--- /dev/null
+/*
+ * 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;
+ set<string> thisnames1;
+
+ 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];
+ thisnames1.insert(names[i]);
+ countName++;
+ }else { //first sighting of this group
+ splitMap[group] = names[i];
+ countName++;
+ thisnames1.insert(names[i]);
+
+ //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);
+ }
+ }
+ }
+
+ allSeqsMap[names[i]] = names[0];
+ }
+
+
+ //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())) {
+ vector<string> groupseqsnames = groupMap->getNamesSeqs();
+
+ for (int i = 0; i < groupseqsnames.size(); i++) {
+ set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
+ if (itnamesfile == thisnames1.end()){
+ cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
+ }
+ }
+
+ 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);
+ }
+}
+/************************************************************/
+int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){
+ try {
+ map<string, vector<Sequence> >::iterator it;
+ vector<Sequence> seqForThisGroup;
+ vector<seqPriorityNode> nameVector;
+
+ it = seqs.find(g);
+ if(it == seqs.end()) {
+ m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
+ }else {
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ seqForThisGroup = it->second;
+
+ if (uchimeFormat) {
+ // format should look like
+ //>seqName /ab=numRedundantSeqs/
+ //sequence
+
+ map<string, string> nameMapForThisGroup = getNameMap(g);
+ map<string, string>::iterator itNameMap;
+ int error = 0;
+
+ for (int i = 0; i < seqForThisGroup.size(); i++) {
+ itNameMap = nameMapForThisGroup.find(seqForThisGroup[i].getName());
+
+ if (itNameMap == nameMapForThisGroup.end()){
+ error = 1;
+ m->mothurOut("[ERROR]: " + seqForThisGroup[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
+ }else {
+ int num = m->getNumNames(itNameMap->second);
+
+ seqPriorityNode temp(num, seqForThisGroup[i].getAligned(), seqForThisGroup[i].getName());
+ nameVector.push_back(temp);
+ }
+ }
+
+ if (error == 1) { out.close(); m->mothurRemove(filename); return 1; }
+
+ //sort by num represented
+ sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
+
+ //print new file in order of
+ for (int i = 0; i < nameVector.size(); i++) {
+
+ if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
+
+ out << ">" << nameVector[i].name << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl;
+ }
+
+ }else {
+ //m->mothurOut("Group " + g + " contains " + toString(seqForThisGroup.size()) + " unique seqs.\n");
+ for (int i = 0; i < seqForThisGroup.size(); i++) {
+
+ if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
+
+ seqForThisGroup[i].printSequence(out);
+ }
+ }
+ out.close();
+ }
+
+ return 0;
+ }
+ 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);
+ }
+}
+/************************************************************/
+int SequenceParser::getNameMap(string g, string filename){
+ 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;
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ for (map<string, string>::iterator itFile = nameMapForThisGroup.begin(); itFile != nameMapForThisGroup.end(); itFile++) {
+
+ if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
+
+ out << itFile->first << '\t' << itFile->second << endl;
+ }
+
+ out.close();
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SequenceParser", "getNameMap");
+ exit(1);
+ }
+}
+/************************************************************/
+
+
+
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