CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter prandom("random", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prandom);
- CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(pdistance);
+ CommandParameter pdistance("distance", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(pdistance);
CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
CommandParameter pconsensus("consensus", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pconsensus);
CommandParameter proot("root", "Boolean", "F", "", "", "", "",false,false); parameters.push_back(proot);
exit(1);
}
}
+//**********************************************************************************************************************
+string UnifracUnweightedCommand::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 == "unweighted") { outputFileName = "unweighted"; }
+ else if (type == "uwsummary") { outputFileName = "uwsummary"; }
+ else if (type == "phylip") { outputFileName = "dist"; }
+ else if (type == "column") { outputFileName = "dist"; }
+ else if (type == "tree") { outputFileName = "tre"; }
+ 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, "UnifracUnweightedCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
UnifracUnweightedCommand::UnifracUnweightedCommand(){
try {
string temp = validParameter.validFile(parameters, "distance", false);
if (temp == "not found") { phylip = false; outputForm = ""; }
else{
+ if (temp=="phylip") { temp = "lt"; }
if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; }
else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
}
T = reader->getTrees();
tmap = T[0]->getTreeMap();
map<string, string> nameMap = reader->getNames();
+ map<string, string> unique2Dup = reader->getNameMap();
delete reader;
- sumFile = outputDir + m->getSimpleName(treefile) + ".uwsummary";
+ sumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("uwsummary");
outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
m->openOutputFile(sumFile, outSum);
int thisSize = thisGroupsSeqs.size();
if (thisSize >= subsampleSize) { Groups.push_back(newGroups[i]); }
- else { m->mothurOut("You have selected a size that is larger than "+newGroups[i]+" number of sequences, removing "+newGroups[i]+".\n"); }
+ else { m->mothurOut("You have selected a size that is larger than "+newGroups[i]+" number of sequences, removing "+newGroups[i]+".\n"); }
}
m->setGroups(Groups);
}
for (int i = 0; i < T.size(); i++) {
if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
- counter = 0;
+ counter = 0;
if (random) {
- output = new ColumnFile(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted", itersString);
- outputNames.push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
- outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
+ output = new ColumnFile(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("unweighted"), itersString);
+ outputNames.push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("unweighted"));
+ outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("unweighted"));
}
if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ int startSubsample = time(NULL);
+
//subsample loop
vector< vector<double> > calcDistsTotals; //each iter, each groupCombos dists. this will be used to make .dist files
for (int thisIter = 0; thisIter < subsampleIters; thisIter++) { //subsampleIters=0, if subsample=f.
-
if (m->control_pressed) { break; }
//copy to preserve old one - would do this in subsample but memory cleanup becomes messy.
TreeMap* newTmap = new TreeMap();
- newTmap->getCopy(*tmap);
+ //newTmap->getCopy(*tmap);
+ //SubSample sample;
+ //Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
+
+ //uses method of setting groups to doNotIncludeMe
SubSample sample;
- Tree* subSampleTree = sample.getSample(T[i], newTmap, nameMap, subsampleSize);
+ Tree* subSampleTree = sample.getSample(T[i], tmap, newTmap, subsampleSize, unique2Dup);
//call new weighted function
vector<double> iterData; iterData.resize(numComp,0);
if((thisIter+1) % 100 == 0){ m->mothurOut(toString(thisIter+1)); m->mothurOutEndLine(); }
}
+ m->mothurOut("It took " + toString(time(NULL) - startSubsample) + " secs to run the subsampling."); m->mothurOutEndLine();
if (m->control_pressed) { delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
}
- string aveFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".unweighted.ave.dist";
- outputNames.push_back(aveFileName); outputTypes["phylip"].push_back(aveFileName);
-
+ string aveFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".unweighted.ave." + getOutputFileNameTag("phylip");
+ if (outputForm != "column") { outputNames.push_back(aveFileName); outputTypes["phylip"].push_back(aveFileName); }
+ else { outputNames.push_back(aveFileName); outputTypes["column"].push_back(aveFileName); }
ofstream out;
m->openOutputFile(aveFileName, out);
- string stdFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".unweighted.std.dist";
- outputNames.push_back(stdFileName); outputTypes["phylip"].push_back(stdFileName);
-
+ string stdFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".unweighted.std." + getOutputFileNameTag("phylip");
+ if (outputForm != "column") { outputNames.push_back(stdFileName); outputTypes["phylip"].push_back(stdFileName); }
+ else { outputNames.push_back(stdFileName); outputTypes["column"].push_back(stdFileName); }
ofstream outStd;
m->openOutputFile(stdFileName, outStd);
Tree* conTree = con.getTree(newTrees);
//create a new filename
- string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.cons.tre";
+ string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.cons." + getOutputFileNameTag("tree");
outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
ofstream outTree;
m->openOutputFile(conFile, outTree);
vector<Tree*> trees;
//create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.all.tre";
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.all." + getOutputFileNameTag("tree");
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream outAll;
try {
string phylipFileName;
if ((outputForm == "lt") || (outputForm == "square")) {
- phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.phylip.dist";
+ phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.phylip." + getOutputFileNameTag("phylip");
outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
}else { //column
- phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.column.dist";
+ phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.column." + getOutputFileNameTag("column");
outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
}
projects / mothur.git / blobdiff