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A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */,
A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */,
A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */,
+ A77A221D139001B600B0BE70 /* deuniquetreecommand.h */,
+ A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */,
A7E9B6CC12D37EC400DA6239 /* distancecommand.h */,
A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
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A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */,
A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */,
+ A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
--- /dev/null
+/*
+ * deuniquetreecommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/27/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "deuniquetreecommand.h"
+
+//**********************************************************************************************************************
+vector<string> DeuniqueTreeCommand::setParameters(){
+ try {
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ 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); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DeuniqueTreeCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The deunique.tree command parameters are tree and name. Both parameters are required unless you have valid current files.\n";
+ helpString += "The deunique.tree command should be in the following format: deunique.tree(tree=yourTreeFile, name=yourNameFile).\n";
+ helpString += "Example deunique.tree(tree=abrecovery.tree, name=abrecovery.names).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreeFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DeuniqueTreeCommand::DeuniqueTreeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
+ exit(1);
+ }
+}
+/***********************************************************/
+DeuniqueTreeCommand::DeuniqueTreeCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = 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);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("tree");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+ m->runParse = true;
+ m->Groups.clear();
+ m->namesOfGroups.clear();
+ m->Treenames.clear();
+ m->names.clear();
+
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { abort = true; }
+ else if (treefile == "not found") { //if there is a current design file, use it
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { //if there is a current design file, use it
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(treefile); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
+ exit(1);
+ }
+}
+
+/***********************************************************/
+int DeuniqueTreeCommand::execute() {
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ m->setTreeFile(treefile);
+
+ //extracts names from tree to make faked out groupmap
+ Tree* tree = new Tree(treefile); delete tree;
+ tmap = new TreeMap();
+ for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+
+ if (m->control_pressed) { delete tmap; return 0; }
+
+ readNamesFile();
+
+ if (m->control_pressed) { delete tmap; return 0; }
+
+ ReadTree* read = new ReadNewickTree(treefile);
+ int readOk = read->read(tmap);
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
+
+ read->AssembleTrees();
+ vector<Tree*> T = read->getTrees();
+ delete read;
+
+ //make sure all files match
+ //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+ int numNamesInTree;
+ if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
+ else { numNamesInTree = m->Treenames.size(); }
+
+ //output any names that are in group file but not in tree
+ if (numNamesInTree < tmap->getNumSeqs()) {
+ for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
+ //is that name in the tree?
+ int count = 0;
+ for (int j = 0; j < m->Treenames.size(); j++) {
+ if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
+ count++;
+ }
+
+ if (m->control_pressed) {
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
+ }
+
+ //then you did not find it so report it
+ if (count == m->Treenames.size()) {
+ //if it is in your namefile then don't remove
+ map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
+
+ if (it == nameMap.end()) {
+ m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
+ tmap->removeSeq(tmap->namesOfSeqs[i]);
+ i--; //need this because removeSeq removes name from namesOfSeqs
+ }
+ }
+ }
+ }
+
+
+ //print new Tree
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + "deunique.tre";
+ outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
+ ofstream out;
+ m->openOutputFile(outputFile, out);
+ T[0]->print(out, "deunique");
+ out.close();
+
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "execute");
+ exit(1);
+ }
+}
+/*****************************************************************/
+int DeuniqueTreeCommand::readNamesFile() {
+ try {
+ m->names.clear();
+ numUniquesInName = 0;
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string first, second;
+ map<string, string>::iterator itNames;
+
+ while(!in.eof()) {
+ in >> first >> second; m->gobble(in);
+
+ numUniquesInName++;
+
+ itNames = m->names.find(first);
+ if (itNames == m->names.end()) {
+ m->names[first] = second;
+
+ //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
+ vector<string> dupNames;
+ m->splitAtComma(second, dupNames);
+
+ for (int i = 0; i < dupNames.size(); i++) {
+ nameMap[dupNames[i]] = dupNames[i];
+ if (i != 0) { tmap->addSeq(dupNames[i], "Group1"); }
+ }
+ }else { m->mothurOut(first + " has already been seen in namefile, aborting."); m->mothurOutEndLine(); in.close(); m->names.clear(); m->control_pressed = true; return 1; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "readNamesFile");
+ exit(1);
+ }
+}
+/***********************************************************/
+
+
+
+
if (tree[node].getBranchLength() != -1) {
out << ":" << tree[node].getBranchLength();
}
+ }else if (mode == "deunique") {
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
}
}else { //you are a leaf
string leafGroup = tmap->getGroup(tree[node].getName());
if (tree[node].getBranchLength() != -1) {
out << ":" << tree[node].getBranchLength();
}
+ }else if (mode == "deunique") {
+ map<string, string>::iterator itNames = m->names.find(tree[node].getName());
+
+ string outputString = "";
+ if (itNames != m->names.end()) {
+
+ vector<string> dupNames;
+ m->splitAtComma((itNames->second), dupNames);
+
+ if (dupNames.size() == 1) {
+ outputString += tree[node].getName();
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(tree[node].getBranchLength());
+ }
+ }else {
+ outputString += "(";
+
+ for (int u = 0; u < dupNames.size()-1; u++) {
+ outputString += dupNames[u];
+
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(0.0);
+ }
+ outputString += ",";
+ }
+
+ outputString += dupNames[dupNames.size()-1];
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(0.0);
+ }
+
+ outputString += ")";
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(tree[node].getBranchLength());
+ }
+ }
+ }else {
+ outputString = tree[node].getName();
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(tree[node].getBranchLength());
+ }
+
+ m->mothurOut("[ERROR]: " + tree[node].getName() + " is not in your namefile, please correct."); m->mothurOutEndLine();
+ }
+
+ out << outputString;
}
}
projects / mothur.git / commitdiff