//**********************************************************************************************************************
vector<string> ChimeraCcodeCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
- CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
- CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "",false,false); parameters.push_back(pnumwanted);
- CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-mapinfo-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
+ CommandParameter pwindow("window", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pwindow);
+ CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pnumwanted);
+ CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
try {
string helpString = "";
helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
- helpString += "This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
+ helpString += "This command was created using the algorithms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\n";
helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n";
helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
}
}
//**********************************************************************************************************************
+string ChimeraCcodeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "chimera") { pattern = "[filename],[tag],ccode.chimeras-[filename],ccode.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],[tag],ccode.accnos-[filename],ccode.accnos"; }
+ else if (type == "mapinfo") { pattern = "[filename],mapinfo"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(){
try {
abort = true; calledHelp = true;
outputTypes["chimera"] = tempOutNames;
outputTypes["mapinfo"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
+
}
catch(exception& e) {
m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
outputTypes["chimera"] = tempOutNames;
outputTypes["mapinfo"] = tempOutNames;
outputTypes["accnos"] = 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);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
- convert(temp, window);
+ m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "20"; }
- convert(temp, numwanted);
+ m->mothurConvert(temp, numwanted);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName, accnosFileName;
- if (maskfile != "") {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras";
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos";
- }else {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.chimeras";
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.accnos";
- }
-
- string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo";
-
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string mapInfo = getOutputFileName("mapinfo", variables);
+ if (maskfile != "") { variables["[tag]"] = maskfile; }
+ outputFileName = getOutputFileName("chimera", variables);
+ accnosFileName = getOutputFileName("accnos", variables);
+
if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); return 0; }
#ifdef USE_MPI
//break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vector<unsigned long long> positions = m->divideFile(fastaFileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) {
}
delete candidateSeq;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
out.close();
out2.close();
int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 0;
int num = 0;
projects / mothur.git / blobdiff