//**********************************************************************************************************************
vector<string> ShhhSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(psigma);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-map",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","name",false,true,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(psigma);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string helpString = "";
helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
- helpString += "The fasta parameter allows you to enter the fasta file containing your potentially sequences, and is required, unless you have a valid current fasta file. \n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
helpString += "The group parameter allows you to provide a group file. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
exit(1);
}
}
+//**********************************************************************************************************************
+string ShhhSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],shhh_seqs.fasta"; }
+ else if (type == "name") { pattern = "[filename],shhh_seqs.names"; }
+ else if (type == "map") { pattern = "[filename],shhh_seqs.map"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
ShhhSeqsCommand::ShhhSeqsCommand(){
else { m->setGroupFile(groupfile); }
string temp = validParameter.validFile(parameters, "sigma", false); if(temp == "not found"){ temp = "0.01"; }
- convert(temp, sigma);
-
+ m->mothurConvert(temp, sigma);
+ sigma = 1/sigma;
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
catch(exception& e) {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- if (outputDir == "") { outputDir = m->hasPath(fastafile); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
- string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.names";
- string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.map";
+ if (outputDir == "") { outputDir = m->hasPath(fastafile); }//if user entered a file with a path then preserve it
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("fasta",variables);
+ string nameFileName = getOutputFileName("name",variables);
+ string mapFileName = getOutputFileName("map",variables);
if (groupfile != "") {
//Parse sequences by group
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(); }
lines.push_back(linePair(startIndex, endIndex));
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
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++){
+ if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ 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 inputString = "fasta=" + fastaFile + ", name=" + nameFile;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
-
+ m->mothurCalling = true;
+
Command* uniqueCommand = new DeconvoluteCommand(inputString);
uniqueCommand->execute();
map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
delete uniqueCommand;
-
+ m->mothurCalling = false;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
string newnameFile = filenames["name"][0];
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;
}
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