X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=68450fb15a7b140803aab2d54d8c5bc84e7ce688;hb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;hp=8864bb3c57d32052220013ebf88267f865ccdbd1;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 8864bb3..68450fb 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -8,181 +8,183 @@
  */
 
 #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');
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doHard() {
-	
-//	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;
-//	}
-
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doTrump() {
-
-	
-	for(int i = 0; i < numSeqs; i++) {
-		string curAligned = db->get(i).getAligned();;
-
-		for(int j = 0; j < alignmentLength; j++) {
-			if(curAligned[j] == trump){
-				filter[j] = '0';
+FilterSeqsCommand::FilterSeqsCommand(string option){
+	try {
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"fasta", "trump", "soft", "hard", "vertical"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			
+			//check to make sure all parameters are valid for command
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
+			
+			//check for required parameters
+			fastafile = validParameter.validFile(parameters, "fasta", true);
+			if (fastafile == "not found") { mothurOut("fasta is a required parameter for the filter.seqs command."); mothurOutEndLine(); abort = true; }
+			else if (fastafile == "not open") { abort = true; }	
+
+			//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;  }
+			
+			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;
+			
+			if (abort == false) {
+			
+				if (soft != 0)			{  F.setSoft(soft);		}
+				if (trump != '*')		{  F.setTrump(trump);	}
+			
+			}
+						
 		}
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
+		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';		}
-//	}
 }
 
-/**************************************************************************************/
-
-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';			
-//		}
-//	}
+void FilterSeqsCommand::help(){
+	try {
+		mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
+		mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
+		mothurOut("The fasta parameter is required.\n");
+		mothurOut("The trump parameter .... The default is ...\n");
+		mothurOut("The soft parameter .... The default is ....\n");
+		mothurOut("The hard parameter .... The default is ....\n");
+		mothurOut("The vertical parameter .... The default is T.\n");
+		mothurOut("The filter.seqs command should be in the following format: \n");
+		mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
+		mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
+		mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "FilterSeqsCommand", "help");
+		exit(1);
+	}
 }
 
 /**************************************************************************************/
 
 int FilterSeqsCommand::execute() {	
 	try {
+	
+		if (abort == true) { return 0; }
 		
 		ifstream inFASTA;
-		openInputFile(globaldata->getFastaFile(), inFASTA);
+		openInputFile(fastafile, inFASTA);
 		
-		Sequence currSequence(inFASTA);
-		alignmentLength = currSequence.getAlignLength();
+		Sequence testSeq(inFASTA);
+		alignmentLength = testSeq.getAlignLength();
+		inFASTA.seekg(0);
 		
-		//while
+		F.setLength(alignmentLength);
 		
+		if(soft != 0 || isTrue(vertical)){
+			F.initialize();
+		}
 		
-		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();		}
+		if(hard.compare("") != 0)	{	F.doHard(hard);		}
+		else						{	F.setFilter(string(alignmentLength, '1'));	}
 
+		if(trump != '*' || isTrue(vertical) || soft != 0){
+			while(!inFASTA.eof()){	//read through and create the filter...
+				Sequence seq(inFASTA);
+				if(trump != '*'){	F.doTrump(seq);	}
+				if(isTrue(vertical) || soft != 0){	F.getFreqs(seq);	}
+				numSeqs++;
+				cout.flush();
+			}
 		
+		}
+		inFASTA.close();
+		F.setNumSeqs(numSeqs);
 		
 		
+		if(isTrue(vertical) == 1)	{	F.doVertical();	}
+		if(soft != 0)				{	F.doSoft();		}
 		
-		
-		
-		ofstream outfile;
-		string filterFile = getRootName(globaldata->inputFileName) + "filter";
-		openOutputFile(filterFile, outfile);
+		filter = F.getFilter();
 
-		outfile << filter << endl;
-		outfile.close();
+		ofstream outFilter;
+		string filterFile = getRootName(fastafile) + "filter";
+		openOutputFile(filterFile, outFilter);
+		outFilter << filter << endl;
+		outFilter.close();
 		
-		string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
-		openOutputFile(filteredFasta, outfile);
+		ifstream inFasta2;
+		openInputFile(fastafile, inFasta2);
+		string filteredFasta = getRootName(fastafile) + "filter.fasta";
+		ofstream outFASTA;
+		openOutputFile(filteredFasta, outFASTA);
 
-		for(int i=0;i<numSeqs;i++){
-			string curAligned = db->get(i).getAligned();
-			outfile << '>' << db->get(i).getName() << endl;
+		numSeqs = 0;
+		while(!inFasta2.eof()){
+			Sequence seq(inFasta2);
+			string align = seq.getAligned();
+			string filterSeq = "";
+	
 			for(int j=0;j<alignmentLength;j++){
 				if(filter[j] == '1'){
-					outfile << curAligned[j];
+					filterSeq += align[j];
 				}
 			}
-			outfile << endl;
+
+			outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+			numSeqs++;
+			gobble(inFasta2);
 		}
-		outfile.close();
+		outFASTA.close();
+		inFasta2.close();
+		
 		
 		int filteredLength = 0;
 		for(int i=0;i<alignmentLength;i++){
 			if(filter[i] == '1'){	filteredLength++;	}
 		}
 		
-		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;
-		
-		globaldata->clear();
+		mothurOutEndLine();
+		mothurOut("Length of filtered alignment: " + toString(filteredLength)); mothurOutEndLine();
+		mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); mothurOutEndLine();
+		mothurOut("Length of the original alignment: " + toString(alignmentLength)); mothurOutEndLine();
+		mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); mothurOutEndLine();
 		
 		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";
+		errorOut(e, "FilterSeqsCommand", "execute");
 		exit(1);
 	}
 }