X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=fa1e93e7c475b9a58cec44ab42af2464a2632c3f;hb=30f2d98fffb579b870c8969ddcc1dfc61ccbb70a;hp=1363216ffe56267adf628c42fe9ede4065c8f626;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 1363216..fa1e93e 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -8,56 +8,113 @@
  */
 
 #include "filterseqscommand.h"
+#include "sequence.hpp"
 
 /**************************************************************************************/
 
-FilterSeqsCommand::FilterSeqsCommand(string option){
+FilterSeqsCommand::FilterSeqsCommand(string option)  {
 	try {
-		globaldata = GlobalData::getInstance();
 		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)));
 			
-			parser = new OptionParser();
-			parser->parse(option, parameters);  delete parser;
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			map<string,string>::iterator it;
 			
-			ValidParameters* validParameter = new ValidParameters();
-		
 			//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 (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 { 
-				globaldata->setFastaFile(fastafile);
+				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 = "."; }
+			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; }
+			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 = ""; }
+			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 = "F"; }
-	
-			delete validParameter;
+			vertical = validParameter.validFile(parameters, "vertical", false);		if (vertical == "not found") { vertical = "T"; }
 			
 			numSeqs = 0;
 			
@@ -65,207 +122,477 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
 		
 	}
 	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 F." << "\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 .... 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) {
-		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; }
+		vector<string> outputNames;
+		
+		ifstream inFASTA;
+		openInputFile(fastafileNames[0], inFASTA);
+		
+		Sequence testSeq(inFASTA);
+		alignmentLength = testSeq.getAlignLength();
+		inFASTA.close();
+		
+		////////////create filter/////////////////
+		
+		filter = createFilter();
+		
+		ofstream outFilter;
+		
+		string filterFile = outputDir + filterFileName + ".filter";
+		openOutputFile(filterFile, outFilter);
+		outFilter << filter << endl;
+		outFilter.close();
+		outputNames.push_back(filterFile);
+		
+		
+		////////////run filter/////////////////
+		
+		numSeqs = 0;
+		for (int i = 0; i < fastafileNames.size(); i++) {
+			ifstream in;
+			openInputFile(fastafileNames[i], in);
+			string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[i])) + "filter.fasta";
+			ofstream outFASTA;
+			openOutputFile(filteredFasta, outFASTA);
+			outputNames.push_back(filteredFasta);
+			
+			
+			while(!in.eof()){
+				if (m->control_pressed) { in.close(); outFASTA.close(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  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];
+						}
+					}
+					
+					outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+					numSeqs++;
+				}
+				gobble(in);
+			}
+			outFASTA.close();
+			in.close();
+		}
+		
+		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);
+	}
 }
-
 /**************************************************************************************/
-
-void FilterSeqsCommand::doTrump(Sequence seq) {
-	
-	string curAligned = seq.getAligned();
-	
-	for(int j = 0; j < alignmentLength; j++) {
-		if(curAligned[j] == trump){
-			filter[j] = '0';
+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++) {
+			
+				for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+			
+#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 = new char(fastafileNames[s].length());
+				tempFileName = &(fastafileNames[s][0]);
+				
+				MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &in);  //comm, filename, mode, info, filepointer
+				
+				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(&lines[j]->numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how many sequences we are sending
+								MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
+							}
+						}
+				
+						char buf[bufferSizes[0]];
+						MPI_File_read_at(in, 0, buf, bufferSizes[0], MPI_CHAR, &status);
+			
+						MPICreateFilter(F, buf);
+												
+						vector<int> temp; temp.resize(alignmentLength+1);
+						
+						//get the frequencies from the child processes
+						for(int i = 0; i < ((processors-1)*5); i++) { 
+				cout << "i = " << i << endl;
+				//vector<int> trial; trial.resize(10);
+				//cout << "trials size = " << trial.size() << endl;
+				//int ierr = MPI_Recv(&trial[0], 10, MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
+							int ierr = MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status); 
+					cout << "recieved something" << endl;		
+			//for (int g = 0; g < trial.size(); g++) {  cout << trial[g] << '\t';  } cout << endl;
+							int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
+					cout << "reciveve tag = " << receiveTag << endl;
+					for (int k = 0; k < alignmentLength; k++) {		cout << k << '\t' << temp[k] << endl;	}
+					cout << "done " << endl << endl;
+							
+							int sender = status.MPI_SOURCE; 
+							
+							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];	}
+							}
+							
+							m->mothurOut("receive tag = " + toString(receiveTag) + " " + toString(sender) + " is complete."); m->mothurOutEndLine();
+						} 
 
-}
+						
+				}else { //i am the child process
+					int startPos, numLines, bufferSize;
+					ierr = MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+					ierr = MPI_Recv(&numLines, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+					ierr = MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+									
+					//send freqs
+					char buf2[bufferSize];
+					MPI_File_read_at( in, startPos, buf2, bufferSize, MPI_CHAR, &status);
+						
+					MPICreateFilter(F, buf2);
+					
+					//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);
+				
+#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;
+					
+					lines.push_back(new linePair(0, numFastaSeqs));
+					
+					driverCreateFilter(F, fastafileNames[s], lines[0]);
+				}else{
+					
+					setLines(fastafileNames[s]);					
+					createProcessesCreateFilter(F, fastafileNames[s]); 
+				}
+		#else
+				ifstream inFASTA;
+				openInputFile(fastafileNames[s], inFASTA);
+				int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				inFASTA.close();
+				
+				numSeqs += numFastaSeqs;
+				
+				lines.push_back(new linePair(0, numFastaSeqs));
+				
+				driverCreateFilter(F, lines[0], fastafileNames[s]);
+		#endif
+#endif
+			
+			}
+		}
 
-/**************************************************************************************/
 
-void FilterSeqsCommand::doVertical() {
+	cout << "made it here, numSeqs = " << numSeqs << endl;	
+		F.setNumSeqs(numSeqs);
+				
+		if(isTrue(vertical) == 1)	{	F.doVertical();	}
+		if(soft != 0)				{	F.doSoft();		}
+//cout << "Filter String = " << F.getFilter() << endl;			
+		filterString = F.getFilter();
 
-	for(int i=0;i<alignmentLength;i++){
-		if(gap[i] == numSeqs)	{	filter[i] = '0';	}
+		return filterString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "createFilter");
+		exit(1);
 	}
-	
 }
-
 /**************************************************************************************/
-
-void FilterSeqsCommand::doSoft() {
-	
-	int threshold = int (soft * numSeqs);
-	bool keep = 0;
-	
-	for(int i=0;i<alignmentLength;i++){
-		if(a[i] >= threshold)		{	keep = 1;	}
-		else if(t[i] >= threshold)	{	keep = 1;	}
-		else if(g[i] >= threshold)	{	keep = 1;	}
-		else if(c[i] >= threshold)	{	keep = 1;	}
+int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {	
+	try {
+		
+		ifstream in;
+		openInputFile(filename, in);
+				
+		in.seekg(line->start);
+		
+		for(int i=0;i<line->numSeqs;i++){
+				
+			if (m->control_pressed) { in.close(); return 1; }
+					
+			Sequence seq(in);
+			if (seq.getName() != "") {
+					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((line->numSeqs) % 100 != 0){	m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();		}
+		
+		in.close();
 		
-		if(keep == 0)	{	filter[i] = 0;		}
+		return 0;
 	}
-}
-
-/**************************************************************************************/
-
-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]++;	}
+	catch(exception& e) {
+		m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
+		exit(1);
 	}
-	
 }
-
 /**************************************************************************************/
-
-int FilterSeqsCommand::execute() {	
+int FilterSeqsCommand::MPICreateFilter(Filters& F, string input) {	
 	try {
-	
-		if (abort == true) { return 0; }
 		
-		ifstream inFASTA;
-		openInputFile(fastafile, inFASTA);
+		vector<string> seqStrings;
+		parseBuffer(input, seqStrings);
 		
-		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<seqStrings.size();i++){
+				
+			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();		}
 		}
 		
-		if(hard.compare("") != 0)	{	doHard();		}
-		else						{	filter = string(alignmentLength, '1');	}
+		//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);
+	}
+}
 
-		if(isTrue(vertical) || soft != 0){
-		
-			while(!inFASTA.eof()){
-				Sequence seq(inFASTA);
-				doTrump(seq);	
-				if(isTrue(vertical) || soft != 0){	getFreqs(seq);	}
-				numSeqs++;
-				cout.flush();
-			}
+/**************************************************************************************************/
+
+int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
+	try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		int process = 0;
+		int exitCommand = 1;
+		vector<int> processIDS;
 		
+		//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); }
 		}
-		inFASTA.close();
 		
-		if(isTrue(vertical) == 1)	{	doVertical();	}
-		if(soft != 0)	{	doSoft();		}			
-
-		ofstream outFilter;
-		string filterFile = getRootName(fastafile) + "filter";
-		openOutputFile(filterFile, outFilter);
-		outFilter << filter << endl;
-		outFilter.close();
+		//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);
-
-		numSeqs = 0;
-		while(!inFASTA.eof()){
-			Sequence seq(inFASTA);
-			string align = seq.getAligned();
-			string filterSeq = "";
+int FilterSeqsCommand::setLines(string filename) {
+	try {
+		vector<int> positions;
+		map<int, int> buf;
+		bufferSizes.clear();
+		
+		int pid;
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 	
-			for(int j=0;j<alignmentLength;j++){
-				if(filter[j] == '1'){
-					filterSeq += align[j];
-				}
-			}
+		ifstream inFASTA;
+		openInputFile(filename, inFASTA);
+			
+		string input;
+		int numbuf = 0;
+		while(!inFASTA.eof()){	
+			input = getline(inFASTA);
 
-			outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
-			numSeqs++;
-			gobble(inFASTA);
+			if (input.length() != 0) {
+				numbuf += input.length();
+				if(input[0] == '>'){	long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	buf[(pos - input.length() - 1)] = numbuf; }
+			}
 		}
-		outFASTA.close();
+
 		inFASTA.close();
 		
+		int numFastaSeqs = positions.size();
 		
-		int filteredLength = 0;
-		for(int i=0;i<alignmentLength;i++){
-			if(filter[i] == '1'){	filteredLength++;	}
-		}
+		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(numbuf-buf[startPos]);
+			}else{  
+				int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+				bufferSizes.push_back(buf[myEnd]-buf[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) {
+			
+			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);
 	}
 }
-
 /**************************************************************************************/