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//
// sequencecountparser.cpp
// Mothur
//
// Created by Sarah Westcott on 8/7/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "sequencecountparser.h"
/************************************************************/
SequenceCountParser::SequenceCountParser(string countfile, string fastafile) {
try {
m = MothurOut::getInstance();
//read count file
CountTable countTable;
countTable.readTable(countfile, true, false);
//initialize maps
namesOfGroups = countTable.getNamesOfGroups();
for (int i = 0; i < namesOfGroups.size(); i++) {
vector<Sequence> temp;
map<string, int> tempMap;
seqs[namesOfGroups[i]] = temp;
countTablePerGroup[namesOfGroups[i]] = tempMap;
}
//read fasta file making sure each sequence is in the group file
ifstream in;
m->openInputFile(fastafile, in);
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() != "") {
allSeqsMap[seq.getName()] = seq.getName();
vector<int> groupCounts = countTable.getGroupCounts(seq.getName());
for (int i = 0; i < namesOfGroups.size(); i++) {
if (groupCounts[i] != 0) {
seqs[namesOfGroups[i]].push_back(seq);
countTablePerGroup[namesOfGroups[i]][seq.getName()] = groupCounts[i];
}
}
}
}
in.close();
}
catch(exception& e) {
m->errorOut(e, "SequenceCountParser", "SequenceCountParser");
exit(1);
}
}
/************************************************************/
SequenceCountParser::SequenceCountParser(string fastafile, CountTable& countTable) {
try {
m = MothurOut::getInstance();
//initialize maps
if (countTable.hasGroupInfo()) {
namesOfGroups = countTable.getNamesOfGroups();
for (int i = 0; i < namesOfGroups.size(); i++) {
vector<Sequence> temp;
map<string, int> tempMap;
seqs[namesOfGroups[i]] = temp;
countTablePerGroup[namesOfGroups[i]] = tempMap;
}
//read fasta file making sure each sequence is in the group file
ifstream in;
m->openInputFile(fastafile, in);
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() != "") {
allSeqsMap[seq.getName()] = seq.getName();
vector<int> groupCounts = countTable.getGroupCounts(seq.getName());
for (int i = 0; i < namesOfGroups.size(); i++) {
if (groupCounts[i] != 0) {
seqs[namesOfGroups[i]].push_back(seq);
countTablePerGroup[namesOfGroups[i]][seq.getName()] = groupCounts[i];
}
}
}
}
in.close();
}else { m->control_pressed = true; m->mothurOut("[ERROR]: cannot parse fasta file by group with a count table that does not include group data, please correct.\n"); }
}
catch(exception& e) {
m->errorOut(e, "SequenceCountParser", "SequenceCountParser");
exit(1);
}
}
/************************************************************/
SequenceCountParser::~SequenceCountParser(){ }
/************************************************************/
int SequenceCountParser::getNumGroups(){ return namesOfGroups.size(); }
/************************************************************/
vector<string> SequenceCountParser::getNamesOfGroups(){ return namesOfGroups; }
/************************************************************/
int SequenceCountParser::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, "SequenceCountParser", "getNumSeqs");
exit(1);
}
}
/************************************************************/
vector<Sequence> SequenceCountParser::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, "SequenceCountParser", "getSeqs");
exit(1);
}
}
/************************************************************/
int SequenceCountParser::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, int> countForThisGroup = getCountTable(g);
map<string, int>::iterator itCount;
int error = 0;
for (int i = 0; i < seqForThisGroup.size(); i++) {
itCount = countForThisGroup.find(seqForThisGroup[i].getName());
if (itCount == countForThisGroup.end()){
error = 1;
m->mothurOut("[ERROR]: " + seqForThisGroup[i].getName() + " is in your fastafile, but is not in your count file, please correct."); m->mothurOutEndLine();
}else {
seqPriorityNode temp(itCount->second, 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, "SequenceCountParser", "getSeqs");
exit(1);
}
}
/************************************************************/
map<string, int> SequenceCountParser::getCountTable(string g){
try {
map<string, map<string, int> >::iterator it;
map<string, int> countForThisGroup;
it = countTablePerGroup.find(g);
if(it == countTablePerGroup.end()) {
m->mothurOut("[ERROR]: No countTable available for group " + g + ", please correct."); m->mothurOutEndLine();
}else {
countForThisGroup = it->second;
if (m->debug) { m->mothurOut("[DEBUG]: group " + g + " count file has " + toString(countForThisGroup.size()) + " unique sequences."); }
}
return countForThisGroup;
}
catch(exception& e) {
m->errorOut(e, "SequenceCountParser", "getCountTable");
exit(1);
}
}
/************************************************************/
int SequenceCountParser::getCountTable(string g, string filename){
try {
map<string, map<string, int> >::iterator it;
map<string, int> countForThisGroup;
it = countTablePerGroup.find(g);
if(it == countTablePerGroup.end()) {
m->mothurOut("[ERROR]: No countTable available for group " + g + ", please correct."); m->mothurOutEndLine();
}else {
countForThisGroup = it->second;
ofstream out;
m->openOutputFile(filename, out);
out << "Representative_Sequence\ttotal\t" << g << endl;
for (map<string, int>::iterator itFile = countForThisGroup.begin(); itFile != countForThisGroup.end(); itFile++) {
if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
out << itFile->first << '\t' << itFile->second << '\t' << itFile->second << endl;
}
out.close();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SequenceParser", "getCountTable");
exit(1);
}
}
/************************************************************/
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