X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=0e33ab2047359b432886384cc41d60a806fbdc7c;hb=5d176c0f8049654ec3ae5a869c9ee3cecb991dc6;hp=aff959ab9359ef0d199ac785d8c43a942ea59255;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index aff959a..0e33ab2 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -3,157 +3,408 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 5/4/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "filterseqscommand.h"
-#include <iostream>
-#include <fstream>
+#include "sequence.hpp"
 
 /**************************************************************************************/
-void FilterSeqsCommand::doTrump() {
-	//trump = globaldata->getTrump();
-//	
-//	for(int i = 0; i < db->size(); i++) {
-//		Sequence cur = db->get(i);
-//		string curAligned = cur.getAligned();
-//		
-//		for(int j = 0; j < curAligned.length-1; j++) {
-//			string curChar = curAligned.substr(j, j+1);
-//			
-//			if(curChar.compare(trump) == 0) 
-//				columnsToRemove[j] = true;
-//		}
-//	}
+
+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::doSoft() {
-	//soft = atoi(globaldata->getSoft().c_str());
-//	vector<vector<int> > columnSymbolSums;
-//	vector<vector<string> > columnSymbols;
-//	for(int i = 0; i < db->get(0).getLength(); i++) {
-//		vector<string> symbols;
-//		vector<int> sums;
-//		columnSymbols[i] = symbols;
-//		columnSymbolSums[i] = sums;
-//	}
-//	
-//	for(int i = 0; i < db->size(); i++) {
-//		Sequence cur = db->get(i);
-//		string curAligned = cur.getAligned();
-//		
-//		for(int j = 0; j < curAligned.length-1; j++) {
-//			string curChar = curAligned.substr(j, j+1);
-//			vector<string> curColumnSymbols = columnSymbols[j];
-//			
-//			bool newSymbol = true;
-//			
-//			for(int k = 0; j < curColumnSymbols.size(); j++) 
-//				if(curChar.compare(curColumnSymbols[k]) == 0) {
-//					newSymbol = false;
-//					columnSymbolSums[j][k]++;
-//				}
-//			
-//			if(newSymbol) {
-//				columnSymbols.push_back(curChar);
-//				columnSymbolSums[j].push_back(1);
-//			}
-//		}
-//	}
-//	
-//	for(int i = 0; i < columnSymbolSums.size(); i++) {
-//		int totalSum = 0;
-//		int max = 0;
-//		vector<int> curColumn = columnSymbolSums[i];
-//		
-//		for(int j = 0; j < curColumn.size(); j++) {
-//			int curSum = curColumn[j];
-//			if(curSum > max)
-//				max = curSum;
-//			totalSum += curSum;
-//		}
-//		
-//		if((double)max/(double)totalSum * 100 < soft)
-//			columnsToRemove[i] = true;
-//	}
+//**********************************************************************************************************************
+
+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::doFilter() {}
+
 /**************************************************************************************/
+
 int FilterSeqsCommand::execute() {	
 	try {
-		globaldata = GlobalData::getInstance();
-		filename = globaldata->inputFileName;
+	
+		if (abort == true) { return 0; }
+		vector<string> outputNames;
 		
-		if(globaldata->getFastaFile().compare("") != 0) {
-			readFasta = new ReadFasta(filename);
-			readFasta->read();
-			db = readFasta->getDB();
-		}
+		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);
 		
-		else if(globaldata->getNexusFile().compare("") != 0) {
-			readNexus = new ReadNexus(filename);
-			readNexus->read();
-			db = readNexus->getDB();
+		
+		////////////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();
 		}
 		
-		else if(globaldata->getClustalFile().compare("") != 0) {
-			readClustal = new ReadClustal(filename);
-			readClustal->read();
-			db = readClustal->getDB();
+		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; }
 
-		else if(globaldata->getPhylipFile().compare("") != 0) {
-			readPhylip = new ReadPhylip(filename);
-			readPhylip->read();
-			db = readPhylip->getDB();
-		}
-	
-		for(int i = 0; i < db->get(0).getLength(); i++) 
-			columnsToRemove[i] = false;
-			
-		// Trump
-		if(globaldata->getTrump().compare("") != 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();
+		
 		
-		// Soft
-		if(globaldata->getSoft().compare("") != 0) {}
+		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);
+	}
+}
+/**************************************************************************************/
+string FilterSeqsCommand::createFilter() {	
+	try {
+		string filterString = "";
 		
-		// Filter
-		//if(globaldata->getFilter().compare("") != 0) {
-//
-//			filter = globaldata->getFilter();
-//			ifstream filehandle;
-//			openInputFile(filter, filehandle);
-//			
-//			char c;
-//			int count = 0;
-//			while(!filehandle.eof()) {
-//				c = filehandle.get();
-//				if(c == '0') 
-//					columnsToRemove[count] = true;
-//				count++;
-//			}
-//		}
+		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();
+				
+				#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{
+						vector<int> positions;
+				
+						ifstream inFASTA;
+						openInputFile(fastafileNames[s], inFASTA);
+				
+						string input;
+						while(!inFASTA.eof()){
+							input = getline(inFASTA);
+							if (input.length() != 0) {
+								if(input[0] == '>'){	long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
+							}
+						}
+						inFASTA.close();
+				
+						int numFastaSeqs = positions.size();
+						
+						numSeqs += numFastaSeqs;
+				
+						int numSeqsPerProcessor = numFastaSeqs / processors;
+				
+						for (int i = 0; i < processors; i++) {
+							long int startPos = positions[ i * numSeqsPerProcessor ];
+							if(i == processors - 1){
+								numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+							}
+							lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+						}
+				
+						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
 			
 			
+			}
+		}
+		
+		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 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();
+			}
+		}
+				
+		in.close();
+		
 		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************************/
+
+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); }
+		}
+		
+		//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);
 	}
 }