if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else if (fastaFile == "not open") { abort = true; }
+ else { m->setFastaFile(fastaFile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligoFile = ""; }
else if(temp == "not open"){ abort = true; }
- else { oligoFile = temp; }
+ else { oligoFile = temp; m->setOligosFile(oligoFile); }
temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
temp = validParameter.validFile(parameters, "qfile", true);
if (temp == "not found") { qFileName = ""; }
else if(temp == "not open") { abort = true; }
- else { qFileName = temp; }
+ else { qFileName = temp; m->setQualFile(qFileName); }
temp = validParameter.validFile(parameters, "name", true);
if (temp == "not found") { nameFile = ""; }
else if(temp == "not open") { nameFile = ""; abort = true; }
- else { nameFile = temp; }
+ else { nameFile = temp; m->setNameFile(nameFile); }
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
convert(temp, qThreshold);
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
+ createGroup = false;
vector<vector<string> > fastaFileNames;
vector<vector<string> > qualFileNames;
vector<vector<string> > nameFileNames;
string outputGroupFileName;
if(oligoFile != ""){
- outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
- outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
- getOligos(fastaFileNames, qualFileNames, nameFileNames);
+ createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
+ if (createGroup) {
+ outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
+ outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
+ }
}
vector<unsigned long int> fastaFilePos;
if (fastaFileNames[i][j] != "") {
if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
if(m->isBlank(fastaFileNames[i][j])){
- remove(fastaFileNames[i][j].c_str());
+ m->mothurRemove(fastaFileNames[i][j]);
namesToRemove.insert(fastaFileNames[i][j]);
if(qFileName != ""){
- remove(qualFileNames[i][j].c_str());
+ m->mothurRemove(qualFileNames[i][j]);
namesToRemove.insert(qualFileNames[i][j]);
}
if(nameFile != ""){
- remove(nameFileNames[i][j].c_str());
+ m->mothurRemove(nameFileNames[i][j]);
namesToRemove.insert(nameFileNames[i][j]);
}
}else{
}
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output group counts
m->mothurOutEndLine();
}
if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//set fasta file as new current fastafile
string current = "";
ofstream outGroupsFile;
- if (oligoFile != ""){ m->openOutputFile(groupFileName, outGroupsFile); }
+ if (createGroup){ m->openOutputFile(groupFileName, outGroupsFile); }
if(allFiles){
for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
if (m->control_pressed) {
inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
- if (oligoFile != "") { outGroupsFile.close(); }
+ if (createGroup) { outGroupsFile.close(); }
if(qFileName != ""){
qFile.close();
}
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
int currentSeqsDiffs = 0;
Sequence currSeq(inFASTA); m->gobble(inFASTA);
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
QualityScores currQual;
if(qFileName != ""){
currQual = QualityScores(qFile); m->gobble(qFile);
}
-
+
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
else { success = 1; }
-
+
//you don't want to trim, if it fails above then scrap it
if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
}
- if(barcodes.size() != 0){
- string thisGroup = barcodeNameVector[barcodeIndex];
- if (primers.size() != 0) { if (primerNameVector[primerIndex] != "") { thisGroup += "." + primerNameVector[primerIndex]; } }
-
- outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
-
- if (nameFile != "") {
- map<string, string>::iterator itName = nameMap.find(currSeq.getName());
- if (itName != nameMap.end()) {
- vector<string> thisSeqsNames;
- m->splitAtChar(itName->second, thisSeqsNames, ',');
- for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
- outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
- }
- }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
- }
-
- map<string, int>::iterator it = groupCounts.find(thisGroup);
- if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
- else { groupCounts[it->first]++; }
+ if (createGroup) {
+ if(barcodes.size() != 0){
+ string thisGroup = barcodeNameVector[barcodeIndex];
+ if (primers.size() != 0) {
+ if (primerNameVector[primerIndex] != "") {
+ if(thisGroup != "") {
+ thisGroup += "." + primerNameVector[primerIndex];
+ }else {
+ thisGroup = primerNameVector[primerIndex];
+ }
+ }
+ }
+
+ outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+
+ if (nameFile != "") {
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ vector<string> thisSeqsNames;
+ m->splitAtChar(itName->second, thisSeqsNames, ',');
+ for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+ outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+ }
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+ map<string, int>::iterator it = groupCounts.find(thisGroup);
+ if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
+ else { groupCounts[it->first]++; }
+
+ }
}
-
if(allFiles){
ofstream output;
m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
unsigned long int pos = inFASTA.tellg();
if ((pos == -1) || (pos >= line->end)) { break; }
+
#else
if (inFASTA.eof()) { break; }
#endif
-
+
//report progress
if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
}
//report progress
if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
+
inFASTA.close();
trimFASTAFile.close();
scrapFASTAFile.close();
- if (oligoFile != "") { outGroupsFile.close(); }
+ if (createGroup) { outGroupsFile.close(); }
if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
qLines[process]);
//pass groupCounts to parent
- ofstream out;
- string tempFile = filename + toString(getpid()) + ".num.temp";
- m->openOutputFile(tempFile, out);
- for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
- out << it->first << '\t' << it->second << endl;
+ if(createGroup){
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << groupCounts.size() << endl;
+
+ for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ }
+ out.close();
}
- out.close();
-
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
m->appendFiles((trimFASTAFileName + toString(processIDS[i]) + ".temp"), trimFASTAFileName);
- remove((trimFASTAFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((trimFASTAFileName + toString(processIDS[i]) + ".temp"));
m->appendFiles((scrapFASTAFileName + toString(processIDS[i]) + ".temp"), scrapFASTAFileName);
- remove((scrapFASTAFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((scrapFASTAFileName + toString(processIDS[i]) + ".temp"));
if(qFileName != ""){
m->appendFiles((trimQualFileName + toString(processIDS[i]) + ".temp"), trimQualFileName);
- remove((trimQualFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((trimQualFileName + toString(processIDS[i]) + ".temp"));
m->appendFiles((scrapQualFileName + toString(processIDS[i]) + ".temp"), scrapQualFileName);
- remove((scrapQualFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((scrapQualFileName + toString(processIDS[i]) + ".temp"));
}
if(nameFile != ""){
m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
- remove((trimNameFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((trimNameFileName + toString(processIDS[i]) + ".temp"));
m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
- remove((scrapNameFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
}
- m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
- remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+ if(createGroup){
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
+ }
if(allFiles){
for(int k=0;k<fastaFileNames[j].size();k++){
if (fastaFileNames[j][k] != "") {
m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
- remove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
if(qFileName != ""){
m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
- remove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
}
if(nameFile != ""){
m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
- remove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"));
}
}
}
}
}
- ifstream in;
- string tempFile = filename + toString(processIDS[i]) + ".num.temp";
- m->openInputFile(tempFile, in);
- int tempNum;
- string group;
- while (!in.eof()) {
- in >> group >> tempNum; m->gobble(in);
+ if(createGroup){
+ ifstream in;
+ string tempFile = filename + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ int tempNum;
+ string group;
+
+ in >> tempNum; m->gobble(in);
+
+ if (tempNum != 0) {
+ while (!in.eof()) {
+ in >> group >> tempNum; m->gobble(in);
- map<string, int>::iterator it = groupCounts.find(group);
- if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
- else { groupCounts[it->first] += tempNum; }
+ map<string, int>::iterator it = groupCounts.find(group);
+ if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
+ else { groupCounts[it->first] += tempNum; }
+ }
+ }
+ in.close(); m->mothurRemove(tempFile);
}
- in.close(); remove(tempFile.c_str());
}
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
+bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
try {
ifstream inOligos;
m->openInputFile(oligoFile, inOligos);
}
numFPrimers = primers.size();
numRPrimers = revPrimer.size();
-
+
+ bool allBlank = true;
+ for (int i = 0; i < barcodeNameVector.size(); i++) {
+ if (barcodeNameVector[i] != "") {
+ allBlank = false;
+ break;
+ }
+ }
+ for (int i = 0; i < primerNameVector.size(); i++) {
+ if (primerNameVector[i] != "") {
+ allBlank = false;
+ break;
+ }
+ }
+
+ if (allBlank) {
+ m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
+ allFiles = false;
+ return false;
+ }
+
+ return true;
+
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "getOligos");
if (alignment != NULL) { delete alignment; }
}
-
+
return success;
}
projects / mothur.git / blobdiff