*/
#include "parsimonycommand.h"
+#include "treereader.h"
//**********************************************************************************************************************
vector<string> ParsimonyCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter prandom("random", "String", "", "", "", "", "",false,false); parameters.push_back(prandom);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- 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 ptree("tree", "InputTypes", "", "", "none", "none", "none","parsimony-psummary",false,true,true); parameters.push_back(ptree);
+ 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 pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter prandom("random", "String", "", "", "", "", "","",false,false); parameters.push_back(prandom);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ 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);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string ParsimonyCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The parsimony command parameters are tree, group, name, random, groups, processors and iters. tree parameter is required unless you have valid current tree file or are using random.\n";
+ helpString += "The parsimony command parameters are tree, group, name, count, random, groups, processors and iters. tree parameter is required unless you have valid current tree file or are using random.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n";
helpString += "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n";
helpString += "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n";
exit(1);
}
}
-
+//**********************************************************************************************************************
+string ParsimonyCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "parsimony") { pattern = "[filename],parsimony"; }
+ else if (type == "psummary") { pattern = "[filename],psummary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ParsimonyCommand::ParsimonyCommand(){
try {
//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();
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //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["count"] = inputDir + it->second; }
+ }
}
- m->runParse = true;
- m->Groups.clear();
- m->namesOfGroups.clear();
- m->Treenames.clear();
- m->names.clear();
-
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; }
if (randomtree == "") {
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
- if (treefile == "not open") { abort = true; }
+ if (treefile == "not open") { treefile = ""; 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; }
- }
+ }else { m->setTreeFile(treefile); }
//check for required parameters
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
}
//if the user changes the output directory command factory will send this info to us in the output parameter
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; m->Groups.clear(); }
+ if (groups == "not found") { groups = ""; m->clearGroups(); }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
- convert(itersString, iters);
+ m->mothurConvert(itersString, iters);
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
+
+ if (countfile=="") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
+ }
}
m->setTreeFile(treefile);
- if (groupfile != "") {
- //read in group map info.
- tmap = new TreeMap(groupfile);
- tmap->readMap();
- }else{ //fake out by putting everyone in one group
- Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- tmap = new TreeMap();
-
- for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
- }
-
- if (namefile != "") { readNamesFile(); }
-
- 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();
- 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 (namefile != "") {
- if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
- else { numNamesInTree = m->Treenames.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
- }
- }
- }
- }
-
+ TreeReader* reader;
+ if (countfile == "") { reader = new TreeReader(treefile, groupfile, namefile); }
+ else { reader = new TreeReader(treefile, countfile); }
+ T = reader->getTrees();
+ ct = T[0]->getCountTable();
+ delete reader;
+
if(outputDir == "") { outputDir += m->hasPath(treefile); }
- output = new ColumnFile(outputDir + m->getSimpleName(treefile) + ".parsimony", itersString);
- outputNames.push_back(outputDir + m->getSimpleName(treefile) + ".parsimony");
- outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile) + ".parsimony");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile) + ".";
+
+ output = new ColumnFile(getOutputFileName("parsimony",variables), itersString);
+ outputNames.push_back(getOutputFileName("parsimony",variables));
+ outputTypes["parsimony"].push_back(getOutputFileName("parsimony",variables));
- sumFile = outputDir + m->getSimpleName(treefile) + ".psummary";
+ sumFile = getOutputFileName("psummary",variables);
m->openOutputFile(sumFile, outSum);
outputNames.push_back(sumFile);
outputTypes["psummary"].push_back(sumFile);
}
//set users groups to analyze
- util = new SharedUtil();
- util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
- util->getCombos(groupComb, m->Groups, numComp);
- delete util;
+ SharedUtil util;
+ vector<string> mGroups = m->getGroups();
+ vector<string> tGroups = ct->getNamesOfGroups();
+ util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
+ util.getCombos(groupComb, mGroups, numComp);
+ m->setGroups(mGroups);
if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
- pars = new Parsimony(tmap);
+ Parsimony pars;
counter = 0;
Progress* reading;
reading = new Progress("Comparing to random:", iters);
if (m->control_pressed) {
- delete reading; delete pars; delete output;
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ delete reading; delete output;
+ delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (randomtree == "") { outSum.close(); }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- m->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->clearGroups();
return 0;
}
if (randomtree == "") {
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
- userData = pars->getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC.
+ userData = pars.getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC.
if (m->control_pressed) {
- delete reading; delete pars; delete output;
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ delete reading; delete output;
+ delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (randomtree == "") { outSum.close(); }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- m->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ m->clearGroups();
return 0;
}
for (int j = 0; j < iters; j++) {
//create new tree with same num nodes and leaves as users
- randT = new Tree(tmap);
+ randT = new Tree(ct);
//create random relationships between nodes
randT->assembleRandomTree();
//get pscore of random tree
- randomData = pars->getValues(randT, processors, outputDir);
+ randomData = pars.getValues(randT, processors, outputDir);
if (m->control_pressed) {
- delete reading; delete pars; delete output; delete randT;
+ delete reading; delete output; delete randT;
if (randomtree == "") { outSum.close(); }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
- m->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ m->clearGroups();
return 0;
}
for (int j = 0; j < iters; j++) {
//create new tree with same num nodes and leaves as users
- randT = new Tree(tmap);
+ randT = new Tree(ct);
//create random relationships between nodes
randT->assembleRandomTree();
if (m->control_pressed) {
- delete reading; delete pars; delete output; delete randT;
- delete tmap;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- m->Groups.clear();
- return 0;
+ delete reading; delete output; delete randT; delete ct;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
}
//get pscore of random tree
- randomData = pars->getValues(randT, processors, outputDir);
+ randomData = pars.getValues(randT, processors, outputDir);
if (m->control_pressed) {
- delete reading; delete pars; delete output; delete randT;
- delete tmap;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- m->Groups.clear();
- return 0;
+ delete reading; delete output; delete randT; delete ct;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
}
for(int r = 0; r < numComp; r++) {
}
if (m->control_pressed) {
- delete reading; delete pars; delete output;
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ delete reading; delete output;
+ delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (randomtree == "") { outSum.close(); }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
- m->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
//finish progress bar
reading->finish();
delete reading;
-
printParsimonyFile();
if (randomtree == "") { printUSummaryFile(); }
+
+ delete output; delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
- //reset groups parameter
- m->Groups.clear();
-
- delete pars; delete output;
- delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;}
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
try {
//create treemap
- tmap = new TreeMap();
+ ct = new CountTable();
m->mothurOut("Please enter the number of groups you would like to analyze: ");
cin >> numGroups;
count = 1;
numEachGroup.resize(numGroups, 0);
+ set<string> nameMap;
+ map<string, string> groupMap;
+ set<string> gps;
+
for (int i = 1; i <= numGroups; i++) {
m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": ");
cin >> num;
m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine();
-
- //set tmaps seqsPerGroup
- tmap->seqsPerGroup[toString(i)] = num;
- tmap->namesOfGroups.push_back(toString(i));
+ gps.insert(toString(i));
+
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
- tmap->namesOfSeqs.push_back(toString(count));
- tmap->treemap[toString(count)].groupname = toString(i);
+ groupMap[toString(count)] = toString(i);
+ nameMap.insert(toString(count));
count++;
}
}
-
+ ct->createTable(nameMap, groupMap, gps);
+
//clears buffer so next command doesn't have error
string s;
getline(cin, s);
- m->Treenames = tmap->namesOfSeqs;
-
+ m->Treenames = ct->getNamesOfSeqs();
+ m->runParse = false;
}
catch(exception& e) {
m->errorOut(e, "ParsimonyCommand", "getUserInput");
exit(1);
}
}
-/*****************************************************************/
-int ParsimonyCommand::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 ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
- }
- }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
- }
- in.close();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ParsimonyCommand", "readNamesFile");
- exit(1);
- }
-}
/***********************************************************/
projects / mothur.git / blobdiff