X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequenceparser.cpp;fp=sequenceparser.cpp;h=44012d8ba8321fea520fbe613e0dac8f8911c760;hb=ae57e166b2ed7b475ec3f466106bd76fabadd063;hp=0000000000000000000000000000000000000000;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
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index 0000000..44012d8
--- /dev/null
+++ b/sequenceparser.cpp
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+/*
+ *  sequenceParser.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 9/9/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "sequenceParser.h"
+
+
+/************************************************************/
+SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFile) {
+	try {
+		
+		m = MothurOut::getInstance();
+		int error;
+		
+		//read group file
+		groupMap = new GroupMap(groupFile);
+		error = groupMap->readMap();
+		
+		if (error == 1) { m->control_pressed = true; }
+		
+		//initialize maps
+		vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			vector<Sequence> temp;
+			map<string, string> tempMap;
+			seqs[namesOfGroups[i]] = temp;
+			nameMapPerGroup[namesOfGroups[i]] = tempMap;
+		}
+		
+		//read fasta file making sure each sequence is in the group file
+		ifstream in;
+		m->openInputFile(fastaFile, in);
+		
+		map<string, string> seqName; //stores name -> sequence string so we can make new "unique" sequences when we parse the name file
+		while (!in.eof()) {
+			
+			if (m->control_pressed) { break; }
+			
+			Sequence seq(in); m->gobble(in);
+			
+			if (seq.getName() != "") {
+				
+				 string group = groupMap->getGroup(seq.getName());
+				 if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
+				 else {	
+					 seqs[group].push_back(seq);	
+					 seqName[seq.getName()] = seq.getAligned();
+				 }
+			}
+		}
+		in.close();
+				 
+		if (error == 1) { m->control_pressed = true; }
+				 
+		//read name file
+		ifstream inName;
+		m->openInputFile(nameFile, inName);
+		
+		string first, second;
+		int countName = 0;
+		while(!inName.eof()) {
+			
+			if (m->control_pressed) { break; }
+			
+			inName >> first; m->gobble(inName);
+			inName >> second; m->gobble(inName);
+			
+			vector<string> names;
+			m->splitAtChar(second, names, ',');
+			
+			//get aligned string for these seqs from the fasta file
+			string alignedString = "";
+			map<string, string>::iterator itAligned = seqName.find(names[0]);
+			if (itAligned == seqName.end()) {
+				error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
+			}else {
+				alignedString = itAligned->second;
+			}
+			
+			//separate by group - parse one line in name file
+			map<string, string> splitMap; //group -> name1,name2,...
+			map<string, string>::iterator it;
+			for (int i = 0; i < names.size(); i++) {
+				
+				string group = groupMap->getGroup(names[i]);
+				if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
+				else {	
+					
+					it = splitMap.find(group);
+					if (it != splitMap.end()) { //adding seqs to this group
+						(it->second) += "," + names[i];
+						countName++;
+					}else { //first sighting of this group
+						splitMap[group] = names[i];
+						countName++;
+						
+						//is this seq in the fasta file?
+						if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
+							Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
+							seqs[group].push_back(tempSeq);
+						}
+					}
+				}
+			}
+			
+			
+			//fill nameMapPerGroup - holds all lines in namefile separated by group
+			for (it = splitMap.begin(); it != splitMap.end(); it++) {
+				//grab first name
+				string firstName = "";
+				for(int i = 0; i < (it->second).length(); i++) {
+					if (((it->second)[i]) != ',') {
+						firstName += ((it->second)[i]);
+					}else { break; }
+				}
+				
+				//group1 -> seq1 -> seq1,seq2,seq3
+				nameMapPerGroup[it->first][firstName] = it->second;
+			}
+		}
+		
+		inName.close();
+		
+		if (error == 1) { m->control_pressed = true; }
+		
+		if (countName != (groupMap->getNumSeqs())) {
+			m->mothurOutEndLine();
+			m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
+			m->mothurOutEndLine();
+			m->control_pressed = true;
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceParser", "SequenceParser");
+		exit(1);
+	}
+}
+/************************************************************/
+SequenceParser::SequenceParser(string groupFile, string fastaFile) {
+	try {
+		
+		m = MothurOut::getInstance();
+		int error;
+		
+		//read group file
+		groupMap = new GroupMap(groupFile);
+		error = groupMap->readMap();
+		
+		if (error == 1) { m->control_pressed = true; }
+		
+		//initialize maps
+		vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			vector<Sequence> temp;
+			seqs[namesOfGroups[i]] = temp;
+		}
+		
+		//read fasta file making sure each sequence is in the group file
+		ifstream in;
+		m->openInputFile(fastaFile, in);
+		int count = 0;
+		
+		while (!in.eof()) {
+			
+			if (m->control_pressed) { break; }
+			
+			Sequence seq(in); m->gobble(in);
+			
+			if (seq.getName() != "") {
+				
+				string group = groupMap->getGroup(seq.getName());
+				if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
+				else {	seqs[group].push_back(seq);	count++; }
+			}
+		}
+		in.close();
+		
+		if (error == 1) { m->control_pressed = true; }
+		
+		if (count != (groupMap->getNumSeqs())) {
+			m->mothurOutEndLine();
+			m->mothurOut("[ERROR]: Your fasta file contains " + toString(count) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
+			if (count < (groupMap->getNumSeqs())) { m->mothurOut(" Did you forget to include the name file?"); }
+			m->mothurOutEndLine();
+			m->control_pressed = true;
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceParser", "SequenceParser");
+		exit(1);
+	}
+}
+/************************************************************/
+SequenceParser::~SequenceParser(){ delete groupMap; }
+/************************************************************/
+int SequenceParser::getNumGroups(){ return groupMap->getNumGroups(); }
+/************************************************************/
+vector<string> SequenceParser::getNamesOfGroups(){ return groupMap->getNamesOfGroups(); }
+/************************************************************/
+bool SequenceParser::isValidGroup(string g){ return groupMap->isValidGroup(g); }
+/************************************************************/
+string SequenceParser::getGroup(string g){ return groupMap->getGroup(g); }
+/************************************************************/
+int SequenceParser::getNumSeqs(string g){ 
+	try {
+		map<string, vector<Sequence> >::iterator it;
+		int num = 0;
+		
+		it = seqs.find(g);
+		if(it == seqs.end()) {
+			m->mothurOut("[ERROR]: " + g + " is not a valid group, please correct."); m->mothurOutEndLine();
+		}else {
+			num = (it->second).size();
+		}
+		
+		return num; 
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceParser", "getNumSeqs");
+		exit(1);
+	}
+}
+/************************************************************/
+vector<Sequence> SequenceParser::getSeqs(string g){ 
+	try {
+		map<string, vector<Sequence> >::iterator it;
+		vector<Sequence> seqForThisGroup;
+		
+		it = seqs.find(g);
+		if(it == seqs.end()) {
+			m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
+		}else {
+			seqForThisGroup = it->second;
+		}
+		
+		return seqForThisGroup; 
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceParser", "getSeqs");
+		exit(1);
+	}
+}
+/************************************************************/
+map<string, string> SequenceParser::getNameMap(string g){ 
+	try {
+		map<string, map<string, string> >::iterator it;
+		map<string, string> nameMapForThisGroup;
+		
+		it = nameMapPerGroup.find(g);
+		if(it == nameMapPerGroup.end()) {
+			m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
+		}else {
+			nameMapForThisGroup = it->second;
+		}
+		
+		return nameMapForThisGroup; 
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceParser", "getNameMap");
+		exit(1);
+	}
+}
+/************************************************************/
+
+
+