//**********************************************************************************************************************
vector<string> TrimFlowsCommand::setParameters(){
try {
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow",false,true,true); parameters.push_back(pflow);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow-file",false,true,true); parameters.push_back(pflow);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
if(allFiles){
set<string> namesAlreadyProcessed;
- variables["[tag]"] = "";
flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
for(int i=0;i<barcodePrimerComboFileNames.size();i++){
for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
if (namesAlreadyProcessed.count(barcodePrimerComboFileNames[i][j]) == 0) {
- FILE * pFile;
- unsigned long long size;
-
- //get num bytes in file
- pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
- if (pFile==NULL) perror ("Error opening file");
- else{
- fseek (pFile, 0, SEEK_END);
- size=ftell(pFile);
- fclose (pFile);
- }
-
- if(size < 10){
- m->mothurRemove(barcodePrimerComboFileNames[i][j]);
- }
- else{
- output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
- outputNames.push_back(barcodePrimerComboFileNames[i][j]);
- outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
- }
- namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
+ if (barcodePrimerComboFileNames[i][j] != "") {
+ FILE * pFile;
+ unsigned long long size;
+
+ //get num bytes in file
+ pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell(pFile);
+ fclose (pFile);
+ }
+
+ if(size < 10){
+ m->mothurRemove(barcodePrimerComboFileNames[i][j]);
+ }
+ else{
+ output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
+ outputNames.push_back(barcodePrimerComboFileNames[i][j]);
+ outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
+ }
+ namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
+ }
}
}
}
output.close();
}
else{
- variables["[tag]"] = "";
flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
}
outputTypes["file"].push_back(flowFilesFileName);
outputNames.push_back(flowFilesFileName);
-
-// 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); }
-// }
-
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
if(allFiles){
for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
- ofstream temp;
- m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
- temp << maxFlows << endl;
- temp.close();
+ if (thisBarcodePrimerComboFileNames[i][j] != "") {
+ ofstream temp;
+ m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
+ temp << maxFlows << endl;
+ temp.close();
+ }
}
}
}
}
if(trashCode.length() == 0){
-
- flowData.printFlows(trimFlowFile);
-
- if(fasta) { currSeq.printSequence(fastaFile); }
-
- if(allFiles){
- ofstream output;
- m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
- output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
-
- flowData.printFlows(output);
- output.close();
- }
+ string thisGroup = "";
+ if(barcodes.size() != 0){
+ thisGroup = barcodeNameVector[barcodeIndex];
+ if (primers.size() != 0) {
+ if (primerNameVector[primerIndex] != "") {
+ if(thisGroup != "") {
+ thisGroup += "." + primerNameVector[primerIndex];
+ }else {
+ thisGroup = primerNameVector[primerIndex];
+ }
+ }
+ }
+ }
+
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+ flowData.printFlows(trimFlowFile);
+
+ if(fasta) { currSeq.printSequence(fastaFile); }
+
+ if(allFiles){
+ ofstream output;
+ m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
+ output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
+
+ flowData.printFlows(output);
+ output.close();
+ }
+ }
}
else{
flowData.printFlows(scrapFlowFile, trashCode);
string primerName = primerNameVector[itPrimer->second];
string barcodeName = barcodeNameVector[itBar->second];
-
- string comboGroupName = "";
- string fileName = "";
-
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
- if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->second];
- variables["[tag]"] = comboGroupName;
- fileName = getOutputFileName("flow", variables);
- }
- else{
- if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->second];
- }
- else{
- comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
- }
- variables["[tag]"] = comboGroupName;
- fileName = getOutputFileName("flow", variables);
- }
-
- outFlowFileNames[itBar->second][itPrimer->second] = fileName;
-
- ofstream temp;
- m->openOutputFile(fileName, temp);
- temp.close();
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fileName = "";
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
+ }
+
+ outFlowFileNames[itBar->second][itPrimer->second] = fileName;
+
+ ofstream temp;
+ m->openOutputFile(fileName, temp);
+ temp.close();
+ }
}
}
}
if(allFiles){
for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
- tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
- ofstream temp;
- m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
- temp.close();
-
+ if (tempBarcodePrimerComboFileNames[i][j] != "") {
+ tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
+ ofstream temp;
+ m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
+ temp.close();
+ }
}
}
}
if(allFiles){
for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
- tempBarcodePrimerComboFileNames[i][j] += extension;
- ofstream temp;
- m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
- temp.close();
-
+ if (tempBarcodePrimerComboFileNames[i][j] != "") {
+ tempBarcodePrimerComboFileNames[i][j] += extension;
+ ofstream temp;
+ m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
+ temp.close();
+ }
}
}
}
if(allFiles){
for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
- tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
- ofstream temp;
- m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
- temp.close();
+ if (tempBarcodePrimerComboFileNames[i][j] != "") {
+ tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
+ ofstream temp;
+ m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
+ temp.close();
+ }
}
}
if(allFiles){
for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
- m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
- m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
+ if (barcodePrimerComboFileNames[j][k] != "") {
+ m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
+ m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
+ }
}
}
}
projects / mothur.git / blobdiff