos, string fastafileTemp) {
try {
//create array of worker threads
vector<std::thread*> workerThreads;
vector<chopData*> data;
vector<linePair> lines;
long long num = 0;
vector<double> positions;
#if defined NON_WINDOWS
positions = util.divideFile(filename, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
if (processors == 1) { lines.push_back(linePair(0, -1)); }//forces it to read whole file
else {
positions = util.setFilePosFasta(filename, num);
if (num < processors) { processors = num; }
//figure out how many sequences you have to process
int numSeqsPerProcessor = num / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = num - i * numSeqsPerProcessor; }
lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
}
}
#endif
auto synchronizedOutputFile = std::make_shared<SynchronizedOutputFile>(outFasta);
auto synchronizedAccnosFile = std::make_shared<SynchronizedOutputFile>(outAccnos);
//Lauch worker threads
for (int i = 0; i < processors-1; i++) {
string extension = toString(i+1) + ".temp";
OutputWriter* threadOutputWriter = new OutputWriter(synchronizedOutputFile);
OutputWriter* threadAccnosWriter = new OutputWriter(synchronizedAccnosFile);
chopData* dataBundle = new chopData(filename, lines[i+1].start, lines[i+1].end, threadOutputWriter, threadAccnosWriter, fastafileTemp+extension);
dataBundle->setVariables(keep, countGaps, numbases, Short, keepN);
data.push_back(dataBundle);
workerThreads.push_back(new std::thread(driverChop, dataBundle));
}
OutputWriter* threadOutputWriter = new OutputWriter(synchronizedOutputFile);
OutputWriter* threadAccnosWriter = new OutputWriter(synchronizedAccnosFile);
chopData* dataBundle = new chopData(filename, lines[0].start, lines[0].end, threadOutputWriter, threadAccnosWriter, fastafileTemp);
dataBundle->setVariables(keep, countGaps, numbases, Short, keepN);
driverChop(dataBundle);
num = dataBundle->count;
bool wroteAccnos = dataBundle->wroteAccnos;
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
num += data[i]->count;
delete data[i]->threadWriterOutput;
delete data[i]->threadWriterAccnos;
if (data[i]->wroteAccnos) { wroteAccnos = true; }
#if defined NON_WINDOWS
#else
if (data[i]->count != data[i]->end) {
m->mothurOut("[ERROR]: process " + toString(i+1) + " only processed " + toString(data[i]->count) + " of " + toString(data[i]->end) + " sequences assigned to it, quitting. \n"); m->setControl_pressed(true);
}
#endif
if (fastafileTemp != "") {
util.appendFiles(data[i]->qualFileOutput, fastafileTemp);
util.mothurRemove(data[i]->qualFileOutput);
}
delete data[i];
delete workerThreads[i];
}
synchronizedOutputFile->close(); synchronizedAccnosFile->close();
delete threadOutputWriter; delete threadAccnosWriter;
delete dataBundle;
return wroteAccnos;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "createProcesses");
exit(1);
}
}
//**********************************************************************************************************************
int ChopSeqsCommand::processQual(string outputFile, string inputFile) {
try {
ofstream out; util.openOutputFile(outputFile, out);
ifstream in; util.openInputFile(inputFile, in);
ifstream inQual; util.openInputFile(qualfile, inQual);
m->mothurOut("Processing the quality file.\n");
int count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { in.close(); out.close(); return 0; }
QualityScores qual(inQual); gobble(inQual);
string name = "";
int start = 0; int end = 0;
in >> name >> start >> end; gobble(in);
if (qual.getName() != "") {
if (qual.getName() != name) { start = 0; end = 0; }
else if (start != 0) {
qual.trimQScores(start, -1);
qual.printQScores(out);
}else if ((start == 0) && (end == 0)) {}
else if ((start == 0) && (end != 0)) {
qual.trimQScores(-1, end);
qual.printQScores(out);
}
}
count++;
//report progress
if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
}
//report progress
if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
in.close(); inQual.close(); out.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "processQual");
exit(1);
}
}
//**********************************************************************************************************************
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