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|
/*
* filterseqscommand.cpp
* Mothur
*
* Created by Thomas Ryabin on 5/4/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "filterseqscommand.h"
#include "sequence.hpp"
//**********************************************************************************************************************
vector<string> FilterSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
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, "FilterSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string FilterSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n";
helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n";
helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n";
helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n";
helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n";
helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n";
helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n";
helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n";
helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
helpString += "The filter.seqs command should be in the following format: \n";
helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n";
helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string FilterSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],filter.fasta"; }
else if (type == "filter") { pattern = "[filename],filter"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
FilterSeqsCommand::FilterSeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["filter"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
exit(1);
}
}
/**************************************************************************************/
FilterSeqsCommand::FilterSeqsCommand(string option) {
try {
abort = false; calledHelp = false;
filterFileName = "";
//allow user to run help
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("filter.seqs");
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
for (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["filter"] = 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("fasta");
//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["fasta"] = inputDir + it->second; }
}
it = parameters.find("hard");
//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["hard"] = inputDir + it->second; }
}
}
//check for required parameters
fasta = validParameter.validFile(parameters, "fasta", false);
if (fasta == "not found") {
fasta = m->getFastaFile();
if (fasta != "") {
fastafileNames.push_back(fasta);
m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
string simpleName = m->getSimpleName(fasta);
filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
}
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else {
m->splitAtDash(fasta, fastafileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastafileNames.size(); i++) {
bool ignore = false;
if (fastafileNames[i] == "current") {
fastafileNames[i] = m->getFastaFile();
if (fastafileNames[i] != "") { m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastafileNames.erase(fastafileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastafileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastafileNames[i] = inputDir + fastafileNames[i]; }
}
ifstream in;
int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastafileNames[i] = tryPath;
}
}
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastafileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastafileNames.erase(fastafileNames.begin()+i);
i--;
}else{
string simpleName = m->getSimpleName(fastafileNames[i]);
filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
m->setFastaFile(fastafileNames[i]);
}
in.close();
}
}
//make sure there is at least one valid file left
if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
if (!abort) {
//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 = "";
outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
}
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
else if (hard == "not open") { hard = ""; abort = true; }
temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; }
trump = temp[0];
temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
else { soft = (float)atoi(temp.c_str()) / 100.0; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
vertical = validParameter.validFile(parameters, "vertical", false);
if (vertical == "not found") {
if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
else { vertical = "F"; }
}
numSeqs = 0;
}
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
exit(1);
}
}
/**************************************************************************************/
int FilterSeqsCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
ifstream inFASTA;
m->openInputFile(fastafileNames[0], inFASTA);
Sequence testSeq(inFASTA);
alignmentLength = testSeq.getAlignLength();
inFASTA.close();
////////////create filter/////////////////
m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
filter = createFilter();
m->mothurOutEndLine(); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); return 0; }
#ifdef USE_MPI
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
if (pid == 0) { //only one process should output the filter
#endif
ofstream outFilter;
//prevent giantic file name
map<string, string> variables;
variables["[filename]"] = outputDir + filterFileName + ".";
if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
string filterFile = getOutputFileName("filter", variables);
m->openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
outFilter.close();
outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
#ifdef USE_MPI
}
#endif
////////////run filter/////////////////
m->mothurOut("Running Filter... "); m->mothurOutEndLine();
filterSequences();
m->mothurOutEndLine(); m->mothurOutEndLine();
int filteredLength = 0;
for(int i=0;i<alignmentLength;i++){
if(filter[i] == '1'){ filteredLength++; }
}
if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
//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); }
}
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, "FilterSeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************/
int FilterSeqsCommand::filterSequences() {
try {
numSeqs = 0;
for (int s = 0; s < fastafileNames.size(); s++) {
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
string filteredFasta = getOutputFileName("fasta", variables);
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;
vector<unsigned long long>MPIPos;
MPI_Status status;
MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_File outMPI;
MPI_File inMPI;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
char outFilename[1024];
strcpy(outFilename, filteredFasta.c_str());
char inFileName[1024];
strcpy(inFileName, fastafileNames[s].c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
if (pid == 0) { //you are the root process
MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
numSeqs += num;
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
}
//figure out how many sequences you have to do
numSeqsPerProcessor = num / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
//do your part
driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
char buf[5];
MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
}
}else { //you are a child process
MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(num+1);
numSeqs += num;
MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = num / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
//align your part
driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
char buf[5];
strcpy(buf, "done");
//tell parent you are done.
MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
MPI_File_close(&outMPI);
MPI_File_close(&inMPI);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
vector<unsigned long long> positions;
if (savedPositions.size() != 0) { positions = savedPositions[s]; }
else {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafileNames[s], processors);
#else
if(processors != 1){
int numFastaSeqs = 0;
positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
if (positions.size() < processors) { processors = positions.size(); }
}
#endif
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) {
lines.push_back(new linePair(positions[i], positions[(i+1)]));
}
if(processors == 1){
int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
}else{
int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
numSeqs += numFastaSeqs;
}
if (m->control_pressed) { return 1; }
#else
if(processors == 1){
lines.push_back(new linePair(0, 1000));
int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
}else {
int numFastaSeqs = positions.size()-1;
//positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
}
numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
numSeqs += numFastaSeqs;
}
if (m->control_pressed) { return 1; }
#endif
#endif
outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "filterSequences");
exit(1);
}
}
#ifdef USE_MPI
/**************************************************************************************/
int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
try {
string outputString = "";
int count = 0;
MPI_Status status;
for(int i=0;i<num;i++){
if (m->control_pressed) { return 0; }
//read next sequence
int length = MPIPos[start+i+1] - MPIPos[start+i];
char* buf4 = new char[length];
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
string tempBuf = buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
istringstream iss (tempBuf,istringstream::in);
delete buf4;
Sequence seq(iss); m->gobble(iss);
if (seq.getName() != "") {
string align = seq.getAligned();
string filterSeq = "";
for(int j=0;j<alignmentLength;j++){
if(filter[j] == '1'){
filterSeq += align[j];
}
}
count++;
outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
if(count % 10 == 0){ //output to file
//send results to parent
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
delete buf;
}
}
if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
if(outputString != ""){ //output to file
//send results to parent
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
delete buf;
}
if((num) % 100 != 0){ cout << (num) << endl; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
exit(1);
}
}
#endif
/**************************************************************************************/
int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
try {
ofstream out;
m->openOutputFile(outputFilename, out);
ifstream in;
m->openInputFile(inputFilename, in);
in.seekg(filePos->start);
bool done = false;
int count = 0;
while (!done) {
if (m->control_pressed) { in.close(); out.close(); return 0; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
string align = seq.getAligned();
string filterSeq = "";
for(int j=0;j<alignmentLength;j++){
if(filter[j] == '1'){
filterSeq += align[j];
}
}
out << '>' << seq.getName() << endl << filterSeq << endl;
count++;
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (in.eof()) { break; }
#endif
//report progress
if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
out.close();
in.close();
return count;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
exit(1);
}
}
/**************************************************************************************************/
int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, string filteredFastaName) {
try {
int process = 1;
int num = 0;
processIDS.clear();
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
string filteredFasta = filename + toString(getpid()) + ".temp";
num = driverRunFilter(F, filteredFasta, filename, lines[process]);
//pass numSeqs to parent
ofstream out;
string tempFile = filename + toString(getpid()) + ".num.temp";
m->openOutputFile(tempFile, out);
out << num << endl;
out.close();
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
exit(0);
}
}
num = driverRunFilter(F, filteredFastaName, filename, lines[0]);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
for (int i = 0; i < processIDS.size(); i++) {
ifstream in;
string tempFile = filename + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); m->mothurRemove(tempFile);
m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filteredFastaName);
m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
}
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the filterData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
//Taking advantage of shared memory to allow both threads to add info to F.
//////////////////////////////////////////////////////////////////////////////////////////////////////
vector<filterRunData*> pDataArray;
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
//Create processor worker threads.
for( int i=0; i<processors-1; i++){
string extension = "";
if (i != 0) { extension = toString(i) + ".temp"; }
filterRunData* tempFilter = new filterRunData(filter, filename, (filteredFastaName + extension), m, lines[i]->start, lines[i]->end, alignmentLength, i);
pDataArray.push_back(tempFilter);
processIDS.push_back(i);
hThreadArray[i] = CreateThread(NULL, 0, MyRunFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}
num = driverRunFilter(F, (filteredFastaName + toString(processors-1) + ".temp"), filename, lines[processors-1]);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
if (pDataArray[i]->count != pDataArray[i]->end) {
m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
}
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
for (int i = 1; i < processors; i++) {
m->appendFiles((filteredFastaName + toString(i) + ".temp"), filteredFastaName);
m->mothurRemove((filteredFastaName + toString(i) + ".temp"));
}
#endif
return num;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
exit(1);
}
}
/**************************************************************************************/
string FilterSeqsCommand::createFilter() {
try {
string filterString = "";
Filters F;
if (soft != 0) { F.setSoft(soft); }
if (trump != '*') { F.setTrump(trump); }
F.setLength(alignmentLength);
if(trump != '*' || m->isTrue(vertical) || soft != 0){
F.initialize();
}
if(hard.compare("") != 0) { F.doHard(hard); }
else { F.setFilter(string(alignmentLength, '1')); }
numSeqs = 0;
if(trump != '*' || m->isTrue(vertical) || soft != 0){
for (int s = 0; s < fastafileNames.size(); s++) {
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;
vector<unsigned long long> MPIPos;
MPI_Status status;
MPI_File inMPI;
MPI_Comm_size(MPI_COMM_WORLD, &processors);
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
//char* tempFileName = new char(fastafileNames[s].length());
//tempFileName = &(fastafileNames[s][0]);
char tempFileName[1024];
strcpy(tempFileName, fastafileNames[s].c_str());
MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
if (pid == 0) { //you are the root process
MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
numSeqs += num;
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
}
//figure out how many sequences you have to do
numSeqsPerProcessor = num / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
//do your part
MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
}else { //i am the child process
MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(num+1);
numSeqs += num;
MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = num / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
//do your part
MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
}
MPI_File_close(&inMPI);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) {
lines.push_back(new linePair(positions[i], positions[(i+1)]));
}
if(processors == 1){
int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
}else{
int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
numSeqs += numFastaSeqs;
}
#else
if(processors == 1){
lines.push_back(new linePair(0, 1000));
int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
}else {
int numFastaSeqs = 0;
positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
}
numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
numSeqs += numFastaSeqs;
}
#endif
//save the file positions so we can reuse them in the runFilter function
savedPositions[s] = positions;
if (m->control_pressed) { return filterString; }
#endif
}
}
#ifdef USE_MPI
int pid;
int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
if(trump != '*' || m->isTrue(vertical) || soft != 0){
if (pid == 0) { //only one process should output the filter
vector<int> temp; temp.resize(alignmentLength+1);
//get the frequencies from the child processes
for(int i = 1; i < processors; i++) {
for (int j = 0; j < 5; j++) {
MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what letter count this is for
if (receiveTag == Atag) { //you are recieveing the A frequencies
for (int k = 0; k < alignmentLength; k++) { F.a[k] += temp[k]; }
}else if (receiveTag == Ttag) { //you are recieveing the T frequencies
for (int k = 0; k < alignmentLength; k++) { F.t[k] += temp[k]; }
}else if (receiveTag == Ctag) { //you are recieveing the C frequencies
for (int k = 0; k < alignmentLength; k++) { F.c[k] += temp[k]; }
}else if (receiveTag == Gtag) { //you are recieveing the G frequencies
for (int k = 0; k < alignmentLength; k++) { F.g[k] += temp[k]; }
}else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
for (int k = 0; k < alignmentLength; k++) { F.gap[k] += temp[k]; }
}
}
}
}else{
//send my fequency counts
F.a.push_back(Atag);
int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
F.t.push_back(Ttag);
ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
F.c.push_back(Ctag);
ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
F.g.push_back(Gtag);
ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
F.gap.push_back(Gaptag);
ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
}
}
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
if (pid == 0) { //only one process should output the filter
#endif
F.setNumSeqs(numSeqs);
if(m->isTrue(vertical) == 1) { F.doVertical(); }
if(soft != 0) { F.doSoft(); }
filterString = F.getFilter();
#ifdef USE_MPI
//send filter string to kids
//for(int i = 1; i < processors; i++) {
// MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
//}
MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
}else{
//recieve filterString
char* tempBuf = new char[alignmentLength];
//MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
filterString = tempBuf;
if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength); }
delete tempBuf;
}
MPI_Barrier(MPI_COMM_WORLD);
#endif
return filterString;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "createFilter");
exit(1);
}
}
/**************************************************************************************/
int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
try {
ifstream in;
m->openInputFile(filename, in);
in.seekg(filePos->start);
bool done = false;
int count = 0;
while (!done) {
if (m->control_pressed) { in.close(); return 1; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
if(trump != '*') { F.doTrump(seq); }
if(m->isTrue(vertical) || soft != 0) { F.getFreqs(seq); }
cout.flush();
count++;
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (in.eof()) { break; }
#endif
//report progress
if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
in.close();
return count;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
exit(1);
}
}
#ifdef USE_MPI
/**************************************************************************************/
int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {
try {
MPI_Status status;
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
for(int i=0;i<num;i++){
if (m->control_pressed) { return 0; }
//read next sequence
int length = MPIPos[start+i+1] - MPIPos[start+i];
char* buf4 = new char[length];
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
string tempBuf = buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
istringstream iss (tempBuf,istringstream::in);
delete buf4;
Sequence seq(iss);
if (seq.getAligned().length() != alignmentLength) { cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1); }
if(trump != '*'){ F.doTrump(seq); }
if(m->isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
cout.flush();
//report progress
if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
//report progress
if((num) % 100 != 0){ cout << num << endl; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
exit(1);
}
}
#endif
/**************************************************************************************************/
int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
try {
int process = 1;
int num = 0;
processIDS.clear();
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
//reset child's filter counts to 0;
F.a.clear(); F.a.resize(alignmentLength, 0);
F.t.clear(); F.t.resize(alignmentLength, 0);
F.g.clear(); F.g.resize(alignmentLength, 0);
F.c.clear(); F.c.resize(alignmentLength, 0);
F.gap.clear(); F.gap.resize(alignmentLength, 0);
num = driverCreateFilter(F, filename, lines[process]);
//write out filter counts to file
filename += toString(getpid()) + "filterValues.temp";
ofstream out;
m->openOutputFile(filename, out);
out << num << endl;
out << F.getFilter() << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.a[k] << '\t'; } out << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.t[k] << '\t'; } out << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.g[k] << '\t'; } out << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.c[k] << '\t'; } out << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.gap[k] << '\t'; } out << endl;
//cout << F.getFilter() << endl;
out.close();
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
exit(0);
}
}
//parent do your part
num = driverCreateFilter(F, filename, lines[0]);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
int temp = processIDS[i];
wait(&temp);
}
//parent reads in and combines Filter info
for (int i = 0; i < processIDS.size(); i++) {
string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
ifstream in;
m->openInputFile(tempFilename, in);
int temp, tempNum;
string tempFilterString;
in >> tempNum; m->gobble(in); num += tempNum;
in >> tempFilterString;
F.mergeFilter(tempFilterString);
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } m->gobble(in);
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } m->gobble(in);
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } m->gobble(in);
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.c[k] += temp; } m->gobble(in);
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } m->gobble(in);
in.close();
m->mothurRemove(tempFilename);
}
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the filterData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
//Taking advantage of shared memory to allow both threads to add info to F.
//////////////////////////////////////////////////////////////////////////////////////////////////////
vector<filterData*> pDataArray;
DWORD dwThreadIdArray[processors];
HANDLE hThreadArray[processors];
//Create processor worker threads.
for( int i=0; i<processors; i++ ){
filterData* tempFilter = new filterData(filename, m, lines[i]->start, lines[i]->end, alignmentLength, trump, vertical, soft, hard, i);
pDataArray.push_back(tempFilter);
processIDS.push_back(i);
hThreadArray[i] = CreateThread(NULL, 0, MyCreateFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}
//Wait until all threads have terminated.
WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
if (pDataArray[i]->count != pDataArray[i]->end) {
m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
}
F.mergeFilter(pDataArray[i]->F.getFilter());
for (int k = 0; k < alignmentLength; k++) { F.a[k] += pDataArray[i]->F.a[k]; }
for (int k = 0; k < alignmentLength; k++) { F.t[k] += pDataArray[i]->F.t[k]; }
for (int k = 0; k < alignmentLength; k++) { F.g[k] += pDataArray[i]->F.g[k]; }
for (int k = 0; k < alignmentLength; k++) { F.c[k] += pDataArray[i]->F.c[k]; }
for (int k = 0; k < alignmentLength; k++) { F.gap[k] += pDataArray[i]->F.gap[k]; }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#endif
return num;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
exit(1);
}
}
/**************************************************************************************/
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