else {
//valid paramters for this command
- string Array[] = {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","outputdir","inputdir"};
+ string Array[] = {"phylip","column","name","cutoff","precision","method","splitmethod","taxonomy","showabund","timing","hard","processors","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//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("taxonomy");
+ //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["taxonomy"] = inputDir + it->second; }
+ }
}
//check for required parameters
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ taxFile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxFile == "not open") { abort = true; }
+ else if (taxFile == "not found") { taxFile = ""; }
+
if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a cluster.split command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster.split command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
if (columnfile != "") {
- if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
+ if (namefile == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "10"; }
convert(temp, cutoff);
- if (!hard) { cutoff += (5 / (precision * 10.0)); }
+ cutoff += (5 / (precision * 10.0));
- method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "furthest"; }
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "furthest"; }
+
+ splitmethod = validParameter.validFile(parameters, "splitmethod", false); if (splitmethod == "not found") { method = "distance"; }
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
+
+ if ((splitmethod == "distance") || (splitmethod == "classify")) { }
+ else { m->mothurOut("Not a valid splitting method. Valid splitting algorithms are distance or classify."); m->mothurOutEndLine(); abort = true; }
+
+ if ((splitmethod == "classify") && (taxFile == "")) { m->mothurOut("You need to provide a taxonomy file if you are going to use the classify splitmethod."); m->mothurOutEndLine(); abort = true; }
showabund = validParameter.validFile(parameters, "showabund", false);
if (showabund == "not found") { showabund = "T"; }
void ClusterSplitCommand::help(){
try {
- m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
- m->mothurOut("The cluster command parameter options are method, cuttoff, hard, precision, showabund and timing. No parameters are required.\n");
- m->mothurOut("The cluster command should be in the following format: \n");
- m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- m->mothurOut("The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n");
+ m->mothurOut("The cluster.split command parameter options are cutoff, splitcutoff, precision, method, splitmethod, phylip, column, name, showabund, timing. Phylip or column and name are required.\n");
+ m->mothurOut("The phylip and column parameter allow you to enter your distance file. \n");
+ m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
+ m->mothurOut("The cluster.split command should be in the following format: \n");
+ m->mothurOut("cluster.split(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+ m->mothurOut("Example: cluster.split(column=abrecovery.dist, name=abrecovery.names, method=furthest, cutoff=0.10, precision=1000, splitmethod=classify) \n");
+
}
catch(exception& e) {
m->errorOut(e, "ClusterSplitCommand", "help");
time_t estart = time(NULL);
//split matrix into non-overlapping groups
- SplitMatrix* split = new SplitMatrix(distfile, namefile, cutoff);
+ SplitMatrix* split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod);
split->split();
if (m->control_pressed) { delete split; return 0; }
vector< map<string, string> > distName = split->getDistanceFiles(); //returns map of distance files -> namefile sorted by distance file size
delete split;
+ if (m->control_pressed) { return 0; }
+
m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to split the distance file."); m->mothurOutEndLine();
estart = time(NULL);
- if (m->control_pressed) { return 0; }
-
//****************** break up files between processes and cluster each file set ******************************//
vector<string> listFileNames;
set<string> labels;
cluster->update(cutoff);
float dist = matrix->getSmallDist();
- float rndDist = roundDist(dist, precision);
+ float rndDist;
+ if (hard) {
+ rndDist = ceilDist(dist, precision);
+ }else{
+ rndDist = roundDist(dist, precision);
+ }
if(previousDist <= 0.0000 && dist != previousDist){
oldList.setLabel("unique");
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