*/
#include "preclustercommand.h"
-#include "sequenceparser.h"
#include "deconvolutecommand.h"
-//**********************************************************************************************************************
-inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); }
-
//**********************************************************************************************************************
vector<string> PreClusterCommand::setParameters(){
try {
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
- CommandParameter pbygroup("bygroup", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pbygroup);
+ 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);
helpString += "The pre.cluster command outputs a new fasta and name file.\n";
helpString += "The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n";
helpString += "The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n";
- helpString += "The group parameter allows you to provide a group file. \n";
+ helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n";
helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
- helpString += "The bygroup parameter allows you to indicate you whether you want to cluster sequences only within each group, default=T, when a groupfile is given. \n";
helpString += "The pre.cluster command should be in the following format: \n";
helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
else { m->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not found") { groupfile = ""; }
+ if (groupfile == "not found") { groupfile = ""; bygroup = false; }
else if (groupfile == "not open") { abort = true; groupfile = ""; }
- else { m->setGroupFile(groupfile); }
+ else { m->setGroupFile(groupfile); bygroup = true; }
string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
convert(temp, diffs);
- temp = validParameter.validFile(parameters, "bygroup", false);
- if (temp == "not found") {
- if (groupfile != "") { temp = "T"; }
- else { temp = "F"; }
- }
- bygroup = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+
- if (bygroup && (groupfile == "")) { m->mothurOut("You cannot set bygroup=T, unless you provide a groupfile."); m->mothurOutEndLine(); abort=true; }
-
}
}
vector<string> groups = parser->getNamesOfGroups();
- //precluster each group
- for (int i = 0; i < groups.size(); i++) {
-
- start = time(NULL);
-
- if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
-
- m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
-
- map<string, string> thisNameMap;
- if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
- vector<Sequence> thisSeqs = parser->getSeqs(groups[i]);
-
- //fill alignSeqs with this groups info.
- int numSeqs = loadSeqs(thisNameMap, thisSeqs);
-
- if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
-
- if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; }
-
- int count = process();
-
- if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
-
- m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
- m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
- printData(newFastaFile, newNamesFile);
-
- m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
-
- }
+//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1) { driverGroups(parser, newFastaFile, newNamesFile, 0, groups.size(), groups); }
+ else { createProcessesGroups(parser, newFastaFile, newNamesFile, groups); }
+//#else
+// driverGroups(parser, newFastaFile, newNamesFile, 0, groups.size(), groups);
+//#endif
delete parser;
+ if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
+
//run unique.seqs for deconvolute results
string inputString = "fasta=" + newFastaFile;
if (namefile != "") { inputString += ", name=" + newNamesFile; }
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->renameFile(filenames["fasta"][0], newFastaFile);
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
}else {
if (namefile != "") { readNameFile(); }
}
}
/**************************************************************************************************/
+int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, vector<string> groups) {
+ try {
+
+ vector<int> processIDS;
+ int process = 1;
+ int num = 0;
+
+ //sanity check
+ if (groups.size() < processors) { processors = groups.size(); }
+
+ //divide the groups between the processors
+ vector<linePair> lines;
+ int numGroupsPerProcessor = groups.size() / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numGroupsPerProcessor;
+ int endIndex = (i+1) * numGroupsPerProcessor;
+ if(i == (processors - 1)){ endIndex = groups.size(); }
+ lines.push_back(linePair(startIndex, endIndex));
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ 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){
+ num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ num = driverGroups(parser, newFName, newNName, 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++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<preClusterData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ // Allocate memory for thread data.
+ string extension = toString(i) + ".temp";
+
+ preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), groups, m, lines[i].start, lines[i].end, diffs, i);
+ pDataArray.push_back(tempPreCluster);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyPreclusterThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+
+ //using the main process as a worker saves time and memory
+ num = driverGroups(parser, newFName, newNName, 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++){
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+#endif
+
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
+ m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
+ m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
+ }
+
+ return num;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int PreClusterCommand::driverGroups(SequenceParser* parser, string newFFile, string newNFile, int start, int end, vector<string> groups){
+ try {
+
+ int numSeqs = 0;
+
+ //precluster each group
+ for (int i = start; i < end; i++) {
+
+ start = time(NULL);
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
+
+ map<string, string> thisNameMap;
+ if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
+ vector<Sequence> thisSeqs = parser->getSeqs(groups[i]);
+
+ //fill alignSeqs with this groups info.
+ numSeqs = loadSeqs(thisNameMap, thisSeqs);
+
+ if (m->control_pressed) { return 0; }
+
+ if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+
+ int count = process();
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+ m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ printData(newFFile, newNFile);
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+
+ }
+
+ return numSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "driverGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
int PreClusterCommand::process(){
try {
projects / mothur.git / blobdiff