X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=d2c7c6bb1f46e9e3ee1eef49ff83b6d4e840d173;hb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff;hp=95d51f329f30d8a639d0772844e54be5246e5005;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 95d51f3..d2c7c6b 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -12,246 +12,929 @@
 
 /**************************************************************************************/
 
-FilterSeqsCommand::FilterSeqsCommand(string option){
+FilterSeqsCommand::FilterSeqsCommand(string option)  {
 	try {
 		abort = false;
+		filterFileName = "";
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; }
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"fasta", "trump", "soft", "hard", "vertical"};
+			string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
 			
-			ValidParameters validParameter;
+			ValidParameters validParameter("filter.seqs");
+			map<string,string>::iterator it;
 			
 			//check to make sure all parameters are valid for command
-			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//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 = 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 = 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
-			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not found") { cout << "fasta is a required parameter for the filter.seqs command." << endl; abort = true; }
-			else if (fastafile == "not open") { abort = true; }	
+			fasta = validParameter.validFile(parameters, "fasta", false);
+			if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
+			else { 
+				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++) {
+					if (inputDir != "") {
+						string path = 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 = 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() + getSimpleName(fastafileNames[i]);
+							m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							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 = getSimpleName(fastafileNames[i]);
+						filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+					}
+					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 += 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;  }
 			
-			hard = validParameter.validFile(parameters, "hard", true);				if (hard == "not found") { hard = ""; }
-			else if (hard == "not open") { abort = true; }	
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = "1";				}
+			convert(temp, processors); 
 			
-			vertical = validParameter.validFile(parameters, "vertical", false);		if (vertical == "not found") { vertical = "T"; }
+			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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FilterSeqsCommand class function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 //**********************************************************************************************************************
 
 void FilterSeqsCommand::help(){
 	try {
-		cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
-		cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical.  " << "\n";
-		cout << "The fasta parameter is required." << "\n";
-		cout << "The trump parameter .... The default is ..." << "\n";
-		cout << "The soft parameter .... The default is ...." << "\n";
-		cout << "The hard parameter .... The default is ...." << "\n";
-		cout << "The vertical parameter .... The default is T." << "\n";
-		cout << "The filter.seqs command should be in the following format: " << "\n";
-		cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
-		cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T)." << "\n";
-		cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+				
+		m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
+		m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
+		m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
+		m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
+		m->mothurOut("The trump parameter .... The default is ...\n");
+		m->mothurOut("The soft parameter .... The default is ....\n");
+		m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
+		m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
+		m->mothurOut("The filter.seqs command should be in the following format: \n");
+		m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
+		m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "FilterSeqsCommand", "help");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FilterSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doHard() {
-	
-	ifstream fileHandle;
-	openInputFile(hard, fileHandle);
+int FilterSeqsCommand::execute() {	
+	try {
 	
-	fileHandle >> filter;
+		if (abort == true) { return 0; }
+		
+		ifstream inFASTA;
+		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) { 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;
+		
+		string filterFile = outputDir + filterFileName + ".filter";
+		openOutputFile(filterFile, outFilter);
+		outFilter << filter << endl;
+		outFilter.close();
+		outputNames.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) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  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();
+		
+		
+		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();
+				
+				string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta";
+#ifdef USE_MPI	
+				int pid, start, end, numSeqsPerProcessor, num; 
+				int tag = 2001;
+				vector<unsigned long int>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 tempMPI;
+				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);
 
-void FilterSeqsCommand::doTrump(Sequence seq) {
-	
-	string curAligned = seq.getAligned();
+				if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 
-	for(int j = 0; j < alignmentLength; j++) {
-		if(curAligned[j] == trump){
-			filter[j] = '0';
+				if (pid == 0) { //you are the root process 
+					
+					MPIPos = 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[4];
+						MPI_Recv(buf, 4, 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[4];
+					strcpy(buf, "done"); 
+					
+					//tell parent you are done.
+					MPI_Send(buf, 4, 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
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if(processors == 1){
+					ifstream inFASTA;
+					int numFastaSeqs;
+					openInputFile(fastafileNames[s], inFASTA);
+					getNumSeqs(inFASTA, numFastaSeqs);
+					inFASTA.close();
+					
+					lines.push_back(new linePair(0, numFastaSeqs));
+					
+					numSeqs += numFastaSeqs;
+					
+					driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
+				}else{
+					setLines(fastafileNames[s]);
+					createProcessesRunFilter(filter, fastafileNames[s]); 
+				
+					rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
+				
+					//append fasta files
+					for(int i=1;i<processors;i++){
+						appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
+						remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
+					}
+				}
+				
+				if (m->control_pressed) {  return 1; }
+		#else
+				ifstream inFASTA;
+				int numFastaSeqs;
+				openInputFile(fastafileNames[s], inFASTA);
+				getNumSeqs(inFASTA, numFastaSeqs);
+				inFASTA.close();
+					
+				lines.push_back(new linePair(0, numFastaSeqs));
+				
+				numSeqs += numFastaSeqs;
+				
+				driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
+
+				if (m->control_pressed) {  return 1; }
+		#endif
+#endif
+			outputNames.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 int>& 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);  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;
+				}
 
-void FilterSeqsCommand::doVertical() {
-
-	for(int i=0;i<alignmentLength;i++){
-		if(gap[i] == numSeqs)	{	filter[i] = '0';	}
+			}
+			
+			if((i+1) % 100 == 0){	cout << (i+1) << endl;	 m->mothurOutJustToLog(toString(i+1) + "\n");	}
+		}
+		
+		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;	 m->mothurOutJustToLog(toString(num) + "\n");	}
+			
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
+		exit(1);
 	}
-	
 }
-
+#endif
 /**************************************************************************************/
-
-void FilterSeqsCommand::doSoft() {
-	
-	int threshold = int (soft * numSeqs);
-	
-	for(int i=0;i<alignmentLength;i++){
-		if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){	filter[i] = 0;	}
+int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {	
+	try {
+		ofstream out;
+		openOutputFile(outputFilename, out);
+		
+		ifstream in;
+		openInputFile(inputFilename, in);
+				
+		in.seekg(line->start);
+		
+		for(int i=0;i<line->num;i++){
+				
+				if (m->control_pressed) { in.close(); out.close(); return 0; }
+				
+				Sequence seq(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;
+				}
+				gobble(in);
+		}
+		out.close();
+		in.close();
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
+		exit(1);
 	}
 }
+/**************************************************************************************************/
 
+int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
+	try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		int process = 0;
+		int exitCommand = 1;
+		processIDS.clear();
+		
+		//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";
+				driverRunFilter(F, filteredFasta, filename, lines[process]);
+				exit(0);
+			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+		}
+		
+		//force parent to wait until all the processes are done
+		for (int i=0;i<processors;i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
+		
+		return exitCommand;
+#endif		
+	}
+	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 != '*' || isTrue(vertical) || soft != 0){
+			F.initialize();
+		}
+		
+		if(hard.compare("") != 0)	{	F.doHard(hard);		}
+		else						{	F.setFilter(string(alignmentLength, '1'));	}
+		
+		numSeqs = 0;
+		if(trump != '*' || 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 int> 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 = 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
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if(processors == 1){
+					ifstream inFASTA;
+					int numFastaSeqs;
+					openInputFile(fastafileNames[s], inFASTA);
+					getNumSeqs(inFASTA, numFastaSeqs);
+					inFASTA.close();
+					
+					numSeqs += numFastaSeqs;
+					
+					lines.push_back(new linePair(0, numFastaSeqs));
+					
+					driverCreateFilter(F, fastafileNames[s], lines[0]);
+				}else{
+					setLines(fastafileNames[s]);					
+					createProcessesCreateFilter(F, fastafileNames[s]); 
+				}
+				
+				if (m->control_pressed) {  return filterString; }
+		#else
+				ifstream inFASTA;
+				int numFastaSeqs;
+				openInputFile(fastafileNames[s], inFASTA);
+				getNumSeqs(inFASTA, numFastaSeqs);
+				inFASTA.close();
+				
+				numSeqs += numFastaSeqs;
+				
+				lines.push_back(new linePair(0, numFastaSeqs));
+				
+				driverCreateFilter(F, fastafileNames[s], lines[0]);
+				if (m->control_pressed) {  return filterString; }
+		#endif
+#endif
+			
+			}
+		}
 
-void FilterSeqsCommand::getFreqs(Sequence seq) {
 
-	string curAligned = seq.getAligned();;
-	
-	for(int j=0;j<alignmentLength;j++){
-		if(toupper(curAligned[j]) == 'A')										{	a[j]++;		}
-		else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U')	{	t[j]++;		}
-		else if(toupper(curAligned[j]) == 'G')									{	g[j]++;		}
-		else if(toupper(curAligned[j]) == 'C')									{	c[j]++;		}
-		else if(curAligned[j] == '-' || curAligned[j] == '.')					{	gap[j]++;	}
+#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 != '*' || 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(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::execute() {	
+int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {	
 	try {
-	
-		if (abort == true) { return 0; }
 		
-		ifstream inFASTA;
-		openInputFile(fastafile, inFASTA);
+		ifstream in;
+		openInputFile(filename, in);
+				
+		in.seekg(line->start);
 		
-		Sequence testSeq(inFASTA);
-		alignmentLength = testSeq.getAlignLength();
-		inFASTA.seekg(0);
-		
-		if(soft != 0 || isTrue(vertical)){
-			a.assign(alignmentLength, 0);
-			t.assign(alignmentLength, 0);
-			g.assign(alignmentLength, 0);
-			c.assign(alignmentLength, 0);
-			gap.assign(alignmentLength, 0);
+		for(int i=0;i<line->num;i++){
+				
+			if (m->control_pressed) { in.close(); return 1; }
+					
+			Sequence seq(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(isTrue(vertical) || soft != 0){	F.getFreqs(seq);	}
+					cout.flush();
+			}
+			
+			//report progress
+			if((i+1) % 100 == 0){	m->mothurOut(toString(i+1)); m->mothurOutEndLine();		}
 		}
 		
-		if(hard.compare("") != 0)	{	doHard();		}
-		else						{	filter = string(alignmentLength, '1');	}
-
-		if(trump != '*' || isTrue(vertical) || soft != 0){
-			while(!inFASTA.eof()){	//read through and create the filter...
-				Sequence seq(inFASTA);
-				if(trump != '*'){	doTrump(seq);	}
-				if(isTrue(vertical) || soft != 0){	getFreqs(seq);	}
-				numSeqs++;
-				cout.flush();
-			}
+		//report progress
+		if((line->num) % 100 != 0){	m->mothurOut(toString(line->num)); m->mothurOutEndLine();		}
+		
+		in.close();
 		
+		return 0;
+	}
+	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 int>& 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(isTrue(vertical) || soft != 0){	F.getFreqs(seq);	}
+			cout.flush();
+						
+			//report progress
+			if((i+1) % 100 == 0){	cout << (i+1) << endl;	 m->mothurOutJustToLog(toString(i+1) + "\n");	}
 		}
-		inFASTA.close();
 		
-		if(isTrue(vertical) == 1)	{	doVertical();	}
-		if(soft != 0)	{	doSoft();		}			
+		//report progress
+		if((num) % 100 != 0){	cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); 	}
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
+		exit(1);
+	}
+}
+#endif
+/**************************************************************************************************/
 
-		ofstream outFilter;
-		string filterFile = getRootName(fastafile) + "filter";
-		openOutputFile(filterFile, outFilter);
-		outFilter << filter << endl;
-		outFilter.close();
+int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
+	try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		int process = 0;
+		int exitCommand = 1;
+		processIDS.clear();
+		
+		//loop through and create all the processes you want
+		while (process != processors) {
+			int pid = vfork();
+			
+			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){
+				driverCreateFilter(F, filename, lines[process]);
+				exit(0);
+			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+		}
 		
+		//force parent to wait until all the processes are done
+		for (int i=0;i<processors;i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
+		
+		return exitCommand;
+#endif		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
 
-		openInputFile(fastafile, inFASTA);
-		string filteredFasta = getRootName(fastafile) + "filter.fasta";
-		ofstream outFASTA;
-		openOutputFile(filteredFasta, outFASTA);
+int FilterSeqsCommand::setLines(string filename) {
+	try {
+		
+		vector<unsigned long int> positions;
+		bufferSizes.clear();
+		
+		ifstream inFASTA;
+		openInputFile(filename, inFASTA);
+			
+		string input;
+		while(!inFASTA.eof()){	
+			input = getline(inFASTA);
 
-		numSeqs = 0;
-		while(!inFASTA.eof()){
-			Sequence seq(inFASTA);
-			string align = seq.getAligned();
-			string filterSeq = "";
-	
-			for(int j=0;j<alignmentLength;j++){
-				if(filter[j] == '1'){
-					filterSeq += align[j];
-				}
+			if (input.length() != 0) {
+				if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
 			}
-
-			outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
-			numSeqs++;
-			gobble(inFASTA);
 		}
-		outFASTA.close();
 		inFASTA.close();
 		
+		int numFastaSeqs = positions.size();
+	
+		FILE * pFile;
+		unsigned long int size;
 		
-		int filteredLength = 0;
-		for(int i=0;i<alignmentLength;i++){
-			if(filter[i] == '1'){	filteredLength++;	}
+		//get num bytes in file
+		pFile = fopen (filename.c_str(),"rb");
+		if (pFile==NULL) perror ("Error opening file");
+		else{
+			fseek (pFile, 0, SEEK_END);
+			size=ftell (pFile);
+			fclose (pFile);
 		}
+	
+		numSeqs += numFastaSeqs;
 		
-		cout << endl;
-		cout << "Length of filtered alignment: " << filteredLength << endl;
-		cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
-		cout << "Length of the original alignment: " << alignmentLength << endl;
-		cout << "Number of sequences used to construct filter: " << numSeqs << endl;
+		int numSeqsPerProcessor = numFastaSeqs / processors;
 		
-		return 0;
+		for (int i = 0; i < processors; i++) {
+
+			unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
+			if(i == processors - 1){
+				numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+				bufferSizes.push_back(size - startPos);
+			}else{  
+				unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+				bufferSizes.push_back(myEnd-startPos);
+			}
+			lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+		}
 		
+		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "FilterSeqsCommand", "setLines");
 		exit(1);
 	}
 }
-
 /**************************************************************************************/