X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=6d894d866a2930eb009d20627cb03f509b94ef2e;hb=cb9c5129766d46fa1a266f724c1ebd41047f3a03;hp=8864bb3c57d32052220013ebf88267f865ccdbd1;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 8864bb3..6d894d8 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -8,183 +8,826 @@
  */
 
 #include "filterseqscommand.h"
+#include "sequence.hpp"
 
 /**************************************************************************************/
 
-FilterSeqsCommand::FilterSeqsCommand(){
-	globaldata = GlobalData::getInstance();
-	
-	if(globaldata->getFastaFile() == "")		{	cout << "You must enter a fasta formatted file" << endl;	}
-	trump = globaldata->getTrump()[0];
-	vertical = 
-//	readSeqs->read();
-//	db = readSeqs->getDB();
-//	numSeqs = db->size();
-//	
-//	alignmentLength = db->get(0).getAlignLength();
-//
-//	filter = string(alignmentLength, '1');
+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", "outputdir","inputdir", "processors"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			map<string,string>::iterator it;
+			
+			//check to make sure all parameters are valid for command
+			for (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
+			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];		}
+					}
+
+					int ableToOpen;
+					ifstream in;
+					ableToOpen = openInputFile(fastafileNames[i], in);
+					if (ableToOpen == 1) { 
+						m->mothurOut(fastafileNames[i] + " 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;
+			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 = "1";				}
+			convert(temp, processors); 
+			
+			hard = validParameter.validFile(parameters, "hard", true);				if (hard == "not found") { hard = ""; }
+			else if (hard == "not open") { abort = true; }	
+			
+			vertical = validParameter.validFile(parameters, "vertical", false);		if (vertical == "not found") { vertical = "T"; }
+			
+			numSeqs = 0;
+			
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************
+
+void FilterSeqsCommand::help(){
+	try {
+				
+		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 .... The default is ....\n");
+		m->mothurOut("The vertical parameter .... 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, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
+		m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "help");
+		exit(1);
+	}
 }
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doHard() {
+int FilterSeqsCommand::execute() {	
+	try {
 	
-//	string hardName = globaldata->getHard();
-//	string hardFilter = "";
-//		
-//	ifstream fileHandle;
-//	openInputFile(hardName, fileHandle);
-//	
-//	fileHandle >> hardFilter;
-//	
-//	if(hardFilter.length() != filter.length()){
-//		cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
-//	}
-//	else{
-//		filter = hardFilter;
-//	}
+		if (abort == true) { return 0; }
+		
+		ifstream inFASTA;
+		openInputFile(fastafileNames[0], inFASTA);
+		
+		Sequence testSeq(inFASTA);
+		alignmentLength = testSeq.getAlignLength();
+		inFASTA.close();
+		
+		////////////create filter/////////////////
+		
+		filter = createFilter();
+		
+		if (m->control_pressed) { return 0; }
+		
+		ofstream outFilter;
+		
+		string filterFile = outputDir + filterFileName + ".filter";
+		openOutputFile(filterFile, outFilter);
+		outFilter << filter << endl;
+		outFilter.close();
+		outputNames.push_back(filterFile);
+		
+		
+		////////////run filter/////////////////
+		
+		filterSequences();
+						
+		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 {
+	
+		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; 
+				int tag = 2001;
+						
+				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[filteredFasta.length()];
+				strcpy(outFilename, filteredFasta.c_str());
+				
+				char inFileName[fastafileNames[s].length()];
+				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 (pid == 0) { //you are the root process 
+					
+					setLines(fastafileNames[s]);
+						
+					for (int j = 0; j < lines.size(); j++) { //each process
+						if (j != 0) { //don't send to yourself
+							MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
+							MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
+						}
+					}
+					
+					//read your peice of file
+					char buf[bufferSizes[0]];
+					MPI_File_read_at(inMPI, lines[0]->start, buf, bufferSizes[0], MPI_CHAR, &status);
+					istringstream iss (buf,istringstream::in);
+					
+					//do your part
+					driverMPIRun(iss, outMPI);
+					
+					//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
+					//receive your section of file
+					int startPos, numLines, bufferSize;
+					MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+					MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+									
+					//read your peice of file
+					char buf2[bufferSize];
+					MPI_File_read_at(inMPI, startPos, buf2, bufferSize, MPI_CHAR, &status);
+					istringstream iss (buf2,istringstream::in);
+					
+					//do your part
+					driverMPIRun(iss, outMPI);
+				
+					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);
+				
+#else
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if(processors == 1){
+					ifstream inFASTA;
+					openInputFile(fastafileNames[s], inFASTA);
+					int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					inFASTA.close();
+					
+					lines.push_back(new linePair(0, 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++){
+						appendAlignFiles((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;
+				openInputFile(fastafileNames[s], inFASTA);
+				int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				inFASTA.close();
+					
+				lines.push_back(new linePair(0, numFastaSeqs));
+				
+				driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 
-void FilterSeqsCommand::doTrump() {
+				if (m->control_pressed) {  return 1; }
+		#endif
+#endif
+			outputNames.push_back(filteredFasta);
+		}
 
-	
-	for(int i = 0; i < numSeqs; i++) {
-		string curAligned = db->get(i).getAligned();;
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "filterSequences");
+		exit(1);
+	}
+}
+/**************************************************************************************/
+int FilterSeqsCommand::driverMPIRun(istringstream& in, MPI_File& outMPI) {	
+	try {
+		string outputString = "";
+		int count = 0;
+		MPI_Status status; 
+		
+		while (!in.eof()) {
+			
+			Sequence seq(in); 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];
+					}
+				}
+				
+				count++;
+				outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
+				
+				if(count % 10 == 0){ //output to file 
+					//send results to parent
+					int length = outputString.length();
+					char buf[length];
+					strcpy(buf, outputString.c_str()); 
+				
+					MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+					outputString = "";
+				}
 
-		for(int j = 0; j < alignmentLength; j++) {
-			if(curAligned[j] == trump){
-				filter[j] = '0';
 			}
 		}
-	}
+		
+		if(outputString != ""){ //output to file 
+			//send results to parent
+			int length = outputString.length();
+			char buf[length];
+			strcpy(buf, outputString.c_str()); 
+			
+			MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+			outputString = "";
+		}
 
+			
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
+		exit(1);
+	}
 }
-
 /**************************************************************************************/
-
-void FilterSeqsCommand::doVertical() {
-
-//	vector<int> counts(alignmentLength, 0);
-//	
-//	for(int i = 0; i < numSeqs; i++) {
-//		string curAligned = db->get(i).getAligned();;
-//		
-//		for(int j = 0; j < alignmentLength; j++) {
-//			if(curAligned[j] == '-' || curAligned[j] == '.'){
-//				counts[j]++;
-//			}
-//		}
-//	}
-//	for(int i=0;i<alignmentLength;i++){
-//		if(counts[i] == numSeqs)	{	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->numSeqs;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(soft != 0 || isTrue(vertical)){
+			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++) {
+			
+#ifdef USE_MPI	
+				int pid, rc, ierr; 
+				int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
+				int tag = 2001;
+				
+				MPI_Status status; 
+				MPI_File in; 
+				rc = MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				rc = MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+							
+				char tempFileName[fastafileNames[s].length()];
+				strcpy(tempFileName, fastafileNames[s].c_str());
+		cout << pid  << " tempFileName " << tempFileName << endl;		
+				MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &in);  //comm, filename, mode, info, filepointer
+		cout << pid  << " here" << endl;			
+				if (pid == 0) { //you are the root process
+						setLines(fastafileNames[s]);
+				cout << pid  << " after setlines" << endl;			
+						for (int j = 0; j < lines.size(); j++) { //each process
+							if (j != 0) { //don't send to yourself
+								MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
+								MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
+							}
+						}
+				cout << pid << " done sending" << endl;
+						char buf[bufferSizes[0]];
+						MPI_File_read_at(in, 0, buf, bufferSizes[0], MPI_CHAR, &status);
+			cout << pid << " done reading" << endl;
+						string tempBuf = buf;
+						if (tempBuf.length() > bufferSizes[0]) { tempBuf = tempBuf.substr(0, bufferSizes[0]); }
 
-void FilterSeqsCommand::doSoft() {
-
-//	int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0;
-//
-//	vector<int> a(alignmentLength, 0);
-//	vector<int> t(alignmentLength, 0);
-//	vector<int> g(alignmentLength, 0);
-//	vector<int> c(alignmentLength, 0);
-//	vector<int> x(alignmentLength, 0);
-//	
-//	for(int i=0;i<numSeqs;i++){
-//		string curAligned = db->get(i).getAligned();;
-//
-//		for(int j=0;j<alignmentLength;j++){
-//			if(toupper(curAligned[j]) == 'A')										{	a[j]++;	}
-//			else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[i]) == 'U')	{	t[j]++;	}
-//			else if(toupper(curAligned[j]) == 'G')									{	g[j]++;	}
-//			else if(toupper(curAligned[j]) == 'C')									{	c[j]++;	}
-//		}
-//	}
-//
-//	for(int i=0;i<alignmentLength;i++){
-//		if(a[i] < softThreshold && t[i] < softThreshold && g[i] < softThreshold && c[i] < softThreshold){
-//			filter[i] = '0';			
-//		}
-//	}
-}
+						MPICreateFilter(F, tempBuf);
+				cout << pid << "done with mpi create filter " << endl;				
+						if (m->control_pressed) { MPI_File_close(&in); return filterString; }
+												
+						vector<int> temp; temp.resize(alignmentLength+1);
+						
+						//get the frequencies from the child processes
+						for(int i = 0; i < ((processors-1)*5); i++) { 
+							MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, tag, 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 { //i am the child process
+			cout << pid << endl;
+					int startPos, bufferSize;
+					ierr = MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+					ierr = MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+			cout << pid << '\t' << startPos << '\t' << bufferSize << endl;						
+					//send freqs
+					char buf2[bufferSize];
+					MPI_File_read_at( in, startPos, buf2, bufferSize, MPI_CHAR, &status);
+			
+					string tempBuf = buf2;
+					if (tempBuf.length() > bufferSize) { tempBuf = tempBuf.substr(0, bufferSize); }
+			
+					MPICreateFilter(F, tempBuf);
+				cout << pid << "done with mpi create filter " << endl;		
+					if (m->control_pressed) { MPI_File_close(&in); return filterString; }
+					
+					//send my fequency counts
+					F.a.push_back(Atag);
+					int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+					F.t.push_back(Ttag);
+					ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+					F.c.push_back(Ctag);
+					ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+					F.g.push_back(Gtag);
+					ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+					F.gap.push_back(Gaptag);
+					ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
+				}
+				
+				MPI_Barrier(MPI_COMM_WORLD);
+				MPI_File_close(&in);
+				
+#else
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if(processors == 1){
+					ifstream inFASTA;
+					openInputFile(fastafileNames[s], inFASTA);
+					int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+					inFASTA.close();
+					
+					numSeqs += numFastaSeqs;
+					
+					for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+					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;
+				openInputFile(fastafileNames[s], inFASTA);
+				int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				inFASTA.close();
+				
+				numSeqs += numFastaSeqs;
+				
+				for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+				lines.push_back(new linePair(0, numFastaSeqs));
+				
+				driverCreateFilter(F, fastafileNames[s], lines[0]);
+				if (m->control_pressed) {  return filterString; }
+		#endif
+#endif
+			
+			}
+		}
 
-int FilterSeqsCommand::execute() {	
+		F.setNumSeqs(numSeqs);
+				
+		if(isTrue(vertical) == 1)	{	F.doVertical();	}
+		if(soft != 0)				{	F.doSoft();		}
+			
+		filterString = F.getFilter();
+
+		return filterString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "createFilter");
+		exit(1);
+	}
+}
+/**************************************************************************************/
+int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {	
 	try {
 		
-		ifstream inFASTA;
-		openInputFile(globaldata->getFastaFile(), inFASTA);
+		ifstream in;
+		openInputFile(filename, in);
+				
+		in.seekg(line->start);
 		
-		Sequence currSequence(inFASTA);
-		alignmentLength = currSequence.getAlignLength();
+		for(int i=0;i<line->numSeqs;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();		}
+		}
 		
-		//while
+		//report progress
+		if((line->numSeqs) % 100 != 0){	m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();		}
 		
+		in.close();
 		
-		if(globaldata->getHard().compare("") != 0)	{	doHard();		}	//	has to be applied first!
-		if(globaldata->getTrump().compare("") != 0)	{	doTrump();		}
-		if(isTrue(globaldata->getVertical()))		{	doVertical();	}
-		if(globaldata->getSoft().compare("") != 0)	{	doSoft();		}
-
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
+		exit(1);
+	}
+}
+/**************************************************************************************/
+int FilterSeqsCommand::MPICreateFilter(Filters& F, string input) {	
+	try {
 		
+		vector<string> seqStrings;
+		parseBuffer(input, seqStrings);
 		
+		for(int i=0;i<seqStrings.size();i++){
+			
+			if (seqStrings[i].length() != alignmentLength) {  cout << i << '\t' << seqStrings[i].length() << "Sequences are not all the same length, please correct." << endl; m->control_pressed = true;  }
+
+			if (m->control_pressed) { return 1; }
+			
+			Sequence seq("", seqStrings[i]);
+			
+			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();		}
+		}
 		
+		//report progress
+		if((seqStrings.size()) % 100 != 0){	m->mothurOut(toString(seqStrings.size())); m->mothurOutEndLine();		}
 		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+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);
+		}
 		
-		ofstream outfile;
-		string filterFile = getRootName(globaldata->inputFileName) + "filter";
-		openOutputFile(filterFile, outfile);
+		return exitCommand;
+#endif		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
 
-		outfile << filter << endl;
-		outfile.close();
+int FilterSeqsCommand::setLines(string filename) {
+	try {
+		for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+		vector<long int> positions;
+		bufferSizes.clear();
 		
-		string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
-		openOutputFile(filteredFasta, outfile);
+		ifstream inFASTA;
+		openInputFile(filename, inFASTA);
+			
+		string input;
+		while(!inFASTA.eof()){	
+			input = getline(inFASTA);
 
-		for(int i=0;i<numSeqs;i++){
-			string curAligned = db->get(i).getAligned();
-			outfile << '>' << db->get(i).getName() << endl;
-			for(int j=0;j<alignmentLength;j++){
-				if(filter[j] == '1'){
-					outfile << curAligned[j];
-				}
+			if (input.length() != 0) {
+				if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
 			}
-			outfile << endl;
 		}
-		outfile.close();
+		inFASTA.close();
 		
-		int filteredLength = 0;
-		for(int i=0;i<alignmentLength;i++){
-			if(filter[i] == '1'){	filteredLength++;	}
+		int numFastaSeqs = positions.size();
+	
+		FILE * pFile;
+		long size;
+		
+		//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;
 		
-		globaldata->clear();
+		for (int i = 0; i < processors; i++) {
+
+			long int startPos = positions[ i * numSeqsPerProcessor ];
+			if(i == processors - 1){
+				numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+				bufferSizes.push_back(size - startPos);
+			}else{  
+				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";
+		m->errorOut(e, "FilterSeqsCommand", "setLines");
 		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";
+}
+/**************************************************************************************************/
+int FilterSeqsCommand::parseBuffer(string file, vector<string>& seqs) {
+	try {	
+		istringstream iss (file); //,istringstream::in
+		string name, seqstring;
+
+		while (!iss.eof()) {
+			
+			if (m->control_pressed) { return 0; }
+				
+			Sequence seq(iss); gobble(iss);
+			
+			if (seq.getName() != "") {
+				seqs.push_back(seq.getAligned());	
+			}
+		}
+		
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "parseBuffer");
 		exit(1);
 	}
 }
-
 /**************************************************************************************/