m->openOutputFile(nameFileName, out1); out1.close();
mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.";
- if(processors == 1) { driverGroups(parser, outputFileName, nameFileName, mapFileName, 0, groups.size(), groups); }
- else { createProcessesGroups(parser, outputFileName, nameFileName, mapFileName, groups); }
+ vector<string> mapFileNames;
+ if(processors == 1) { mapFileNames = driverGroups(parser, outputFileName, nameFileName, mapFileName, 0, groups.size(), groups); }
+ else { mapFileNames = createProcessesGroups(parser, outputFileName, nameFileName, mapFileName, groups); }
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { return 0; }
- //deconvolute results by running unique.seqs
+ for (int j = 0; j < mapFileNames.size(); j++) { outputNames.push_back(mapFileNames[j]); outputTypes["map"].push_back(mapFileNames[j]); }
+ //deconvolute results by running unique.seqs
+ deconvoluteResults(outputFileName, nameFileName);
if (m->control_pressed) { return 0; }
if (m->control_pressed) { m->mothurRemove(distFileName); return 0; }
driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, outputFileName, nameFileName, mapFileName);
+ outputNames.push_back(mapFileName); outputTypes["map"].push_back(mapFileName);
}
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
- outputNames.push_back(mapFileName); outputTypes["map"].push_back(mapFileName);
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
/**************************************************************************************************/
-int ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, string newFName, string newNName, string newMName, vector<string> groups) {
+vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, string newFName, string newNName, string newMName, vector<string> groups) {
try {
vector<int> processIDS;
int process = 1;
+ vector<string> mapfileNames;
//sanity check
if (groups.size() < processors) { processors = groups.size(); }
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMName, lines[process].start, lines[process].end, groups);
+ mapfileNames = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMName, lines[process].start, lines[process].end, groups);
+
+ //pass filenames to parent
+ ofstream out;
+ string tempFile = newMName + toString(getpid()) + ".temp";
+ m->openOutputFile(tempFile, out);
+ out << mapfileNames.size() << endl;
+ for (int i = 0; i < mapfileNames.size(); i++) {
+ out << mapfileNames[i] << endl;
+ }
+ out.close();
+
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
}
//do my part
- driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
+ mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
wait(&temp);
}
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ ifstream in;
+ string tempFile = newMName + toString(processIDS[i]) + ".temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) {
+ int tempNum = 0; in >> tempNum; m->gobble(in);
+ for (int j = 0; j < tempNum; j++) {
+ string filename;
+ in >> filename; m->gobble(in);
+ mapfileNames.push_back(filename);
+ }
+ }
+ in.close(); m->mothurRemove(tempFile);
+
+ }
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
for( int i=1; i<processors; i++ ){
// Allocate memory for thread data.
string extension = toString(i) + ".temp";
-
+
shhhseqsData* tempShhhseqs = new shhhseqsData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), newMName, groups, m, lines[i].start, lines[i].end, sigma, i);
pDataArray.push_back(tempShhhseqs);
processIDS.push_back(i);
//using the main process as a worker saves time and memory
- driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
+ mapfileNames = driverGroups(parser, newFName, newNName, newMName, lines[0].start, lines[0].end, groups);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->mapfileNames.size(); j++) {
+ mapfileNames.push_back(pDataArray[i]->mapfileNames[j]);
+ }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
}
- return 0;
+ return mapfileNames;
}
catch(exception& e) {
}
}
/**************************************************************************************************/
-int ShhhSeqsCommand::driverGroups(SequenceParser& parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
+vector<string> ShhhSeqsCommand::driverGroups(SequenceParser& parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
try {
+ vector<string> mapFileNames;
+
for (int i = start; i < end; i++) {
start = time(NULL);
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { return mapFileNames; }
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
//load this groups info in order
loadData(correct, noise, sequences, uniqueNames, redundantNames, seqFreq, thisNameMap, thisSeqs);
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { return mapFileNames; }
//calc distances for cluster
string distFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + groups[i] + ".shhh.dist";
correct->execute(distFileName);
delete correct;
- if (m->control_pressed) { m->mothurRemove(distFileName); return 0; }
+ if (m->control_pressed) { m->mothurRemove(distFileName); return mapFileNames; }
driver(noise, sequences, uniqueNames, redundantNames, seqFreq, distFileName, newFFile+groups[i], newNFile+groups[i], newMFile+groups[i]+".map");
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { return mapFileNames; }
m->appendFiles(newFFile+groups[i], newFFile); m->mothurRemove(newFFile+groups[i]);
m->appendFiles(newNFile+groups[i], newNFile); m->mothurRemove(newNFile+groups[i]);
+ mapFileNames.push_back(newMFile+groups[i]+".map");
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + groups[i] + "."); m->mothurOutEndLine();
}
- return 0;
+ return mapFileNames;
}
catch(exception& e) {
m->errorOut(e, "ShhhSeqsCommand", "driverGroups");
string newfastaFile = filenames["fasta"][0];
m->mothurRemove(fastaFile); rename(newfastaFile.c_str(), fastaFile.c_str());
- m->mothurRemove(nameFile); rename(newnameFile.c_str(), nameFile.c_str());
+ if (nameFile != newnameFile) { m->mothurRemove(nameFile); rename(newnameFile.c_str(), nameFile.c_str()); }
return 0;
}
projects / mothur.git / blobdiff