*/
#include "preclustercommand.h"
+#include "deconvolutecommand.h"
//**********************************************************************************************************************
-inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); }
+vector<string> PreClusterCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pdiffs("diffs", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pdiffs);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter ptopdown("topdown", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptopdown);
+
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PreClusterCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n";
+ helpString += "The pre.cluster command outputs a new fasta and name file.\n";
+ helpString += "The pre.cluster command parameters are fasta, name, group, count, topdown, processors and diffs. The fasta parameter is required. \n";
+ helpString += "The name 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 so you can cluster by group. \n";
+ helpString += "The count parameter allows you to provide a count 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 topdown parameter allows you to specify whether to cluster from largest abundance to smallest or smallest to largest. Default=T, meaning largest to smallest.\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";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PreClusterCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],precluster,[extension]"; }
+ else if (type == "name") { pattern = "[filename],precluster.names"; }
+ else if (type == "count") { pattern = "[filename],precluster.count_table"; }
+ else if (type == "map") { pattern = "[filename],precluster.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, "PreClusterCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PreClusterCommand::PreClusterCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ outputTypes["map"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-PreClusterCommand::PreClusterCommand(string option){
+PreClusterCommand::PreClusterCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta", "name", "diffs", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["map"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//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("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not found") { namefile = ""; }
- else if (namefile == "not open") { abort = true; }
- else { readNameFile(); }
+ else if (namefile == "not open") { namefile = ""; abort = true; }
+ else { m->setNameFile(namefile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not found") { groupfile = ""; bygroup = false; }
+ else if (groupfile == "not open") { abort = true; groupfile = ""; }
+ else { m->setGroupFile(groupfile); bygroup = true; }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not found") { countfile = ""; }
+ else if (countfile == "not open") { abort = true; countfile = ""; }
+ else {
+ m->setCountTableFile(countfile);
+ ct.readTable(countfile);
+ if (ct.hasGroupInfo()) { bygroup = true; }
+ else { bygroup = false; }
+ }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
- string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
- convert(temp, diffs);
+ string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
+ m->mothurConvert(temp, diffs);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "topdown", false); if(temp == "not found"){ temp = "T"; }
+ topdown = m->isTrue(temp);
+
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "PreClusterCommand");
+ m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
exit(1);
}
}
-
-//**********************************************************************************************************************
-PreClusterCommand::~PreClusterCommand(){}
//**********************************************************************************************************************
-void PreClusterCommand::help(){
+int PreClusterCommand::execute(){
try {
- mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
- mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
- mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
- mothurOut("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");
- mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
- mothurOut("The pre.cluster command should be in the following format: \n");
- mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
- mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int start = time(NULL);
+
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ string newNamesFile = getOutputFileName("name",variables);
+ string newCountFile = getOutputFileName("count",variables);
+ string newMapFile = getOutputFileName("map",variables); //add group name if by group
+ variables["[extension]"] = m->getExtension(fastafile);
+ string newFastaFile = getOutputFileName("fasta", variables);
+ outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
+ if (countfile == "") { outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); }
+ else { outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile); }
+
+ if (bygroup) {
+ //clear out old files
+ ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
+ ofstream outNames; m->openOutputFile(newNamesFile, outNames); outNames.close();
+ newMapFile = fileroot + "precluster.";
+
+ //parse fasta and name file by group
+ vector<string> groups;
+ if (countfile != "") {
+ cparser = new SequenceCountParser(countfile, fastafile);
+ groups = cparser->getNamesOfGroups();
+ }else {
+ if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile); }
+ else { parser = new SequenceParser(groupfile, fastafile); }
+ groups = parser->getNamesOfGroups();
+ }
+
+ if(processors == 1) { driverGroups(newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); }
+ else { createProcessesGroups(newFastaFile, newNamesFile, newMapFile, groups); }
+
+ if (countfile != "") {
+ mergeGroupCounts(newCountFile, newNamesFile, newFastaFile);
+ delete cparser;
+ }else {
+ delete parser;
+ //run unique.seqs for deconvolute results
+ string inputString = "fasta=" + newFastaFile;
+ if (namefile != "") { inputString += ", name=" + newNamesFile; }
+ m->mothurOutEndLine();
+ 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();
+
+ m->renameFile(filenames["fasta"][0], newFastaFile);
+ m->renameFile(filenames["name"][0], newNamesFile);
+ }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
+
+ }else {
+ if (namefile != "") { readNameFile(); }
+
+ //reads fasta file and return number of seqs
+ int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; }
+ if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; }
+
+ int count = process(newMapFile);
+ outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile);
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
+ m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ if (countfile != "") { newNamesFile = newCountFile; }
+ printData(newFastaFile, newNamesFile, "");
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+
+ return 0;
+
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "help");
+ m->errorOut(e, "PreClusterCommand", "execute");
exit(1);
}
}
-//**********************************************************************************************************************
-
-int PreClusterCommand::execute(){
+/**************************************************************************************************/
+int PreClusterCommand::createProcessesGroups(string newFName, string newNName, string newMFile, vector<string> groups) {
try {
- if (abort == true) { return 0; }
+ vector<int> processIDS;
+ int process = 1;
+ int num = 0;
- //reads fasta file and return number of seqs
- int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
-
- if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0; }
- if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); return 0; }
+ //sanity check
+ if (groups.size() < processors) { processors = groups.size(); }
- //clear sizes since you only needed this info to build the alignSeqs seqPNode structs
-// sizes.clear();
-
- //sort seqs by number of identical seqs
- sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
-
- int count = 0;
-
- //think about running through twice...
- for (int i = 0; i < numSeqs; i++) {
+ //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) || (__linux__) || (__unix__) || (__unix)
+
+ //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){
+ outputNames.clear();
+ num = driverGroups(newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
+
+ string tempFile = toString(getpid()) + ".outputNames.temp";
+ ofstream outTemp;
+ m->openOutputFile(tempFile, outTemp);
+
+ outTemp << outputNames.size();
+ for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
+ outTemp.close();
+
+ 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(newFName, newNName, newMFile, 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);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFile = toString(processIDS[i]) + ".outputNames.temp";
+ ifstream intemp;
+ m->openInputFile(tempFile, intemp);
+
+ int num;
+ intemp >> num;
+ for (int k = 0; k < num; k++) {
+ string name = "";
+ intemp >> name; m->gobble(intemp);
+
+ outputNames.push_back(name); outputTypes["map"].push_back(name);
+ }
+ intemp.close();
+ m->mothurRemove(tempFile);
+ }
+#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";
- //are you active
- // itActive = active.find(alignSeqs[i].seq.getName());
+ preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, topdown, i);
+ pDataArray.push_back(tempPreCluster);
+ processIDS.push_back(i);
- if (alignSeqs[i].active) { //this sequence has not been merged yet
+ //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]);
+ }
+
- //try to merge it with all smaller seqs
- for (int j = i+1; j < numSeqs; j++) {
- if (alignSeqs[j].active) { //this sequence has not been merged yet
- //are you within "diff" bases
- int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
-
- if (mismatch <= diffs) {
- //merge
- alignSeqs[i].names += ',' + alignSeqs[j].names;
- alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
-
- alignSeqs[j].active = 0;
- alignSeqs[j].numIdentical = 0;
- count++;
- }
- }//end if j active
- }//end if i != j
-
- //remove from active list
- alignSeqs[i].active = 0;
- }//end if active i
- if(i % 100 == 0) { cout << i << '\t' << numSeqs - count << '\t' << count << endl; }
+ //using the main process as a worker saves time and memory
+ num = driverGroups(newFName, newNName, newMFile, 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++) {
+ outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]);
+ }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
}
- string fileroot = outputDir + getRootName(getSimpleName(fastafile));
+#endif
- string newFastaFile = fileroot + "precluster" + getExtension(fastafile);
- string newNamesFile = fileroot + "precluster.names";
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ //newFName = m->getFullPathName(".\\" + newFName);
+ //newNName = m->getFullPathName(".\\" + newNName);
+
+ 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;
- mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();
- mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine();
- printData(newFastaFile, newNamesFile);
-
- return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int PreClusterCommand::driverGroups(string newFFile, string newNFile, string newMFile, 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;
+ vector<Sequence> thisSeqs;
+ if (groupfile != "") {
+ thisSeqs = parser->getSeqs(groups[i]);
+ }else if (countfile != "") {
+ thisSeqs = cparser->getSeqs(groups[i]);
+ }
+ if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
+
+ //fill alignSeqs with this groups info.
+ numSeqs = loadSeqs(thisNameMap, thisSeqs, groups[i]);
+
+ 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(newMFile+groups[i]+".map");
+ outputNames.push_back(newMFile+groups[i]+".map"); outputTypes["map"].push_back(newMFile+groups[i]+".map");
+
+ 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, groups[i]);
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+
+ }
+
+ return numSeqs;
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "execute");
+ m->errorOut(e, "PreClusterCommand", "driverGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int PreClusterCommand::process(string newMapFile){
+ try {
+ ofstream out;
+ m->openOutputFile(newMapFile, out);
+
+ //sort seqs by number of identical seqs
+ if (topdown) { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityTopDown); }
+ else { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityDownTop); }
+
+ int count = 0;
+ int numSeqs = alignSeqs.size();
+
+ if (topdown) {
+ //think about running through twice...
+ for (int i = 0; i < numSeqs; i++) {
+
+ if (alignSeqs[i].active) { //this sequence has not been merged yet
+
+ string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
+
+ //try to merge it with all smaller seqs
+ for (int j = i+1; j < numSeqs; j++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ if (alignSeqs[j].active) { //this sequence has not been merged yet
+ //are you within "diff" bases
+ int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
+
+ if (mismatch <= diffs) {
+ //merge
+ alignSeqs[i].names += ',' + alignSeqs[j].names;
+ alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
+
+ chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
+
+ alignSeqs[j].active = 0;
+ alignSeqs[j].numIdentical = 0;
+ count++;
+ }
+ }//end if j active
+ }//end for loop j
+
+ //remove from active list
+ alignSeqs[i].active = 0;
+
+ out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
+
+ }//end if active i
+ if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+ }
+ }else {
+ map<int, string> mapFile;
+ map<int, int> originalCount;
+ map<int, int>::iterator itCount;
+ for (int i = 0; i < numSeqs; i++) { mapFile[i] = ""; originalCount[i] = alignSeqs[i].numIdentical; }
+
+ //think about running through twice...
+ for (int i = 0; i < numSeqs; i++) {
+
+ //try to merge it into larger seqs
+ for (int j = i+1; j < numSeqs; j++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ if (originalCount[j] > originalCount[i]) { //this sequence is more abundant than I am
+ //are you within "diff" bases
+ int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
+
+ if (mismatch <= diffs) {
+ //merge
+ alignSeqs[j].names += ',' + alignSeqs[i].names;
+ alignSeqs[j].numIdentical += alignSeqs[i].numIdentical;
+
+ mapFile[j] = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[i].seq.getAligned() + "\n" + mapFile[i];
+ alignSeqs[i].numIdentical = 0;
+ originalCount.erase(i);
+ mapFile[i] = "";
+ count++;
+ j+=numSeqs; //exit search, we merged this one in.
+ }
+ }//end abundance check
+ }//end for loop j
+
+ if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+ }
+
+ for (int i = 0; i < numSeqs; i++) {
+ if (alignSeqs[i].numIdentical != 0) {
+ out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n" << mapFile[i] << endl;
+ }
+ }
+
+ }
+ out.close();
+
+ if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+
+ return count;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "process");
exit(1);
}
}
-
/**************************************************************************************************/
-
-//this requires the names and fasta file to be in the same order
-
int PreClusterCommand::readFASTA(){
try {
//ifstream inNames;
ifstream inFasta;
- //openInputFile(namefile, inNames);
- openInputFile(fastafile, inFasta);
-
- //string firstCol, secondCol, nameString;
- length = 0;
+ m->openInputFile(fastafile, inFasta);
+ set<int> lengths;
while (!inFasta.eof()) {
-
- //inNames >> firstCol >> secondCol;
- //nameString = secondCol;
- //gobble(inNames);
- //int size = 1;
- //while (secondCol.find_first_of(',') != -1) {
- // size++;
- // secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
- //}
-
- Sequence seq(inFasta); gobble(inFasta);
+ if (m->control_pressed) { inFasta.close(); return 0; }
+
+ Sequence seq(inFasta); m->gobble(inFasta);
if (seq.getName() != "") { //can get "" if commented line is at end of fasta file
if (namefile != "") {
itSize = sizes.find(seq.getName());
- if (itSize == sizes.end()) { mothurOut(seq.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
+ if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
else{
seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
alignSeqs.push_back(tempNode);
- if (seq.getAligned().length() > length) { length = alignSeqs[0].seq.getAligned().length(); }
+ lengths.insert(seq.getAligned().length());
}
}else { //no names file, you are identical to yourself
- seqPNode tempNode(1, seq, seq.getName());
+ int numRep = 1;
+ if (countfile != "") { numRep = ct.getNumSeqs(seq.getName()); }
+ seqPNode tempNode(numRep, seq, seq.getName());
alignSeqs.push_back(tempNode);
- if (seq.getAligned().length() > length) { length = alignSeqs[0].seq.getAligned().length(); }
+ lengths.insert(seq.getAligned().length());
}
}
}
inFasta.close();
- //inNames.close();
+
+ if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+ else if (lengths.size() == 1) { length = *(lengths.begin()); }
+
return alignSeqs.size();
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readFASTA");
+ m->errorOut(e, "PreClusterCommand", "readFASTA");
exit(1);
}
}
-
+/**************************************************************************************************/
+int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs, string group){
+ try {
+ set<int> lengths;
+ alignSeqs.clear();
+ map<string, string>::iterator it;
+ bool error = false;
+ map<string, int> thisCount;
+ if (countfile != "") { thisCount = cparser->getCountTable(group); }
+
+ for (int i = 0; i < thisSeqs.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ if (namefile != "") {
+ it = thisName.find(thisSeqs[i].getName());
+
+ //should never be true since parser checks for this
+ if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
+ else{
+ //get number of reps
+ int numReps = 1;
+ for(int j=0;j<(it->second).length();j++){
+ if((it->second)[j] == ','){ numReps++; }
+ }
+
+ seqPNode tempNode(numReps, thisSeqs[i], it->second);
+ alignSeqs.push_back(tempNode);
+ lengths.insert(thisSeqs[i].getAligned().length());
+ }
+ }else { //no names file, you are identical to yourself
+ int numRep = 1;
+ if (countfile != "") {
+ map<string, int>::iterator it2 = thisCount.find(thisSeqs[i].getName());
+
+ //should never be true since parser checks for this
+ if (it2 == thisCount.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); error = true; }
+ else { numRep = it2->second; }
+ }
+ seqPNode tempNode(numRep, thisSeqs[i], thisSeqs[i].getName());
+ alignSeqs.push_back(tempNode);
+ lengths.insert(thisSeqs[i].getAligned().length());
+ }
+ }
+
+ if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+ else if (lengths.size() == 1) { length = *(lengths.begin()); }
+
+ //sanity check
+ if (error) { m->control_pressed = true; }
+
+ thisSeqs.clear();
+
+ return alignSeqs.size();
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "loadSeqs");
+ exit(1);
+ }
+}
+
/**************************************************************************************************/
int PreClusterCommand::calcMisMatches(string seq1, string seq2){
return numBad;
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "calcMisMatches");
+ m->errorOut(e, "PreClusterCommand", "calcMisMatches");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int PreClusterCommand::mergeGroupCounts(string newcount, string newname, string newfasta){
+ try {
+ ifstream inNames;
+ m->openInputFile(newname, inNames);
+
+ string group, first, second;
+ set<string> uniqueNames;
+ while (!inNames.eof()) {
+ if (m->control_pressed) { break; }
+ inNames >> group; m->gobble(inNames);
+ inNames >> first; m->gobble(inNames);
+ inNames >> second; m->gobble(inNames);
+
+ vector<string> names;
+ m->splitAtComma(second, names);
+
+ uniqueNames.insert(first);
+
+ int total = ct.getGroupCount(first, group);
+ for (int i = 1; i < names.size(); i++) {
+ total += ct.getGroupCount(names[i], group);
+ ct.setAbund(names[i], group, 0);
+ }
+ ct.setAbund(first, group, total);
+ }
+ inNames.close();
+
+ vector<string> namesOfSeqs = ct.getNamesOfSeqs();
+ for (int i = 0; i < namesOfSeqs.size(); i++) {
+ if (ct.getNumSeqs(namesOfSeqs[i]) == 0) {
+ ct.remove(namesOfSeqs[i]);
+ }
+ }
+
+ ct.printTable(newcount);
+ m->mothurRemove(newname);
+
+ if (bygroup) { //if by group, must remove the duplicate seqs that are named the same
+ ifstream in;
+ m->openInputFile(newfasta, in);
+
+ ofstream out;
+ m->openOutputFile(newfasta+"temp", out);
+
+ int count = 0;
+ set<string> already;
+ while(!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+ count++;
+ if (already.count(seq.getName()) == 0) {
+ seq.printSequence(out);
+ already.insert(seq.getName());
+ }
+ }
+ }
+ in.close();
+ out.close();
+ m->mothurRemove(newfasta);
+ m->renameFile(newfasta+"temp", newfasta);
+ }
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "mergeGroupCounts");
exit(1);
}
}
/**************************************************************************************************/
-void PreClusterCommand::printData(string newfasta, string newname){
+void PreClusterCommand::printData(string newfasta, string newname, string group){
try {
ofstream outFasta;
ofstream outNames;
- openOutputFile(newfasta, outFasta);
- openOutputFile(newname, outNames);
-
+ if (bygroup) {
+ m->openOutputFileAppend(newfasta, outFasta);
+ m->openOutputFileAppend(newname, outNames);
+ }else {
+ m->openOutputFile(newfasta, outFasta);
+ m->openOutputFile(newname, outNames);
+ }
+ if ((countfile != "") && (group == "")) { outNames << "Representative_Sequence\ttotal\n"; }
for (int i = 0; i < alignSeqs.size(); i++) {
if (alignSeqs[i].numIdentical != 0) {
alignSeqs[i].seq.printSequence(outFasta);
- outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
+ if (countfile != "") {
+ if (group != "") { outNames << group << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
+ else { outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].numIdentical << endl; }
+ }else { outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
}
}
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "printData");
+ m->errorOut(e, "PreClusterCommand", "printData");
exit(1);
}
}
-
/**************************************************************************************************/
void PreClusterCommand::readNameFile(){
try {
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
string firstCol, secondCol;
while (!in.eof()) {
- in >> firstCol >> secondCol; gobble(in);
+ in >> firstCol >> secondCol; m->gobble(in);
+
+ for (int i = 0; i < firstCol.length(); i++) {
+ if (firstCol[i] == ':') { firstCol[i] = '_'; m->changedSeqNames = true; }
+ }
+
+ int size = 1;
+ for (int i = 0; i < secondCol.length(); i++) {
+ if (secondCol[i] == ':') { secondCol[i] = '_'; m->changedSeqNames = true; }
+ else if(secondCol[i] == ','){ size++; }
+ }
+
names[firstCol] = secondCol;
- int size = 1;
- while (secondCol.find_first_of(',') != -1) {
- size++;
- secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
- }
- sizes[firstCol] = size;
+ sizes[firstCol] = size;
}
in.close();
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readNameFile");
+ m->errorOut(e, "PreClusterCommand", "readNameFile");
exit(1);
}
}
projects / mothur.git / blobdiff