X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=026e91b01f188ce180c3b645de8451138efe0e02;hb=d2390ede25cc211f95f99e377d5654bad7e6950e;hp=e08909bc89993db47ed80836a417b7020f68d068;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp index e08909b..026e91b 100644 --- a/chimerauchimecommand.cpp +++ b/chimerauchimecommand.cpp @@ -418,7 +418,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); abskew = validParameter.validFile(parameters, "abskew", false); if (abskew == "not found"){ useAbskew = false; abskew = "1.9"; }else{ useAbskew = true; } if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; } @@ -461,7 +461,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { path = path.substr(0, (tempPath.find_last_of('m'))); string uchimeCommand; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) uchimeCommand = path + "uchime"; // format the database, -o option gives us the ability #else uchimeCommand = path + "uchime.exe"; @@ -509,7 +509,7 @@ int ChimeraUchimeCommand::execute(){ if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one nameFile = nameFileNames[s]; }else { nameFile = getNamesFile(fastaFileNames[s]); } - + map seqs; readFasta(fastaFileNames[s], seqs); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } @@ -544,7 +544,7 @@ int ChimeraUchimeCommand::execute(){ int totalSeqs = 0; if(processors == 1) { totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); } - else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups); } + else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]); } if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } @@ -560,12 +560,19 @@ int ChimeraUchimeCommand::execute(){ int numSeqs = 0; int numChimeras = 0; - //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); } else{ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); } - //#else - // numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); - //#endif + + //add headings + ofstream out; + m->openOutputFile(outputFileName+".temp", out); + out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n"; + out.close(); + + m->appendFiles(outputFileName, outputFileName+".temp"); + m->mothurRemove(outputFileName); rename((outputFileName+".temp").c_str(), outputFileName.c_str()); + if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } //remove file made for uchime @@ -653,6 +660,7 @@ int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outp ofstream out; m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n"; float temp1; string parent1, parent2, temp2, temp3, temp4, temp5, temp6, temp7, temp8, temp9, temp10, temp11, temp12, temp13, flag; @@ -919,14 +927,15 @@ string ChimeraUchimeCommand::getNamesFile(string& inputFile){ string inputString = "fasta=" + inputFile; m->mothurOut("/******************************************/"); m->mothurOutEndLine(); m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); - + m->mothurCalling = true; + Command* uniqueCommand = new DeconvoluteCommand(inputString); uniqueCommand->execute(); map > filenames = uniqueCommand->getOutputFiles(); delete uniqueCommand; - + m->mothurCalling = false; m->mothurOut("/******************************************/"); m->mothurOutEndLine(); nameFile = filenames["name"][0]; @@ -979,23 +988,35 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){ try { + + outputFName = m->getFullPathName(outputFName); + filename = m->getFullPathName(filename); + alns = m->getFullPathName(alns); + //to allow for spaces in the path outputFName = "\"" + outputFName + "\""; filename = "\"" + filename + "\""; alns = "\"" + alns + "\""; vector cPara; - - char* tempUchime; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - tempUchime= new char[10]; - *tempUchime = '\0'; - strncat(tempUchime, "./uchime ", 9); + + string path = m->argv; + string tempPath = path; + for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); } + path = path.substr(0, (tempPath.find_last_of('m'))); + + string uchimeCommand = path; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + uchimeCommand += "uchime "; #else - tempUchime= new char[8]; - *tempUchime = '\0'; - strncat(tempUchime, "uchime ", 7); + uchimeCommand += "uchime"; + uchimeCommand = "\"" + uchimeCommand + "\""; #endif + + char* tempUchime; + tempUchime= new char[uchimeCommand.length()+1]; + *tempUchime = '\0'; + strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length()); cPara.push_back(tempUchime); char* tempIn = new char[8]; @@ -1223,6 +1244,10 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc //uchime_main(numArgs, uchimeParameters); //cout << "commandString = " << commandString << endl; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) +#else + commandString = "\"" + commandString + "\""; +#endif system(commandString.c_str()); //free memory @@ -1285,7 +1310,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename int num = 0; vector files; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //break up file into multiple files m->divideFile(filename, processors, files); @@ -1448,7 +1473,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename } /**************************************************************************************************/ -int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector groups) { +int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector groups, string nameFile, string groupFile, string fastaFile) { try { processIDS.clear(); @@ -1468,7 +1493,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o lines.push_back(linePair(startIndex, endIndex)); } -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //loop through and create all the processes you want while (process != processors) { @@ -1514,7 +1539,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o #else ////////////////////////////////////////////////////////////////////////////////////////////////////// - //Windows version shared memory, so be careful when passing variables through the preClusterData struct. + //Windows version shared memory, so be careful when passing variables through the uchimeData struct. //Above fork() will clone, so memory is separate, but that's not the case with windows, ////////////////////////////////////////////////////////////////////////////////////////////////////// @@ -1527,14 +1552,14 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o // Allocate memory for thread data. string extension = toString(i) + ".temp"; - uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastafile, namefile, groupfile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end, i); + uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end, i); tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract); tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract); pDataArray.push_back(tempUchime); processIDS.push_back(i); - //MySeqSumThreadFunction is in header. It must be global or static to work with the threads. + //MyUchimeThreadFunction 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, MyUchimeThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]); }