CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FastaTaxName",false,false); parameters.push_back(ptaxonomy);
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "none",false,false); parameters.push_back(pphylip);
CommandParameter pfasta("fasta", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "FastaTaxName",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName-FastaTaxName",false,false); parameters.push_back(pname);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName-FastaTaxName",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "",false,false); parameters.push_back(pcount);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "ColumnName",false,false); parameters.push_back(pcolumn);
CommandParameter ptaxlevel("taxlevel", "Number", "", "3", "", "", "",false,false); parameters.push_back(ptaxlevel);
CommandParameter psplitmethod("splitmethod", "Multiple", "classify-fasta-distance", "distance", "", "", "",false,false); parameters.push_back(psplitmethod);
string ClusterSplitCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The cluster.split command parameter options are fasta, phylip, column, name, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, large, processors. Fasta or Phylip or column and name are required.\n";
+ helpString += "The cluster.split command parameter options are fasta, phylip, column, name, count, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, large, processors. Fasta or Phylip or column and name are required.\n";
helpString += "The cluster.split command can split your files in 3 ways. Splitting by distance file, by classification, or by classification also using a fasta file. \n";
helpString += "For the distance file method, you need only provide your distance file and mothur will split the file into distinct groups. \n";
helpString += "For the classification method, you need to provide your distance file and taxonomy file, and set the splitmethod to classify. \n";
helpString += "You will also need to set the taxlevel you want to split by. mothur will split the sequence into distinct taxonomy groups, and create distance files for each grouping. \n";
helpString += "The phylip and column parameter allow you to enter your distance file. \n";
helpString += "The fasta parameter allows you to enter your aligned fasta file. \n";
- helpString += "The name parameter allows you to enter your name file and is required if your distance file is in column format. \n";
+ helpString += "The name parameter allows you to enter your name file. \n";
+ helpString += "The count parameter allows you to enter your count file. \n A count or name file is required if your distance file is in column format";
helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 0.25. \n";
helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
helpString += "The method allows you to specify what clustering algorythm you want to use, default=average, option furthest, nearest, or average. \n";
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = 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; }
+ }
}
//check for required parameters
else { distfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { abort = true; namefile = "";}
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = "";}
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
}
}
else if ((phylipfile != "") && (columnfile != "") && (fastafile != "")) { m->mothurOut("When executing a cluster.split command you must enter ONLY ONE of the following: fasta, phylip or column."); m->mothurOutEndLine(); abort = true; }
-
+
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.split command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
if (columnfile != "") {
- if (namefile == "") {
+ if ((namefile == "") && (countfile == "")) {
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
- abort = true;
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a namefile or countfile if you are going to use the column format."); m->mothurOutEndLine();
+ abort = true;
+ }
}
}
}
}
}
- if (namefile == "") {
+ if ((namefile == "") && (countfile == "")) {
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("You need to provide a namefile if you are if you are using a fasta file to generate the split."); m->mothurOutEndLine();
- abort = true;
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a namefile or countfile if you are going to use the fasta file to generate the split."); m->mothurOutEndLine();
+ abort = true;
+ }
}
}
}
//if no names file given with phylip file, create it
ListVector* listToMakeNameFile = convert->getListVector();
- if (namefile == "") { //you need to make a namefile for split matrix
+ if ((namefile == "") && (countfile == "")) { //you need to make a namefile for split matrix
ofstream out;
namefile = phylipfile + ".names";
m->openOutputFile(namefile, out);
//split matrix into non-overlapping groups
SplitMatrix* split;
- if (splitmethod == "distance") { split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod, large); }
- else if (splitmethod == "classify") { split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod, large); }
- else if (splitmethod == "fasta") { split = new SplitMatrix(fastafile, namefile, taxFile, taxLevelCutoff, cutoff, splitmethod, processors, classic, outputDir); }
+ if (splitmethod == "distance") { split = new SplitMatrix(distfile, namefile, countfile, taxFile, cutoff, splitmethod, large); }
+ else if (splitmethod == "classify") { split = new SplitMatrix(distfile, namefile, countfile, taxFile, taxLevelCutoff, splitmethod, large); }
+ else if (splitmethod == "fasta") { split = new SplitMatrix(fastafile, namefile, countfile, taxFile, taxLevelCutoff, cutoff, splitmethod, processors, classic, outputDir); }
else { m->mothurOut("Not a valid splitting method. Valid splitting algorithms are distance, classify or fasta."); m->mothurOutEndLine(); return 0; }
split->split();
//read in singletons
if (singleton != "none") {
- ifstream in;
- m->openInputFile(singleton, in);
+
+ ifstream in;
+ m->openInputFile(singleton, in);
string firstCol, secondCol;
listSingle = new ListVector();
+
+ if (countfile != "") { m->getline(in); m->gobble(in); }
+
while (!in.eof()) {
- in >> firstCol >> secondCol; m->gobble(in);
- listSingle->push_back(secondCol);
+ in >> firstCol >> secondCol; m->getline(in); m->gobble(in);
+ if (countfile == "") { listSingle->push_back(secondCol); }
+ else { listSingle->push_back(firstCol); }
}
+
in.close();
m->mothurRemove(singleton);
string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+ string listFileName = fileroot+ tag + ".";
+ if (countfile != "") { listFileName += "unique_"; }
+ listFileName += getOutputFileNameTag("list");
- m->openOutputFile(sabundFileName, outSabund);
- m->openOutputFile(rabundFileName, outRabund);
+ if (countfile == "") {
+ m->openOutputFile(sabundFileName, outSabund);
+ m->openOutputFile(rabundFileName, outRabund);
+ outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+ outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+
+ }
m->openOutputFile(listFileName, outList);
+ outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+
- outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
- outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
- outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
map<float, int>::iterator itLabel;
//for each label needed
else { thisLabel = toString(itLabel->first, length-1); }
outList << thisLabel << '\t' << itLabel->second << '\t';
-
- RAbundVector* rabund = new RAbundVector();
- rabund->setLabel(thisLabel);
+
+ RAbundVector* rabund = NULL;
+ if (countfile == "") {
+ rabund = new RAbundVector();
+ rabund->setLabel(thisLabel);
+ }
//add in singletons
if (listSingle != NULL) {
for (int j = 0; j < listSingle->getNumBins(); j++) {
outList << listSingle->get(j) << '\t';
- rabund->push_back(m->getNumNames(listSingle->get(j)));
+ if (countfile == "") { rabund->push_back(m->getNumNames(listSingle->get(j))); }
}
}
//get the list info from each file
for (int k = 0; k < listNames.size(); k++) {
- if (m->control_pressed) { if (listSingle != NULL) { delete listSingle; } for (int i = 0; i < listNames.size(); i++) { m->mothurRemove(listNames[i]); } delete rabund; return 0; }
+ if (m->control_pressed) { if (listSingle != NULL) { delete listSingle; } for (int i = 0; i < listNames.size(); i++) { m->mothurRemove(listNames[i]); } if (rabund != NULL) { delete rabund; } return 0; }
InputData* input = new InputData(listNames[k], "list");
ListVector* list = input->getListVector(thisLabel);
else {
for (int j = 0; j < list->getNumBins(); j++) {
outList << list->get(j) << '\t';
- rabund->push_back(m->getNumNames(list->get(j)));
+ if (countfile == "") { rabund->push_back(m->getNumNames(list->get(j))); }
}
delete list;
}
delete input;
}
- SAbundVector sabund = rabund->getSAbundVector();
-
- sabund.print(outSabund);
- rabund->print(outRabund);
+ if (countfile == "") {
+ SAbundVector sabund = rabund->getSAbundVector();
+ sabund.print(outSabund);
+ rabund->print(outRabund);
+ }
outList << endl;
- delete rabund;
+ if (rabund != NULL) { delete rabund; }
}
outList.close();
- outRabund.close();
- outSabund.close();
-
+ if (countfile == "") {
+ outRabund.close();
+ outSabund.close();
+ }
if (listSingle != NULL) { delete listSingle; }
for (int i = 0; i < listNames.size(); i++) { m->mothurRemove(listNames[i]); }
m->mothurOutEndLine(); m->mothurOut("Reading " + thisDistFile); m->mothurOutEndLine();
- NameAssignment* nameMap = new NameAssignment(thisNamefile);
- nameMap->readMap();
-
- //reads phylip file storing data in 2D vector, also fills list and rabund
+ //reads phylip file storing data in 2D vector, also fills list and rabund
bool sim = false;
ClusterClassic* cluster = new ClusterClassic(cutoff, method, sim);
- cluster->readPhylipFile(thisDistFile, nameMap);
- tag = cluster->getTag();
- if (m->control_pressed) { delete cluster; return 0; }
+ NameAssignment* nameMap = NULL;
+ CountTable* ct = NULL;
+ if(namefile != ""){
+ nameMap = new NameAssignment(thisNamefile);
+ nameMap->readMap();
+ cluster->readPhylipFile(thisDistFile, nameMap);
+ }else if (countfile != "") {
+ ct = new CountTable();
+ ct->readTable(thisNamefile);
+ cluster->readPhylipFile(thisDistFile, ct);
+ }
+ tag = cluster->getTag();
+
+ if (m->control_pressed) { if(namefile != ""){ delete nameMap; }
+ else { delete ct; } delete cluster; return 0; }
list = cluster->getListVector();
rabund = cluster->getRAbundVector();
m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
- if (m->control_pressed) { delete cluster; delete list; delete rabund; listFile.close(); return listFileName; }
+ if (m->control_pressed) { delete cluster; delete list; delete rabund; listFile.close(); if(namefile != ""){ delete nameMap; }
+ else { delete ct; } return listFileName; }
cluster->update(cutoff);
listFile.close();
- delete cluster; delete nameMap; delete list; delete rabund;
-
+ delete cluster; delete list; delete rabund;
+ if(namefile != ""){ delete nameMap; }
+ else { delete ct; }
+
+ m->mothurRemove(thisDistFile);
+ m->mothurRemove(thisNamefile);
return listFileName;
ReadMatrix* read = new ReadColumnMatrix(thisDistFile);
read->setCutoff(cutoff);
- NameAssignment* nameMap = new NameAssignment(thisNamefile);
- nameMap->readMap();
- read->read(nameMap);
-
- if (m->control_pressed) { delete read; delete nameMap; return listFileName; }
-
- list = read->getListVector();
+ NameAssignment* nameMap = NULL;
+ CountTable* ct = NULL;
+ if(namefile != ""){
+ nameMap = new NameAssignment(thisNamefile);
+ nameMap->readMap();
+ read->read(nameMap);
+ }else if (countfile != "") {
+ ct = new CountTable();
+ ct->readTable(thisNamefile);
+ read->read(ct);
+ }
+
+ list = read->getListVector();
oldList = *list;
- matrix = read->getDMatrix();
+ matrix = read->getDMatrix();
+ if(countfile != "") {
+ rabund = new RAbundVector();
+ createRabund(ct, list, rabund); //creates an rabund that includes the counts for the unique list
+ delete ct;
+ }else { rabund = new RAbundVector(list->getRAbundVector()); }
+
delete read; read = NULL;
- delete nameMap; nameMap = NULL;
+ if (namefile != "") { delete nameMap; nameMap = NULL; }
#ifdef USE_MPI
m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
- rabund = new RAbundVector(list->getRAbundVector());
-
//create cluster
if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
}
}
//**********************************************************************************************************************
+int ClusterSplitCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund){
+ try {
+ rabund->setLabel(list->getLabel());
+ for(int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+ vector<string> binNames;
+ string bin = list->get(i);
+ m->splitAtComma(bin, binNames);
+ int total = 0;
+ for (int j = 0; j < binNames.size(); j++) { total += ct->getNumSeqs(binNames[j]); }
+ rabund->push_back(total);
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "createRabund");
+ exit(1);
+ }
+
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff