+++ /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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