*/
#include "countseqscommand.h"
-#include "groupmap.h"
#include "sharedutilities.h"
+#include "counttable.h"
//**********************************************************************************************************************
vector<string> CountSeqsCommand::setParameters(){
try {
- 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 pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","count",false,true,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ 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); }
string CountSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.seqs command reads a name file and outputs a .seq.count file. You may also provide a group file to get the counts broken down by group.\n";
+ helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count_table file. You may also provide a group file to get the counts broken down by group.\n";
helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
+ helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
- helpString += "Example count.seqs(name=amazon.names).\n";
+ helpString += "Example count.seqs(name=amazon.names) or make.table(name=amazon.names).\n";
helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourNameFile).\n";
return helpString;
}
exit(1);
}
}
-
+//**********************************************************************************************************************
+string CountSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "count") { pattern = "[filename],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
CountSeqsCommand::CountSeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
m->splitAtDash(groups, Groups);
+
+ string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
+ large = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
//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 = m->hasPath(namefile); }
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count";
- m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
- out << "Representative_Sequence\ttotal\t";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+ string outputFileName = getOutputFileName("count", variables);
+
+ int total = 0;
+ int start = time(NULL);
+ if (!large) { total = processSmall(outputFileName); }
+ else { total = processLarge(outputFileName); }
+
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create a table for " + toString(total) + " sequences.");
+ m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ //set rabund file as new current rabundfile
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { string current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
- GroupMap* groupMap;
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountSeqsCommand::processSmall(string outputFileName){
+ try {
+ ofstream out;
+ m->openOutputFile(outputFileName, out); outputTypes["count"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
+ out << "Representative_Sequence\ttotal\t";
+
+ GroupMap* groupMap;
if (groupfile != "") {
groupMap = new GroupMap(groupfile); groupMap->readMap();
//make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
SharedUtil* util = new SharedUtil();
- util->setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> nameGroups = groupMap->getNamesOfGroups();
+ util->setGroups(Groups, nameGroups);
delete util;
//sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
}
}
out << endl;
+ out.close();
+
+ int total = createProcesses(groupMap, outputFileName);
+
+ if (groupfile != "") { delete groupMap; }
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processSmall");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int CountSeqsCommand::createProcesses(GroupMap*& groupMap, string outputFileName) {
+ try {
- //open input file
- ifstream in;
- m->openInputFile(namefile, in);
+ vector<int> processIDS;
+ int process = 0;
+ vector<unsigned long long> positions;
+ vector<linePair> lines;
+ int numSeqs = 0;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFilePerLine(namefile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ if(processors == 1){ lines.push_back(linePair(0, 1000)); }
+ else {
+ int numSeqs = 0;
+ positions = m->setFilePosEachLine(namefile, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+ }
+#endif
+
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- while (!in.eof()) {
+ //loop through and create all the processes you want
+ while (process != processors-1) {
+ 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){
+ string filename = toString(getpid()) + ".temp";
+ numSeqs = driver(lines[process].start, lines[process].end, filename, groupMap);
+
+ string tempFile = toString(getpid()) + ".num.temp";
+ ofstream outTemp;
+ m->openOutputFile(tempFile, outTemp);
+
+ outTemp << numSeqs << 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);
+ }
+ }
+
+ string filename = toString(getpid()) + ".temp";
+ numSeqs = driver(lines[processors-1].start, lines[processors-1].end, filename, groupMap);
+
+ //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]) + ".num.temp";
+ ifstream intemp;
+ m->openInputFile(tempFile, intemp);
+
+ int num;
+ intemp >> num; intemp.close();
+ numSeqs += num;
+ m->mothurRemove(tempFile);
+ }
+#else
+ vector<countData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<GroupMap*> copies;
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ string filename = toString(i) + ".temp";
+
+ GroupMap* copyGroup = new GroupMap();
+ copyGroup->getCopy(groupMap);
+ copies.push_back(copyGroup);
+ vector<string> cGroups = Groups;
+
+ countData* temp = new countData(filename, copyGroup, m, lines[i].start, lines[i].end, groupfile, namefile, cGroups);
+ pDataArray.push_back(temp);
+ processIDS.push_back(i);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MyCountThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ string filename = toString(processors-1) + ".temp";
+ numSeqs = driver(lines[processors-1].start, lines[processors-1].end, filename, groupMap);
+
+ //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++){
+ numSeqs += pDataArray[i]->total;
+ delete copies[i];
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
+ //append output files
+ for(int i=0;i<processIDS.size();i++){
+ m->appendFiles((toString(processIDS[i]) + ".temp"), outputFileName);
+ m->mothurRemove((toString(processIDS[i]) + ".temp"));
+ }
+ m->appendFiles(filename, outputFileName);
+ m->mothurRemove(filename);
+
+
+ //sanity check
+ if (groupfile != "") {
+ if (numSeqs != groupMap->getNumSeqs()) {
+ m->mothurOut("[ERROR]: processes reported processing " + toString(numSeqs) + " sequences, but group file indicates you have " + toString(groupMap->getNumSeqs()) + " sequences.");
+ if (processors == 1) { m->mothurOut(" Could you have a file mismatch?\n"); }
+ else { m->mothurOut(" Either you have a file mismatch or a process failed to complete the task assigned to it.\n"); m->control_pressed = true; }
+ }
+ }
+ return numSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int CountSeqsCommand::driver(unsigned long long start, unsigned long long end, string outputFileName, GroupMap*& groupMap) {
+ try {
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+ in.seekg(start);
+
+ bool done = false;
+ int total = 0;
+ while (!done) {
if (m->control_pressed) { break; }
string firstCol, secondCol;
- in >> firstCol >> secondCol; m->gobble(in);
-
+ in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in);
+ //cout << firstCol << '\t' << secondCol << endl;
+ m->checkName(firstCol);
+ m->checkName(secondCol);
+ //cout << firstCol << '\t' << secondCol << endl;
+
vector<string> names;
m->splitAtChar(secondCol, names, ',');
out << firstCol << '\t' << names.size() << endl;
}
-
+ total += names.size();
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= end)) { break; }
+#else
+ if (in.eof()) { break; }
+#endif
+
}
in.close();
+ out.close();
+
+ return total;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountSeqsCommand::processLarge(string outputFileName){
+ try {
+ set<string> namesOfGroups;
+ map<string, int> initial;
+ for (set<string>::iterator it = namesOfGroups.begin(); it != namesOfGroups.end(); it++) { initial[(*it)] = 0; }
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
+ out << "Representative_Sequence\ttotal\t";
+ if (groupfile == "") { out << endl; }
+
+ map<string, unsigned long long> namesToIndex;
+ string outfile = m->getRootName(groupfile) + "sorted.groups.temp";
+ string outName = m->getRootName(namefile) + "sorted.name.temp";
+ map<int, string> indexToName;
+ map<int, string> indexToGroup;
+ if (groupfile != "") {
+ time_t estart = time(NULL);
+ //convert name file to redundant -> unique. set unique name equal to index so we can use vectors, save name for later.
+ string newNameFile = m->getRootName(namefile) + ".name.temp";
+ string newGroupFile = m->getRootName(groupfile) + ".group.temp";
+ indexToName = processNameFile(newNameFile);
+ indexToGroup = getGroupNames(newGroupFile, namesOfGroups);
+
+ //sort file by first column so the names of sequences will be easier to find
+ //use the unix sort
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ string command = "sort -n " + newGroupFile + " -o " + outfile;
+ system(command.c_str());
+ command = "sort -n " + newNameFile + " -o " + outName;
+ system(command.c_str());
+ #else //sort using windows sort
+ string command = "sort " + newGroupFile + " /O " + outfile;
+ system(command.c_str());
+ command = "sort " + newNameFile + " /O " + outName;
+ system(command.c_str());
+ #endif
+ m->mothurRemove(newNameFile);
+ m->mothurRemove(newGroupFile);
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort and index the group and name files. "); m->mothurOutEndLine();
+ }else { outName = namefile; }
+
+ time_t estart = time(NULL);
+ //open input file
+ ifstream in;
+ m->openInputFile(outName, in);
+
+ //open input file
+ ifstream in2;
- if (groupfile != "") { delete groupMap; }
-
- if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+ int total = 0;
+ vector< vector<int> > nameMapCount;
+ if (groupfile != "") {
+ m->openInputFile(outfile, in2);
+ nameMapCount.resize(indexToName.size());
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ nameMapCount[i].resize(indexToGroup.size(), 0);
+ }
+ }
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol;
+ in >> firstCol; m->gobble(in);
+
+ if (groupfile != "") {
+ int uniqueIndex;
+ in >> uniqueIndex; m->gobble(in);
+
+ string name; int groupIndex;
+ in2 >> name >> groupIndex; m->gobble(in2);
+
+ if (name != firstCol) { m->mothurOut("[ERROR]: found " + name + " in your groupfile, but " + firstCol + " was in your namefile, please correct.\n"); m->control_pressed = true; }
+
+ nameMapCount[uniqueIndex][groupIndex]++;
+ total++;
+ }else {
+ string secondCol;
+ in >> secondCol; m->gobble(in);
+ int num = m->getNumNames(secondCol);
+ out << firstCol << '\t' << num << endl;
+ total += num;
+ }
+ }
+ in.close();
+
+ if (groupfile != "") {
+ m->mothurRemove(outfile);
+ m->mothurRemove(outName);
+ in2.close();
+ for (map<int, string>::iterator it = indexToGroup.begin(); it != indexToGroup.end(); it++) { out << it->second << '\t'; }
+ out << endl;
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ string totalsLine = "";
+ int seqTotal = 0;
+ for (int j = 0; j < nameMapCount[i].size(); j++) {
+ seqTotal += nameMapCount[i][j];
+ totalsLine += toString(nameMapCount[i][j]) + '\t';
+ }
+ out << indexToName[i] << '\t' << seqTotal << '\t' << totalsLine << endl;
+ }
+ }
+
+ out.close();
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to create the count table file. "); m->mothurOutEndLine();
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processLarge");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<int, string> CountSeqsCommand::processNameFile(string name) {
+ try {
+ map<int, string> indexToNames;
+
+ ofstream out;
+ m->openOutputFile(name, out);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+ int count = 0;
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ m->checkName(firstCol);
+ m->checkName(secondCol);
+ //parse names into vector
+ vector<string> theseNames;
+ m->splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { out << theseNames[i] << '\t' << count << endl; }
+ indexToNames[count] = firstCol;
+ pairDone = false;
+ count++;
+ }
+ }
+ }
+ in.close();
+ out.close();
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
- m->mothurOutEndLine();
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ m->checkName(firstCol);
+ m->checkName(secondCol);
+ //parse names into vector
+ vector<string> theseNames;
+ m->splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { out << theseNames[i] << '\t' << count << endl; }
+ indexToNames[count] = firstCol;
+ pairDone = false;
+ count++;
+ }
+ }
+
+ }
+
+ return indexToNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processNameFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<int, string> CountSeqsCommand::getGroupNames(string filename, set<string>& namesOfGroups) {
+ try {
+ map<int, string> indexToGroups;
+ map<string, int> groupIndex;
+ map<string, int>::iterator it;
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(groupfile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+ int count = 0;
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ m->checkName(firstCol);
+ it = groupIndex.find(secondCol);
+ if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
+ groupIndex[secondCol] = count;
+ count++;
+ }
+ out << firstCol << '\t' << groupIndex[secondCol] << endl;
+ namesOfGroups.insert(secondCol);
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+ out.close();
+
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ m->checkName(firstCol);
+ it = groupIndex.find(secondCol);
+ if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
+ groupIndex[secondCol] = count;
+ count++;
+ }
+ out << firstCol << '\t' << groupIndex[secondCol] << endl;
+ namesOfGroups.insert(secondCol);
+ pairDone = false;
+ }
+ }
+ }
- return 0;
+ for (it = groupIndex.begin(); it != groupIndex.end(); it++) { indexToGroups[it->second] = it->first; }
+
+ return indexToGroups;
}
-
catch(exception& e) {
- m->errorOut(e, "CountSeqsCommand", "execute");
+ m->errorOut(e, "CountSeqsCommand", "getGroupNames");
exit(1);
}
}
//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff