X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=ae4cb524cba877f5a9ec843e1686569032c6528d;hb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;hp=3205ae794165a5b8c045c473403d8a66b1b54f90;hpb=a150db3c2bfd7b76420048a1e94ebe397f2c6045;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 3205ae7..ae4cb52 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -40,6 +40,7 @@ void MothurOut::printCurrentFiles() { if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); } if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); } if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); } + if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); } if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); } } @@ -73,6 +74,7 @@ bool MothurOut::hasCurrentFiles() { if (taxonomyfile != "") { return true; } if (treefile != "") { return true; } if (flowfile != "") { return true; } + if (biomfile != "") { return true; } if (processors != "1") { return true; } return hasCurrent; @@ -107,6 +109,7 @@ void MothurOut::clearCurrentFiles() { accnosfile = ""; taxonomyfile = ""; flowfile = ""; + biomfile = ""; processors = "1"; } catch(exception& e) { @@ -143,7 +146,7 @@ void MothurOut::setDefaultPath(string pathname) { //add / to name if needed string lastChar = pathname.substr(pathname.length()-1); - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if (lastChar != "/") { pathname += "/"; } #else if (lastChar != "\\") { pathname += "\\"; } @@ -212,8 +215,8 @@ void MothurOut::mothurOut(string output) { if (pid == 0) { //only one process should output to screen #endif - cout << output; out << output; + logger() << output; #ifdef USE_MPI } @@ -234,8 +237,8 @@ void MothurOut::mothurOutEndLine() { if (pid == 0) { //only one process should output to screen #endif - cout << endl; out << endl; + logger() << endl; #ifdef USE_MPI } @@ -247,6 +250,55 @@ void MothurOut::mothurOutEndLine() { } } /*********************************************************************************************/ +void MothurOut::mothurOut(string output, ofstream& outputFile) { + try { + +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen +#endif + + + out << output; + outputFile << output; + logger() << output; + +#ifdef USE_MPI + } +#endif + + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOut"); + exit(1); + } +} +/*********************************************************************************************/ +void MothurOut::mothurOutEndLine(ofstream& outputFile) { + try { +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen +#endif + + out << endl; + outputFile << endl; + logger() << endl; + +#ifdef USE_MPI + } +#endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOutEndLine"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::mothurOutJustToLog(string output) { try { #ifdef USE_MPI @@ -285,7 +337,7 @@ void MothurOut::errorOut(exception& e, string object, string function) { // // On failure, returns 0.0, 0.0 int MothurOut::mem_usage(double& vm_usage, double& resident_set) { - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) vm_usage = 0.0; resident_set = 0.0; @@ -387,7 +439,7 @@ void MothurOut::gobble(istream& f){ char d; while(isspace(d=f.get())) { ;} - f.putback(d); + if(!f.eof()) { f.putback(d); } } catch(exception& e) { errorOut(e, "MothurOut", "gobble"); @@ -399,7 +451,7 @@ void MothurOut::gobble(istringstream& f){ try { char d; while(isspace(d=f.get())) {;} - f.putback(d); + if(!f.eof()) { f.putback(d); } } catch(exception& e) { errorOut(e, "MothurOut", "gobble"); @@ -457,7 +509,7 @@ string MothurOut::getline(ifstream& fileHandle) { } /***********************************************************************/ -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_COMPRESSION inline bool endsWith(string s, const char * suffix){ size_t suffixLength = strlen(suffix); @@ -471,7 +523,7 @@ string MothurOut::getRootName(string longName){ string rootName = longName; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_COMPRESSION if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) { int pos = rootName.find_last_of('.'); @@ -515,6 +567,21 @@ string MothurOut::getSimpleName(string longName){ /***********************************************************************/ +int MothurOut::getRandomIndex(int highest){ + try { + + int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0)); + + return random; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getRandomIndex"); + exit(1); + } + +} +/**********************************************************************/ + string MothurOut::getPathName(string longName){ try { string rootPathName = longName; @@ -534,6 +601,48 @@ string MothurOut::getPathName(string longName){ } /***********************************************************************/ +bool MothurOut::dirCheck(string& dirName){ + try { + + string tag = ""; + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + tag = toString(pid); + #endif + + //add / to name if needed + string lastChar = dirName.substr(dirName.length()-1); + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + if (lastChar != "/") { dirName += "/"; } + #else + if (lastChar != "\\") { dirName += "\\"; } + #endif + + //test to make sure directory exists + dirName = getFullPathName(dirName); + string outTemp = dirName + tag + "temp"; + ofstream out; + out.open(outTemp.c_str(), ios::trunc); + if(!out) { + mothurOut(dirName + " directory does not exist or is not writable."); mothurOutEndLine(); + }else{ + out.close(); + mothurRemove(outTemp); + return true; + } + + return false; + } + catch(exception& e) { + errorOut(e, "MothurOut", "dirCheck"); + exit(1); + } + +} +/***********************************************************************/ + string MothurOut::hasPath(string longName){ try { string path = ""; @@ -557,7 +666,7 @@ string MothurOut::hasPath(string longName){ string MothurOut::getExtension(string longName){ try { - string extension = longName; + string extension = ""; if(longName.find_last_of('.') != longName.npos){ int pos = longName.find_last_of('.'); @@ -611,7 +720,7 @@ string MothurOut::getFullPathName(string fileName){ string cwd; //get current working directory - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if (path.find("~") != -1) { //go to home directory string homeDir; @@ -664,7 +773,7 @@ string MothurOut::getFullPathName(string fileName){ }else if (path[(pos-1)] == '/') { //you want the current working dir ./ path = path.substr(0, pos); }else if (pos == 1) { break; //you are at the end - }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + }else { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; } } for (int i = index; i >= 0; i--) { @@ -710,7 +819,7 @@ string MothurOut::getFullPathName(string fileName){ }else if (path[(pos-1)] == '\\') { //you want the current working dir ./ path = path.substr(0, pos); }else if (pos == 1) { break; //you are at the end - }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + }else { mothurOut("cannot resolve path for " + fileName + "\n"); return fileName; } } for (int i = index; i >= 0; i--) { @@ -734,7 +843,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){ try { //get full path name string completeFileName = getFullPathName(fileName); -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_COMPRESSION // check for gzipped or bzipped file if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) { @@ -749,7 +858,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){ cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n"; system(command.c_str()); cerr << "Done decompressing " << completeFileName << "\n"; - remove(tempName.c_str()); + mothurRemove(tempName); exit(EXIT_SUCCESS); } else { cerr << "waiting on child process " << fork_result << "\n"; @@ -780,7 +889,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){ //get full path name string completeFileName = getFullPathName(fileName); -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_COMPRESSION // check for gzipped or bzipped file if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) { @@ -795,7 +904,7 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){ cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n"; system(command.c_str()); cerr << "Done decompressing " << completeFileName << "\n"; - remove(tempName.c_str()); + mothurRemove(tempName); exit(EXIT_SUCCESS); } else { cerr << "waiting on child process " << fork_result << "\n"; @@ -829,10 +938,10 @@ int MothurOut::renameFile(string oldName, string newName){ try { ifstream inTest; int exist = openInputFile(newName, inTest, ""); + inTest.close(); - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if (exist == 0) { //you could open it so you want to delete it - inTest.close(); string command = "rm " + newName; system(command.c_str()); } @@ -840,7 +949,7 @@ int MothurOut::renameFile(string oldName, string newName){ string command = "mv " + oldName + " " + newName; system(command.c_str()); #else - remove(newName.c_str()); + mothurRemove(newName); int renameOk = rename(oldName.c_str(), newName.c_str()); #endif return 0; @@ -858,7 +967,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){ try { string completeFileName = getFullPathName(fileName); -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_COMPRESSION // check for gzipped file if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) { @@ -896,7 +1005,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){ } /**************************************************************************************************/ -void MothurOut::appendFiles(string temp, string filename) { +int MothurOut::appendFiles(string temp, string filename) { try{ ofstream output; ifstream input; @@ -906,15 +1015,19 @@ void MothurOut::appendFiles(string temp, string filename) { int ableToOpen = openInputFile(temp, input, "no error"); //int ableToOpen = openInputFile(temp, input); + int numLines = 0; if (ableToOpen == 0) { //you opened it - while(char c = input.get()){ + while(!input.eof()){ + char c = input.get(); if(input.eof()) { break; } - else { output << c; } + else { output << c; if (c == '\n') {numLines++;} } } input.close(); } output.close(); + + return numLines; } catch(exception& e) { errorOut(e, "MothurOut", "appendFiles"); @@ -931,7 +1044,7 @@ string MothurOut::sortFile(string distFile, string outputDir){ //if you can, use the unix sort since its been optimized for years - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) string command = "sort -n -k +3 " + distFile + " -o " + outfile; system(command.c_str()); #else //you are stuck with my best attempt... @@ -976,8 +1089,8 @@ string MothurOut::sortFile(string distFile, string outputDir){ output.close(); //remove temp files - remove(tempDistFile.c_str()); - remove(tempOutfile.c_str()); + mothurRemove(tempDistFile); + mothurRemove(tempOutfile); #endif return outfile; @@ -988,19 +1101,27 @@ string MothurOut::sortFile(string distFile, string outputDir){ } } /**************************************************************************************************/ -vector MothurOut::setFilePosFasta(string filename, int& num) { +vector MothurOut::setFilePosFasta(string filename, int& num) { try { - vector positions; + vector positions; ifstream inFASTA; - openInputFile(filename, inFASTA); + //openInputFile(filename, inFASTA); + inFASTA.open(filename.c_str(), ios::binary); string input; + unsigned long long count = 0; while(!inFASTA.eof()){ - input = getline(inFASTA); - if (input.length() != 0) { - if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + //input = getline(inFASTA); + //cout << input << '\t' << inFASTA.tellg() << endl; + //if (input.length() != 0) { + // if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); cout << (pos - input.length() - 1) << endl; } + //} + //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions + char c = inFASTA.get(); count++; + if (c == '>') { + positions.push_back(count-1); + //cout << count << endl; } - gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions } inFASTA.close(); @@ -1018,7 +1139,7 @@ vector MothurOut::setFilePosFasta(string filename, int& num) fclose (pFile); }*/ - unsigned long int size = positions[(positions.size()-1)]; + unsigned long long size = positions[(positions.size()-1)]; ifstream in; openInputFile(filename, in); @@ -1031,6 +1152,7 @@ vector MothurOut::setFilePosFasta(string filename, int& num) in.close(); positions.push_back(size); + positions[0] = 0; return positions; } @@ -1040,31 +1162,51 @@ vector MothurOut::setFilePosFasta(string filename, int& num) } } /**************************************************************************************************/ -vector MothurOut::setFilePosEachLine(string filename, int& num) { +vector MothurOut::setFilePosEachLine(string filename, int& num) { try { filename = getFullPathName(filename); - vector positions; + vector positions; ifstream in; - openInputFile(filename, in); - + //openInputFile(filename, in); + in.open(filename.c_str(), ios::binary); + string input; + unsigned long long count = 0; + positions.push_back(0); + while(!in.eof()){ - unsigned long int lastpos = in.tellg(); - input = getline(in); - if (input.length() != 0) { - unsigned long int pos = in.tellg(); - if (pos != -1) { positions.push_back(pos - input.length() - 1); } - else { positions.push_back(lastpos); } + //unsigned long long lastpos = in.tellg(); + //input = getline(in); + //if (input.length() != 0) { + //unsigned long long pos = in.tellg(); + //if (pos != -1) { positions.push_back(pos - input.length() - 1); } + //else { positions.push_back(lastpos); } + //} + //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions + + + //getline counting reads + char d = in.get(); count++; + while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) { + //get next character + d = in.get(); + count++; } - gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions + + if (!in.eof()) { + d=in.get(); count++; + while(isspace(d) && (d != in.eof())) { d=in.get(); count++;} + } + positions.push_back(count-1); + //cout << count-1 << endl; } in.close(); - num = positions.size(); + num = positions.size()-1; FILE * pFile; - unsigned long int size; + unsigned long long size; //get num bytes in file pFile = fopen (filename.c_str(),"rb"); @@ -1075,7 +1217,7 @@ vector MothurOut::setFilePosEachLine(string filename, int& nu fclose (pFile); } - positions.push_back(size); + positions[(positions.size()-1)] = size; return positions; } @@ -1086,17 +1228,16 @@ vector MothurOut::setFilePosEachLine(string filename, int& nu } /**************************************************************************************************/ -vector MothurOut::divideFile(string filename, int& proc) { +vector MothurOut::divideFile(string filename, int& proc) { try{ - - vector filePos; + vector filePos; filePos.push_back(0); FILE * pFile; - unsigned long int size; + unsigned long long size; filename = getFullPathName(filename); - + //get num bytes in file pFile = fopen (filename.c_str(),"rb"); if (pFile==NULL) perror ("Error opening file"); @@ -1105,9 +1246,11 @@ vector MothurOut::divideFile(string filename, int& proc) { size=ftell (pFile); fclose (pFile); } - + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + //estimate file breaks - unsigned long int chunkSize = 0; + unsigned long long chunkSize = 0; chunkSize = size / proc; //file to small to divide by processors @@ -1115,21 +1258,24 @@ vector MothurOut::divideFile(string filename, int& proc) { //for each process seekg to closest file break and search for next '>' char. make that the filebreak for (int i = 0; i < proc; i++) { - unsigned long int spot = (i+1) * chunkSize; + unsigned long long spot = (i+1) * chunkSize; ifstream in; openInputFile(filename, in); in.seekg(spot); //look for next '>' - unsigned long int newSpot = spot; + unsigned long long newSpot = spot; while (!in.eof()) { char c = in.get(); + if (c == '>') { in.putback(c); newSpot = in.tellg(); break; } + else if (int(c) == -1) { break; } + } //there was not another sequence before the end of the file - unsigned long int sanityPos = in.tellg(); + unsigned long long sanityPos = in.tellg(); if (sanityPos == -1) { break; } else { filePos.push_back(newSpot); } @@ -1139,14 +1285,18 @@ vector MothurOut::divideFile(string filename, int& proc) { //save end pos filePos.push_back(size); - + //sanity check filePos for (int i = 0; i < (filePos.size()-1); i++) { if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; } } proc = (filePos.size() - 1); - +#else + mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine(); + proc=1; + filePos.push_back(size); +#endif return filePos; } catch(exception& e) { @@ -1158,7 +1308,7 @@ vector MothurOut::divideFile(string filename, int& proc) { int MothurOut::divideFile(string filename, int& proc, vector& files) { try{ - vector filePos = divideFile(filename, proc); + vector filePos = divideFile(filename, proc); for (int i = 0; i < (filePos.size()-1); i++) { @@ -1166,7 +1316,7 @@ int MothurOut::divideFile(string filename, int& proc, vector& files) { ifstream in; openInputFile(filename, in); in.seekg(filePos[i]); - unsigned long int size = filePos[(i+1)] - filePos[i]; + unsigned long long size = filePos[(i+1)] - filePos[i]; char* chunk = new char[size]; in.read(chunk, size); in.close(); @@ -1230,6 +1380,61 @@ float MothurOut::ceilDist(float dist, int precision){ } } /**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map& nameMap) { + try { + + //open input file + ifstream in; + openInputFile(namefile, in); + + while (!in.eof()) { + if (control_pressed) { break; } + + string firstCol, secondCol; + in >> firstCol >> secondCol; gobble(in); + + nameMap[firstCol] = secondCol; + } + in.close(); + + return nameMap.size(); + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map >& nameMap) { + try { + + //open input file + ifstream in; + openInputFile(namefile, in); + + while (!in.eof()) { + if (control_pressed) { break; } + + string firstCol, secondCol; + in >> firstCol >> secondCol; gobble(in); + + vector temp; + splitAtComma(secondCol, temp); + + nameMap[firstCol] = temp; + } + in.close(); + + return nameMap.size(); + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} +/**********************************************************************************************************************/ map MothurOut::readNames(string namefile) { try { @@ -1318,7 +1523,123 @@ int MothurOut::getNumNames(string names){ exit(1); } } +/***********************************************************************/ +int MothurOut::getNumChar(string line, char c){ + try { + int count = 0; + + if(line != ""){ + for(int i=0;i > MothurOut::binomial(int maxOrder){ @@ -1644,6 +1965,25 @@ void MothurOut::splitAtComma(string& estim, vector& container) { exit(1); } } +/***********************************************************************/ +//This function splits up the various option parameters +void MothurOut::splitAtChar(string& prefix, string& suffix, char c){ + try { + prefix = suffix.substr(0,suffix.find_first_of(c)); + if ((suffix.find_first_of(c)+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string + suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length()); + string space = " "; + while(suffix.at(0) == ' ') + suffix = suffix.substr(1, suffix.length()); + } + + } + catch(exception& e) { + errorOut(e, "MothurOut", "splitAtComma"); + exit(1); + } +} + /***********************************************************************/ //This function splits up the various option parameters @@ -1860,6 +2200,46 @@ bool MothurOut::isContainingOnlyDigits(string input) { } } /**************************************************************************************************/ +int MothurOut::removeConfidences(string& tax) { + try { + + string taxon; + string newTax = ""; + + while (tax.find_first_of(';') != -1) { + + if (control_pressed) { return 0; } + + //get taxon + taxon = tax.substr(0,tax.find_first_of(';')); + + int pos = taxon.find_last_of('('); + if (pos != -1) { + //is it a number? + int pos2 = taxon.find_last_of(')'); + if (pos2 != -1) { + string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1))); + if (isNumeric1(confidenceScore)) { + taxon = taxon.substr(0, pos); //rip off confidence + } + } + } + taxon += ";"; + + tax = tax.substr(tax.find_first_of(';')+1, tax.length()); + newTax += taxon; + } + + tax = newTax; + + return 0; + } + catch(exception& e) { + errorOut(e, "MothurOut", "removeConfidences"); + exit(1); + } +} +/**************************************************************************************************/