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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
int fastaCount = 0;
while (!in.eof()) {
if (m->control_pressed) { break; }
Sequence seq(in); m->gobble(in);
fastaCount++;
if (m->debug) { if((fastaCount) % 1000 == 0){ m->mothurOut("[DEBUG]: reading seq " + toString(fastaCount) + "\n."); } }
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;
string rest = "";
char buffer[4096];
bool pairDone = false;
bool columnOne = true;
string firstCol, secondCol;
while (!inName.eof()) {
if (m->control_pressed) { break; }
inName.read(buffer, 4096);
vector<string> pieces = m->splitWhiteSpace(rest, buffer, inName.gcount());
for (int i = 0; i < pieces.size(); i++) {
if (columnOne) { firstCol = pieces[i]; columnOne=false; }
else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
if (pairDone) { //save one line
if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
vector<string> names;
m->splitAtChar(secondCol, 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;
}
pairDone = false;
}
}
}
inName.close();
//in case file does not end in white space
if (rest != "") {
vector<string> pieces = m->splitWhiteSpace(rest);
for (int i = 0; i < pieces.size(); i++) {
if (columnOne) { firstCol = pieces[i]; columnOne=false; }
else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
if (pairDone) { //save one line
if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
vector<string> names;
m->splitAtChar(secondCol, 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;
}
pairDone = false;
}
}
}
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); }
/************************************************************/
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;
if (m->debug) { m->mothurOut("[DEBUG]: group " + g + " fasta file has " + toString(seqForThisGroup.size()) + " sequences."); }
}
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;
if (m->debug) { m->mothurOut("[DEBUG]: group " + g + " name file has " + toString(nameMapForThisGroup.size()) + " unique sequences."); }
}
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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