//**********************************************************************************************************************
vector<string> ClassifyOtuCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(preftaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pbasis("basis", "Multiple", "otu-sequence", "otu", "", "", "",false,false); parameters.push_back(pbasis);
- CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "",false,true); parameters.push_back(pcutoff);
- CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","constaxonomy",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppersample);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pbasis("basis", "Multiple", "otu-sequence", "otu", "", "", "","",false,false); parameters.push_back(pbasis);
+ CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "","",false,true); parameters.push_back(pcutoff);
+ CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string ClassifyOtuCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The classify.otu command parameters are list, taxonomy, reftaxonomy, name, group, count, cutoff, label, basis and probs. The taxonomy and list parameters are required unless you have a valid current file.\n";
+ helpString += "The classify.otu command parameters are list, taxonomy, reftaxonomy, name, group, count, persample, cutoff, label, basis and probs. The taxonomy and list parameters are required unless you have a valid current file.\n";
helpString += "The reftaxonomy parameter allows you give the name of the reference taxonomy file used when you classified your sequences. Providing it will keep the rankIDs in the summary file static.\n";
helpString += "The name parameter allows you add a names file with your taxonomy file.\n";
helpString += "The group parameter allows you provide a group file to use in creating the summary file breakdown.\n";
helpString += "Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales.\n";
helpString += "6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC.\n";
helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n";
+ helpString += "The persample parameter allows you to find a consensus taxonomy for each group. Default=f\n";
helpString += "The default value for label is all labels in your inputfile.\n";
helpString += "The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy. The default is 51, meaning 51%. Cutoff cannot be below 51.\n";
helpString += "The probs parameter shuts off the outputting of the consensus confidence results. The default is true, meaning you want the confidence to be shown.\n";
}
}
//**********************************************************************************************************************
-string ClassifyOtuCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClassifyOtuCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //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 == "constaxonomy") { outputFileName = "cons.taxonomy"; }
- else if (type == "taxsummary") { outputFileName = "cons.tax.summary"; }
- 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, "ClassifyOtuCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "constaxonomy") { pattern = "[filename],[distance],cons.taxonomy"; }
+ else if (type == "taxsummary") { pattern = "[filename],[distance],cons.tax.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyOtuCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClassifyOtuCommand::ClassifyOtuCommand(){
if (namefile != "") { m->readNames(namefile, nameMap, true); }
if (groupfile != "") { groupMap = new GroupMap(groupfile); groupMap->readMap(); groups = groupMap->getNamesOfGroups(); }
else { groupMap = NULL; }
- if (countfile != "") { ct = new CountTable(); ct->readTable(countfile); if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+ if (countfile != "") { ct = new CountTable(); ct->readTable(countfile, true, false); if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
else { ct = NULL; }
//read taxonomy file and save in map for easy access in building bin trees
if (outputDir == "") { outputDir += m->hasPath(listfile); }
ofstream out;
- string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." +getOutputFileNameTag("constaxonomy");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = processList->getLabel();
+ string outputFile = getOutputFileName("constaxonomy", variables);
m->openOutputFile(outputFile, out);
outputNames.push_back(outputFile); outputTypes["constaxonomy"].push_back(outputFile);
ofstream outSum;
- string outputSumFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." +getOutputFileNameTag("taxsummary");
+ string outputSumFile = getOutputFileName("taxsummary", variables);
m->openOutputFile(outputSumFile, outSum);
outputNames.push_back(outputSumFile); outputTypes["taxsummary"].push_back(outputSumFile);
for (int i = 0; i < groups.size(); i++) {
groupIndex[groups[i]] = i;
ofstream* temp = new ofstream();
- string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + groups[i] + "." +getOutputFileNameTag("constaxonomy");
+ variables["[distance]"] = processList->getLabel() + "." + groups[i];
+ string outputFile = getOutputFileName("constaxonomy", variables);
m->openOutputFile(outputFile, *temp);
(*temp) << "OTU\tSize\tTaxonomy" << endl;
outs.push_back(temp);
outputNames.push_back(outputFile); outputTypes["constaxonomy"].push_back(outputFile);
ofstream* tempSum = new ofstream();
- string outputSumFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + groups[i] + "." +getOutputFileNameTag("taxsummary");
+ string outputSumFile = getOutputFileName("taxsummary", variables);
m->openOutputFile(outputSumFile, *tempSum);
outSums.push_back(tempSum);
outputNames.push_back(outputSumFile); outputTypes["taxsummary"].push_back(outputSumFile);
//for each bin in the list vector
string snumBins = toString(processList->getNumBins());
+ vector<string> binLabels = processList->getLabels();
for (int i = 0; i < processList->getNumBins(); i++) {
if (m->control_pressed) { break; }
names = findConsensusTaxonomy(thisNames, size, conTax);
if (m->control_pressed) { break; }
-
- //output to new names file
- string binLabel = "Otu";
- string sbinNumber = toString(i+1);
- if (sbinNumber.length() < snumBins.length()) {
- int diff = snumBins.length() - sbinNumber.length();
- for (int h = 0; h < diff; h++) { binLabel += "0"; }
- }
- binLabel += sbinNumber;
- out << binLabel << '\t' << size << '\t' << conTax << endl;
+ out << binLabels[i] << '\t' << size << '\t' << conTax << endl;
string noConfidenceConTax = conTax;
m->removeConfidences(noConfidenceConTax);
//add this bins taxonomy to summary
if (basis == "sequence") {
for(int j = 0; j < names.size(); j++) {
- int numReps = 1;
- if (countfile != "") { numReps = ct->getNumSeqs(names[j]); }
- for(int k = 0; k < numReps; k++) { taxaSum->addSeqToTree(names[j], noConfidenceConTax); }
+ //int numReps = 1;
+ //if (countfile != "") { numReps = ct->getNumSeqs(names[j]); }
+ //for(int k = 0; k < numReps; k++) { taxaSum->addSeqToTree(names[j], noConfidenceConTax); }
+ taxaSum->addSeqToTree(names[j], noConfidenceConTax);
}
}else { //otu
map<string, bool> containsGroup;
if (m->control_pressed) { break; }
- //output to new names file
- string binLabel = "Otu";
- string sbinNumber = toString(i+1);
- if (sbinNumber.length() < snumBins.length()) {
- int diff = snumBins.length() - sbinNumber.length();
- for (int h = 0; h < diff; h++) { binLabel += "0"; }
- }
- binLabel += sbinNumber;
- (*outs[groupIndex[itParsed->first]]) << binLabel << '\t' << size << '\t' << conTax << endl;
+ (*outs[groupIndex[itParsed->first]]) << binLabels[i] << '\t' << size << '\t' << conTax << endl;
string noConfidenceConTax = conTax;
m->removeConfidences(noConfidenceConTax);
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