else {
//valid paramters for this command
- string Array[] = {"label","calc","groups","all","outputdir","inputdir", "processors"};
+ string Array[] = {"label","calc","groups","all","outputdir","distance","inputdir", "processors"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
all = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; }
+ createPhylip = m->isTrue(temp);
+
temp = validParameter.validFile(parameters, "processors", false); if(temp == "not found"){ temp = "1"; }
convert(temp, processors);
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine();
if (mult) { m->mothurOut(outAllFileName); m->mothurOutEndLine(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
/***********************************************************/
int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
try {
+ vector< vector<seqDist> > calcDists; //vector containing vectors that contains the summary results for each group compare
+ calcDists.resize(sumCalculators.size()); //one for each calc, this will be used to make .dist files
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp");
+ driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
m->appendFiles((sumFileName + ".temp"), sumFileName);
remove((sumFileName + ".temp").c_str());
if (mult) {
remove((sumAllFileName + ".temp").c_str());
}
}else{
- int process = 0;
+ int process = 1;
vector<int> processIDS;
//loop through and create all the processes you want
processIDS.push_back(pid);
process++;
}else if (pid == 0){
- driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp");
+ driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
+
+ //only do this if you want a distance file
+ if (createPhylip) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist";
+ ofstream outtemp;
+ m->openOutputFile(tempdistFileName, outtemp);
+
+ for (int i = 0; i < calcDists.size(); i++) {
+ outtemp << calcDists[i].size() << endl;
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
+ }
+ }
+ outtemp.close();
+ }
+
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
-
+
+ //parent do your part
+ driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);
+ m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
+ remove((sumFileName + toString(getpid()) + ".temp").c_str());
+ if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
+
//force parent to wait until all the processes are done
for (int i = 0; i < processIDS.size(); i++) {
int temp = processIDS[i];
for (int i = 0; i < processIDS.size(); i++) {
m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
remove((sumFileName + toString(processIDS[i]) + ".temp").c_str());
- if (mult) {
- if (i == 0) { m->appendFiles((sumAllFileName + toString(processIDS[i]) + ".temp"), sumAllFileName); }
- remove((sumAllFileName + toString(processIDS[i]) + ".temp").c_str());
+ if (mult) { remove((sumAllFileName + toString(processIDS[i]) + ".temp").c_str()); }
+
+ if (createPhylip) {
+ string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist";
+ ifstream intemp;
+ m->openInputFile(tempdistFileName, intemp);
+
+ for (int i = 0; i < calcDists.size(); i++) {
+ int size = 0;
+ intemp >> size; m->gobble(intemp);
+
+ for (int j = 0; j < size; j++) {
+ int seq1 = 0;
+ int seq2 = 0;
+ float dist = 1.0;
+
+ intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
+
+ seqDist tempDist(seq1, seq2, dist);
+ calcDists[i].push_back(tempDist);
+ }
+ }
+ intemp.close();
+ remove(tempdistFileName.c_str());
}
}
}
#else
- driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"));
+ driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"), calcDists);
m->appendFiles((sumFileName + ".temp"), sumFileName);
remove((sumFileName + ".temp").c_str());
if (mult) {
remove((sumAllFileName + ".temp").c_str());
}
#endif
+
+ if (createPhylip) {
+ for (int i = 0; i < calcDists.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sumFileName)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
+ outputNames.push_back(distFileName);
+ ofstream outDist;
+ m->openOutputFile(distFileName, outDist);
+ outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+
+ //initialize matrix
+ vector< vector<float> > matrix; //square matrix to represent the distance
+ matrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
+
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ int row = calcDists[i][j].seq1;
+ int column = calcDists[i][j].seq2;
+ float dist = calcDists[i][j].dist;
+
+ matrix[row][column] = dist;
+ matrix[column][row] = dist;
+ }
+
+ //output to file
+ outDist << thisLookup.size() << endl;
+ for (int r=0; r<thisLookup.size(); r++) {
+ //output name
+ string name = thisLookup[r]->getGroup();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+ outDist << name << '\t';
+
+ //output distances
+ for (int l = 0; l < r; l++) { outDist << matrix[r][l] << '\t'; }
+ outDist << endl;
+ }
+
+ outDist.close();
+ }
+ }
}
catch(exception& e) {
m->errorOut(e, "SummarySharedCommand", "process");
}
}
/**************************************************************************************************/
-int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, string sumFile, string sumAllFile) {
+int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, string sumFile, string sumAllFile, vector< vector<seqDist> >& calcDists) {
try {
//loop through calculators and add to file all for all calcs that can do mutiple groups
for(int i=0;i<sumCalculators.size();i++) {
- sumCalculators[i]->getValues(subset); //saves the calculator outputs
+ vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
if (m->control_pressed) { outputFileHandle.close(); return 1; }
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
+
+ seqDist temp(l, k, tempdata[0]);
+ calcDists[i].push_back(temp);
}
outputFileHandle << endl;
}
projects / mothur.git / blobdiff