//**********************************************************************************************************************
int ListSeqsCommand::readFasta(){
try {
ifstream in;
util.openInputFile(fastafile, in);
string name;
int count = 1;
while(!in.eof()){
if (m->getControl_pressed()) { in.close(); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
if (name != "") { names.push_back(name); }
util.gobble(in);
if (m->getDebug()) { count++; m->mothurOut("[DEBUG]: count = " + toString(count) + ", name = " + currSeq.getName() + "\n"); }
}
in.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ListSeqsCommand", "readFasta");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::readFasta(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
variables["[extension]"] = m->getExtension(fastafile);
string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(fastafile, in);
string name;
bool wroteSomething = false;
int removedCount = 0;
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
if (name != "") {
//if this name is in the accnos file
if (names.count(name) == 0) {
wroteSomething = true;
currSeq.printSequence(out);
}else {
//if you are not in the accnos file check if you are a name that needs to be changed
map<string, string>::iterator it = uniqueToRedundant.find(name);
if (it != uniqueToRedundant.end()) {
wroteSomething = true;
currSeq.setName(it->second);
currSeq.printSequence(out);
}else { removedCount++; }
}
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readFasta");
exit(1);
}
}
void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data
ifstream oldNameFile;
util.openInputFile(oldNameFileName, oldNameFile);
map<string,string> oldNameMap;
map<string, string>::iterator itName;
string name, list;
while(!oldNameFile.eof()){
if (m->getControl_pressed()) { break; }
oldNameFile >> name; util.gobble(oldNameFile);
oldNameFile >> list;
oldNameMap[name] = list;
util.gobble(oldNameFile);
}
oldNameFile.close();
ifstream inFASTA;
util.openInputFile(inFastaFile, inFASTA);
string sequence;
while(!inFASTA.eof()){
if (m->getControl_pressed()) { break; }
Sequence currSeq(inFASTA);
name = currSeq.getName();
if (name != "") {
sequence = currSeq.getAligned();
itName = seqmap.find(name);
if (itName == seqmap.end()) { seqmap[name] = sequence; }
else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
seqmap[name] = sequence;
map<string,group>::iterator it = data.find(sequence);
if (it == data.end()) { //it's unique.
data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
// data[sequence].groupnumber = 1;
data[sequence].names = oldNameMap[name];
}else { // its a duplicate.
data[sequence].names += "," + oldNameMap[name];
// data[sequence].groupnumber++;
}
}
util.gobble(inFASTA);
}
inFASTA.close();
}
//**********************************************************************************************************************
int GetSeqsCommand::readFasta(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(fastafile, in);
string name;
bool wroteSomething = false;
int selectedCount = 0;
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
if (name != "") {
//if this name is in the accnos file
if (names.count(name) != 0) {
wroteSomething = true;
currSeq.printSequence(out);
selectedCount++;
}
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readFasta");
exit(1);
}
}
void FastaMap::readFastaFile(string inFileName) {
try {
ifstream in;
util.openInputFile(inFileName, in);
string name, sequence, line;
sequence = "";
string temp;
map<string, string>::iterator itName;
while(!in.eof()){
if (m->getControl_pressed()) { break; }
Sequence currSeq(in);
name = currSeq.getName();
if (name != "") {
sequence = currSeq.getAligned();
itName = seqmap.find(name);
if (itName == seqmap.end()) { seqmap[name] = sequence; }
else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
map<string,group>::iterator it = data.find(sequence);
if (it == data.end()) { //it's unique.
data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
// data[sequence].groupnumber = 1;
data[sequence].names = name;
}else { // its a duplicate.
data[sequence].names += "," + name;
// data[sequence].groupnumber++;
}
}
util.gobble(in);
}
in.close();
}
catch(exception& e) {
m->errorOut(e, "FastaMap", "readFastaFile");
exit(1);
}
}
//***************************************************************************************************************
void driverDegap(degapData* params){
try{
ifstream inFASTA;
params->util.openInputFile(params->filename, inFASTA);
inFASTA.seekg(params->start);
if (params->start == 0) { params->util.zapGremlins(inFASTA); params->util.gobble(inFASTA); }
while(!inFASTA.eof()){
if (params->m->getControl_pressed()) { break; }
Sequence currSeq(inFASTA); params->util.gobble(inFASTA);
if (currSeq.getName() != "") {
params->threadWriter->write(">"+currSeq.getName()+"\n"+currSeq.getUnaligned()+"\n");
params->count++;
}
//report progress
if((params->count) % 1000 == 0){ params->m->mothurOutJustToScreen(toString(params->count) + "\n"); }
#if defined NON_WINDOWS
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= params->end)) { break; }
#else
if (params->count == params->end) { break; }
#endif
}
//report progress
if((params->count) % 1000 != 0){ params->m->mothurOutJustToScreen(toString(params->count) + "\n"); }
inFASTA.close();
}
catch(exception& e) {
params->m->errorOut(e, "DegapSeqsCommand", "driver");
exit(1);
}
}
//**********************************************************************************************************************
int ListSeqsCommand::readFasta(){
try {
ifstream in;
m->openInputFile(fastafile, in);
string name;
//ofstream out;
//string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
//m->openOutputFile(newFastaName, out);
int count = 1;
//string lastName = "";
while(!in.eof()){
if (m->control_pressed) { in.close(); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
if (name != "") { names.push_back(name); }
m->gobble(in);
if (m->debug) { count++; cout << "[DEBUG]: count = " + toString(count) + ", name = " + currSeq.getName() + "\n"; }
}
in.close();
//out.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ListSeqsCommand", "readFasta");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readFasta(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
variables["[extension]"] = m->getExtension(fastafile);
string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(fastafile, in);
string name;
bool wroteSomething = false;
int selectedCount = 0;
if (m->debug) { set<string> temp; sanity["fasta"] = temp; }
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { currSeq.setName(it->second); }
}
name = currSeq.getName();
if (name != "") {
//if this name is in the accnos file
if (names.count(name) != 0) {
wroteSomething = true;
currSeq.printSequence(out);
selectedCount++;
if (m->debug) { sanity["fasta"].insert(name); }
}
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readFasta");
exit(1);
}
}
int ReverseSeqsCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
string fastaReverseFileName;
if(fastaFileName != ""){
ifstream inFASTA;
m->openInputFile(fastaFileName, inFASTA);
ofstream outFASTA;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
map<string, string> variables;
variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
variables["[extension]"] = m->getExtension(fastaFileName);
fastaReverseFileName = getOutputFileName("fasta", variables);
m->openOutputFile(fastaReverseFileName, outFASTA);
while(!inFASTA.eof()){
if (m->control_pressed) { inFASTA.close(); outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
Sequence currSeq(inFASTA); m->gobble(inFASTA);
if (currSeq.getName() != "") {
currSeq.reverseComplement();
currSeq.printSequence(outFASTA);
}
}
inFASTA.close();
outFASTA.close();
outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName);
}
string qualReverseFileName;
if(qualFileName != ""){
QualityScores currQual;
ifstream inQual;
m->openInputFile(qualFileName, inQual);
ofstream outQual;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
map<string, string> variables;
variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
variables["[extension]"] = m->getExtension(qualFileName);
string qualReverseFileName = getOutputFileName("qfile", variables);
m->openOutputFile(qualReverseFileName, outQual);
while(!inQual.eof()){
if (m->control_pressed) { inQual.close(); outQual.close(); m->mothurRemove(qualReverseFileName); return 0; }
currQual = QualityScores(inQual); m->gobble(inQual);
currQual.flipQScores();
currQual.printQScores(outQual);
}
inQual.close();
outQual.close();
outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName);
}
if (m->control_pressed) { m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; }
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for(int i=0;i<outputNames.size();i++){
m->mothurOut(outputNames[i]);
m->mothurOutEndLine();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "ReverseSeqsCommand", "execute");
exit(1);
}
}
