#include "readmatrix.hpp"
#include "clusterdoturcommand.h"
+
//**********************************************************************************************************************
vector<string> ClusterCommand::setParameters(){
try {
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pcount);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
string ClusterCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The cluster command parameter options are phylip, column, name, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
+ helpString += "The cluster command parameter options are phylip, column, name, count, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
helpString += "The cluster command should be in the following format: \n";
helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
helpString += "The acceptable cluster methods are furthest, nearest, average and weighted. If no method is provided then average is assumed.\n";
//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; }
+ }
}
//check for required parameters
if (namefile == "not open") { abort = true; }
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); }
if ((phylipfile == "") && (columnfile == "")) {
//is there are current file available for either of these?
else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: phylip or column."); 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 ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
//get user cutoff and precision or use defaults
//run unique.seqs for deconvolute results
string inputString = "phylip=" + distfile;
if (namefile != "") { inputString += ", name=" + namefile; }
+ else if (countfile != "") { inputString += ", count=" + countfile; }
inputString += ", precision=" + toString(precision);
inputString += ", method=" + method;
if (hard) { inputString += ", hard=T"; }
read->setCutoff(cutoff);
NameAssignment* nameMap = NULL;
+ CountTable* ct = NULL;
if(namefile != ""){
nameMap = new NameAssignment(namefile);
nameMap->readMap();
- }
+ read->read(nameMap);
+ }else if (countfile != "") {
+ ct = new CountTable();
+ ct->readTable(countfile);
+ read->read(ct);
+ }else { read->read(nameMap); }
- read->read(nameMap);
list = read->getListVector();
- matrix = read->getMatrix();
- rabund = new RAbundVector(list->getRAbundVector());
+ 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;
if (m->control_pressed) { //clean up
- delete list; delete matrix; delete rabund;
- sabundFile.close();rabundFile.close();listFile.close();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- return 0;
+ delete list; delete matrix; delete rabund; if(countfile == ""){rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); }
+ listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0;
}
//create cluster
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, sabundFile);
- m->openOutputFile(rabundFileName, rabundFile);
+ if (countfile == "") {
+ m->openOutputFile(sabundFileName, sabundFile);
+ m->openOutputFile(rabundFileName, rabundFile);
+ outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+ outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+
+ }
m->openOutputFile(listFileName, listFile);
-
- 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);
+ outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
time_t estart = time(NULL);
loops = 0;
double saveCutoff = cutoff;
- while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
+ while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
if (m->control_pressed) { //clean up
delete list; delete matrix; delete rabund; delete cluster;
- sabundFile.close();rabundFile.close();listFile.close();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- return 0;
+ if(countfile == "") {rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); }
+ listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0;
}
if (print_start && m->isTrue(timing)) {
loops++;
cluster->update(cutoff);
-
- float dist = matrix->getSmallDist();
+
+ float dist = matrix->getSmallDist();
float rndDist;
if (hard) {
rndDist = m->ceilDist(dist, precision);
delete list;
delete rabund;
delete cluster;
-
- sabundFile.close();
- rabundFile.close();
+ if (countfile == "") {
+ sabundFile.close();
+ rabundFile.close();
+ }
listFile.close();
if (saveCutoff != cutoff) {
print_start = true;
loops = 0;
start = time(NULL);
-
- oldRAbund.setLabel(label);
- if (m->isTrue(showabund)) {
- oldRAbund.getSAbundVector().print(cout);
- }
- oldRAbund.print(rabundFile);
- oldRAbund.getSAbundVector().print(sabundFile);
-
+
+ oldRAbund.setLabel(label);
+ if (countfile == "") {
+ oldRAbund.print(rabundFile);
+ oldRAbund.getSAbundVector().print(sabundFile);
+ }
+
+ if (m->isTrue(showabund)) {
+ oldRAbund.getSAbundVector().print(cout);
+ }
+
oldList.setLabel(label);
oldList.print(listFile);
}
}
//**********************************************************************************************************************
+
+int ClusterCommand::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