X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=countseqscommand.cpp;h=411a814d73671ebb69b43a783e36e31d6263fe45;hp=e83c6035731aa5509655dcd25a7a45995c1a0004;hb=d3e27ba055f6765044b885cded5302d9cece161a;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc diff --git a/countseqscommand.cpp b/countseqscommand.cpp index e83c603..411a814 100644 --- a/countseqscommand.cpp +++ b/countseqscommand.cpp @@ -8,17 +8,19 @@ */ #include "countseqscommand.h" -#include "groupmap.h" #include "sharedutilities.h" +#include "counttable.h" //********************************************************************************************************************** vector 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 myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -33,11 +35,13 @@ vector CountSeqsCommand::setParameters(){ 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; } @@ -46,14 +50,28 @@ string CountSeqsCommand::getHelpString(){ 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 tempOutNames; - outputTypes["summary"] = tempOutNames; + outputTypes["count"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand"); @@ -85,7 +103,7 @@ CountSeqsCommand::CountSeqsCommand(string option) { //initialize outputTypes vector 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 @@ -127,6 +145,13 @@ CountSeqsCommand::CountSeqsCommand(string option) { 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); } @@ -146,12 +171,52 @@ int CountSeqsCommand::execute(){ 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 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(); @@ -170,18 +235,181 @@ int CountSeqsCommand::execute(){ } } 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; + vector processIDS; + int process = 0; + vector positions; + vector 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) + + //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;iopenInputFile(tempFile, intemp); + + int num; + intemp >> num; intemp.close(); + numSeqs += num; + m->mothurRemove(tempFile); + } +#else + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + vector copies; + + //Create processor worker threads. + for( int i=0; igetCopy(groupMap); + copies.push_back(copyGroup); + vector 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;iappendFiles((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); - int total = 0; - while (!in.eof()) { + 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 names; m->splitAtChar(secondCol, names, ','); @@ -219,26 +447,296 @@ int CountSeqsCommand::execute(){ } 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 namesOfGroups; + map initial; + for (set::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 namesToIndex; + string outfile = m->getRootName(groupfile) + "sorted.groups.temp"; + string outName = m->getRootName(namefile) + "sorted.name.temp"; + map indexToName; + map 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 > 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::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 CountSeqsCommand::processNameFile(string name) { + try { + map 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 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 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("Total number of sequences: " + toString(total)); m->mothurOutEndLine(); - m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); - m->mothurOutEndLine(); + if (rest != "") { + vector 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 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 CountSeqsCommand::getGroupNames(string filename, set& namesOfGroups) { + try { + map indexToGroups; + map groupIndex; + map::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 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 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); } } //********************************************************************************************************************** + + +