X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=68450fb15a7b140803aab2d54d8c5bc84e7ce688;hb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;hp=aff959ab9359ef0d199ac785d8c43a942ea59255;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index aff959a..68450fb 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -3,158 +3,190 @@
  *  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;
+		
+		//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::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 {
+		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);
+	}
 }
-void FilterSeqsCommand::doFilter() {}
+
 /**************************************************************************************/
+
 int FilterSeqsCommand::execute() {	
 	try {
-		globaldata = GlobalData::getInstance();
-		filename = globaldata->inputFileName;
+	
+		if (abort == true) { return 0; }
 		
-		if(globaldata->getFastaFile().compare("") != 0) {
-			readFasta = new ReadFasta(filename);
-			readFasta->read();
-			db = readFasta->getDB();
-		}
+		ifstream inFASTA;
+		openInputFile(fastafile, inFASTA);
 		
-		else if(globaldata->getNexusFile().compare("") != 0) {
-			readNexus = new ReadNexus(filename);
-			readNexus->read();
-			db = readNexus->getDB();
-		}
+		Sequence testSeq(inFASTA);
+		alignmentLength = testSeq.getAlignLength();
+		inFASTA.seekg(0);
+		
+		F.setLength(alignmentLength);
 		
-		else if(globaldata->getClustalFile().compare("") != 0) {
-			readClustal = new ReadClustal(filename);
-			readClustal->read();
-			db = readClustal->getDB();
+		if(soft != 0 || isTrue(vertical)){
+			F.initialize();
 		}
+		
+		if(hard.compare("") != 0)	{	F.doHard(hard);		}
+		else						{	F.setFilter(string(alignmentLength, '1'));	}
 
-		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) {
+		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);
 		
-		// Soft
-		if(globaldata->getSoft().compare("") != 0) {}
+		
+		if(isTrue(vertical) == 1)	{	F.doVertical();	}
+		if(soft != 0)				{	F.doSoft();		}
+		
+		filter = F.getFilter();
 
+		ofstream outFilter;
+		string filterFile = getRootName(fastafile) + "filter";
+		openOutputFile(filterFile, outFilter);
+		outFilter << filter << endl;
+		outFilter.close();
 		
-			
+		ifstream inFasta2;
+		openInputFile(fastafile, inFasta2);
+		string filteredFasta = getRootName(fastafile) + "filter.fasta";
+		ofstream outFASTA;
+		openOutputFile(filteredFasta, outFASTA);
+
+		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'){
+					filterSeq += align[j];
+				}
+			}
+
+			outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+			numSeqs++;
+			gobble(inFasta2);
+		}
+		outFASTA.close();
+		inFasta2.close();
 		
-		// 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++;
-//			}
-//		}
 		
+		int filteredLength = 0;
+		for(int i=0;i<alignmentLength;i++){
+			if(filter[i] == '1'){	filteredLength++;	}
+		}
 		
+		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 DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		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";
+		errorOut(e, "FilterSeqsCommand", "execute");
 		exit(1);
 	}
 }
+
 /**************************************************************************************/