CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pmaxflows("maxflows", "Number", "", "720", "", "", "",false,false); parameters.push_back(pmaxflows);
- CommandParameter pminflows("minflows", "Number", "", "360", "", "", "",false,false); parameters.push_back(pminflows);
+ CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
+ CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
+ CommandParameter porder("order", "String", "", "TACG", "", "", "",false,false); parameters.push_back(porder);
CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
exit(1);
}
}
-
+//**********************************************************************************************************************
+string TrimFlowsCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "flow") { outputFileName = "flow"; }
+ else if (type == "fasta") { outputFileName = "flow.fasta"; }
+ else if (type == "file") { outputFileName = "flow.files"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimFlowsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
TrimFlowsCommand::TrimFlowsCommand(){
vector<string> tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
+ outputTypes["file"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
vector<string> tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
+ outputTypes["file"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
string temp;
temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
- convert(temp, minFlows);
+ m->mothurConvert(temp, minFlows);
temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
- convert(temp, maxFlows);
+ m->mothurConvert(temp, maxFlows);
temp = validParameter.validFile(parameters, "oligos", true);
else if(m->isTrue(temp)) { fasta = 1; }
temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found"){ temp = "9"; }
- convert(temp, maxHomoP);
+ m->mothurConvert(temp, maxHomoP);
temp = validParameter.validFile(parameters, "signal", false); if (temp == "not found"){ temp = "0.50"; }
- convert(temp, signal);
+ m->mothurConvert(temp, signal);
temp = validParameter.validFile(parameters, "noise", false); if (temp == "not found"){ temp = "0.70"; }
- convert(temp, noise);
+ m->mothurConvert(temp, noise);
temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, bdiffs);
+ m->mothurConvert(temp, bdiffs);
temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, pdiffs);
+ m->mothurConvert(temp, pdiffs);
- temp = validParameter.validFile(parameters, "tdiffs", false);
- if (temp == "not found"){ int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); }
- convert(temp, tdiffs);
- if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; }
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
+
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
flowOrder = validParameter.validFile(parameters, "order", false);
if (flowOrder == "not found"){ flowOrder = "TACG"; }
numFPrimers = 0;
numRPrimers = 0;
+ numLinkers = 0;
+ numSpacers = 0;
}
}
catch(exception& e) {
- m->errorOut(e, "TrimFlowsCommand", "TrimSeqsCommand");
+ m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
exit(1);
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
+ string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim." + getOutputFileNameTag("flow");
outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
- string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
+ string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap." + getOutputFileNameTag("flow");;
outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
- string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
+ string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
if(fasta){
outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
}
vector<unsigned long long> flowFilePos;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
flowFilePos = getFlowFileBreaks();
for (int i = 0; i < (flowFilePos.size()-1); i++) {
lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
ofstream output;
if(allFiles){
-
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+ set<string> namesAlreadyProcessed;
+ flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
m->openOutputFile(flowFilesFileName, output);
for(int i=0;i<barcodePrimerComboFileNames.size();i++){
for(int j=0;j<barcodePrimerComboFileNames[0].size();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 << barcodePrimerComboFileNames[i][j] << endl;
- outputNames.push_back(barcodePrimerComboFileNames[i][j]);
- outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][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]);
}
}
}
output.close();
}
else{
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+ flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
m->openOutputFile(flowFilesFileName, output);
- output << trimFlowFileName << endl;
+ output << m->getFullPathName(trimFlowFileName) << endl;
output.close();
}
- outputTypes["flow.files"].push_back(flowFilesFileName);
+ outputTypes["file"].push_back(flowFilesFileName);
outputNames.push_back(flowFilesFileName);
// set fasta file as new current fastafile
int count = 0;
bool moreSeqs = 1;
- TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
+ TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
while(moreSeqs) {
- //cout << "driver " << count << endl;
-
-
+
if (m->control_pressed) { break; }
int success = 1;
string trashCode = "";
flowData.getNext(flowFile);
- //cout << "driver good bit " << flowFile.good() << endl;
flowData.capFlows(maxFlows);
Sequence currSeq = flowData.getSequence();
-
if(!flowData.hasMinFlows(minFlows)){ //screen to see if sequence is of a minimum number of flows
success = 0;
trashCode += 'l';
int primerIndex = 0;
int barcodeIndex = 0;
+ if(numLinkers != 0){
+ success = trimOligos.stripLinker(currSeq);
+ if(success > ldiffs) { trashCode += 'k'; }
+ else{ currentSeqDiffs += success; }
+
+ }
+
if(barcodes.size() != 0){
success = trimOligos.stripBarcode(currSeq, barcodeIndex);
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqDiffs += success; }
}
+ if(numSpacers != 0){
+ success = trimOligos.stripSpacer(currSeq);
+ if(success > sdiffs) { trashCode += 's'; }
+ else{ currentSeqDiffs += success; }
+
+ }
+
if(numFPrimers != 0){
success = trimOligos.stripForward(currSeq, primerIndex);
if(success > pdiffs) { trashCode += 'f'; }
//report progress
if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = flowFile.tellg();
if ((pos == -1) || (pos >= line->end)) { break; }
}
else if(type == "REVERSE"){
- Sequence oligoRC("reverse", oligo);
- oligoRC.reverseComplement();
- revPrimer.push_back(oligoRC.getUnaligned());
+ string oligoRC = reverseOligo(oligo);
+ revPrimer.push_back(oligoRC);
}
else if(type == "BARCODE"){
oligosFile >> group;
barcodes[oligo]=indexBarcode; indexBarcode++;
barcodeNameVector.push_back(group);
+ }else if(type == "LINKER"){
+ linker.push_back(oligo);
+ }else if(type == "SPACER"){
+ spacer.push_back(oligo);
}
else{
m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
numFPrimers = primers.size();
numRPrimers = revPrimer.size();
+ numLinkers = linker.size();
+ numSpacers = spacer.size();
}
catch(exception& e) {
exit(1);
}
}
+//********************************************************************/
+string TrimFlowsCommand::reverseOligo(string oligo){
+ try {
+ string reverse = "";
+
+ for(int i=oligo.length()-1;i>=0;i--){
+
+ if(oligo[i] == 'A') { reverse += 'T'; }
+ else if(oligo[i] == 'T'){ reverse += 'A'; }
+ else if(oligo[i] == 'U'){ reverse += 'A'; }
+
+ else if(oligo[i] == 'G'){ reverse += 'C'; }
+ else if(oligo[i] == 'C'){ reverse += 'G'; }
+
+ else if(oligo[i] == 'R'){ reverse += 'Y'; }
+ else if(oligo[i] == 'Y'){ reverse += 'R'; }
+
+ else if(oligo[i] == 'M'){ reverse += 'K'; }
+ else if(oligo[i] == 'K'){ reverse += 'M'; }
+
+ else if(oligo[i] == 'W'){ reverse += 'W'; }
+ else if(oligo[i] == 'S'){ reverse += 'S'; }
+
+ else if(oligo[i] == 'B'){ reverse += 'V'; }
+ else if(oligo[i] == 'V'){ reverse += 'B'; }
+
+ else if(oligo[i] == 'D'){ reverse += 'H'; }
+ else if(oligo[i] == 'H'){ reverse += 'D'; }
+
+ else { reverse += 'N'; }
+ }
+
+
+ return reverse;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
+ exit(1);
+ }
+}
+
/**************************************************************************************************/
vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
processIDS.clear();
int exitCommand = 1;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
//loop through and create all the processes you want
projects / mothur.git / blobdiff