else {
//valid paramters for this command
- string Array[] = {"cutoff","precision","method","showabund","timing","phylip","column","name","sorted"};
+ string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
abort = true;
}
globaldata->newRead();
+ //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("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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; }
+ }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
//check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
cutoff += (5 / (precision * 10.0));
method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "nearest"; }
+ if (method == "not found") { method = "furthest"; }
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
else { mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; }
if (abort == false) {
-
- fileroot = getRootName(distfile);
- tag = "fn"; //until we figure out average and nearest methods
+ if (outputDir == "") { outputDir += hasPath(distfile); }
+ fileroot = outputDir + getRootName(getSimpleName(distfile));
+
+ if (method == "furthest") { tag = "fn"; }
+ else if (method == "nearest") { tag = "nn"; }
+ else { tag = "an"; }
openOutputFile(fileroot+ tag + ".sabund", sabundFile);
openOutputFile(fileroot+ tag + ".rabund", rabundFile);
void HClusterCommand::help(){
try {
- mothurOut("The hcluster command parameter options are cutoff, precision, method, showabund, timing, phylip, column, name and sorted. Phylip or column and name are required.\n");
+ mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
mothurOut("The hcluster command should be in the following format: \n");
mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- mothurOut("The acceptable hcluster methods is furthest, but we hope to add nearest and average in the future.\n\n");
+ mothurOut("The acceptable hcluster methods are furthest and nearest, but we hope to add average in the future.\n\n");
}
catch(exception& e) {
errorOut(e, "HClusterCommand", "help");
mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine();
estart = time(NULL);
-
+
//list vector made by read contains all sequence names
if(list != NULL){
rabund = new RAbundVector(list->getRAbundVector());
print_start = true;
start = time(NULL);
-
-//cout << "here" << endl;
- ifstream in;
- openInputFile(distfile, in);
- string firstName, secondName;
- float distance;
-
- cluster = new HCluster(rabund, list);
- bool clusteredSomething;
+
+ cluster = new HCluster(rabund, list, method, distfile, globaldata->nameMap, cutoff);
vector<seqDist> seqs; seqs.resize(1); // to start loop
- exitedBreak = false; //lets you know if there is a distance stored in next
while (seqs.size() != 0){
- seqs = getSeqs(in);
- random_shuffle(seqs.begin(), seqs.end());
-
- if (seqs.size() == 0) { break; } //there are no more distances
-
+ seqs = cluster->getSeqs();
+
for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
- if (print_start && isTrue(timing)) {
- mothurOut("Clustering (" + tag + ") dist " + toString(distance) + "/"
- + toString(roundDist(distance, precision))
- + "\t(precision: " + toString(precision) + ")");
- cout.flush();
- print_start = false;
- }
-
- ///cout << "before cluster update" << endl;
if (seqs[i].seq1 != seqs[i].seq2) {
- clusteredSomething = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+ cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
float rndDist = roundDist(seqs[i].dist, precision);
- //cout << "after cluster update clusterSomething = " << clusteredSomething << " rndDist = " << rndDist << " rndPreviousDist = " << rndPreviousDist << endl;
-
if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
printData("unique");
else if((rndDist != rndPreviousDist)){
printData(toString(rndPreviousDist, length-1));
}
-
+
previousDist = seqs[i].dist;
rndPreviousDist = rndDist;
oldRAbund = *rabund;
}
}
}
-
- in.close();
- if (print_start && isTrue(timing)) {
- //mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist)
- //+ "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
- cout.flush();
- print_start = false;
- }
-
if(previousDist <= 0.0000){
printData("unique");
}
sabundFile.close();
rabundFile.close();
listFile.close();
-
delete cluster;
- //if (isTrue(timing)) {
- mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); mothurOutEndLine();
- //}
+
+ mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
}
//**********************************************************************************************************************
-vector<seqDist> HClusterCommand::getSeqs(ifstream& filehandle){
- try {
- string firstName, secondName;
- float distance, prevDistance;
- vector<seqDist> sameSeqs;
- prevDistance = -1;
-
- //if you are not at the beginning of the file
- if (exitedBreak) {
- sameSeqs.push_back(next);
- prevDistance = next.dist;
- exitedBreak = false;
- }
-
- //get entry
- while (filehandle) {
-
- filehandle >> firstName >> secondName >> distance;
-//cout << firstName << '\t' << secondName << '\t' << distance << endl;
- gobble(filehandle);
-
- //save first one
- if (prevDistance == -1) { prevDistance = distance; }
-
- map<string,int>::iterator itA = globaldata->nameMap->find(firstName);
- map<string,int>::iterator itB = globaldata->nameMap->find(secondName);
-
- if(itA == globaldata->nameMap->end()){
- cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);
- }
- if(itB == globaldata->nameMap->end()){
- cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
- }
-
- //using cutoff
- if (distance > cutoff) { break; }
-
- if (distance != -1) { //-1 means skip me
-
- //are the distances the same
- if (distance == prevDistance) { //save in vector
- seqDist temp;
- temp.seq1 = itA->second;
- temp.seq2 = itB->second;
- temp.dist = distance;
- sameSeqs.push_back(temp);
- exitedBreak = false;
- //what about precision??
-
- }else{
- next.seq1 = itA->second;
- next.seq2 = itB->second;
- next.dist = distance;
- exitedBreak = true;
- break;
- }
-
- }
- }
-
- return sameSeqs;
- }
- catch(exception& e) {
- errorOut(e, "HClusterCommand", "getSeqs");
- exit(1);
- }
-
-
-}
-
-//**********************************************************************************************************************
-
projects / mothur.git / blobdiff