X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.cpp;h=0f24cb2dc362c679dd16ed0eb7c50444f07e7a6e;hp=713bafd0c2a79ec637abdf9d481a0c96c183ee77;hb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;hpb=3a5dd9e428ab93a6dcdce7912e8ebb977be0b893 diff --git a/mothurout.cpp b/mothurout.cpp index 713bafd..0f24cb2 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -779,6 +779,8 @@ string MothurOut::getPathName(string longName){ bool MothurOut::dirCheck(string& dirName){ try { + if (dirName == "") { return false; } + string tag = ""; #ifdef USE_MPI int pid; @@ -797,7 +799,7 @@ bool MothurOut::dirCheck(string& dirName){ //test to make sure directory exists dirName = getFullPathName(dirName); - string outTemp = dirName + tag + "temp"; + string outTemp = dirName + tag + "temp"+ toString(time(NULL)); ofstream out; out.open(outTemp.c_str(), ios::trunc); if(!out) { @@ -1140,6 +1142,105 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){ exit(1); } } +/***********************************************************************/ +int MothurOut::openInputFileBinary(string fileName, ifstream& fileHandle){ + try { + + //get full path name + string completeFileName = getFullPathName(fileName); +#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")) { + string tempName = string(tmpnam(0)); + mkfifo(tempName.c_str(), 0666); + int fork_result = fork(); + if (fork_result < 0) { + cerr << "Error forking.\n"; + exit(1); + } else if (fork_result == 0) { + string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName; + cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n"; + system(command.c_str()); + cerr << "Done decompressing " << completeFileName << "\n"; + mothurRemove(tempName); + exit(EXIT_SUCCESS); + } else { + cerr << "waiting on child process " << fork_result << "\n"; + completeFileName = tempName; + } + } +#endif +#endif + + fileHandle.open(completeFileName.c_str(), ios::binary); + if(!fileHandle) { + mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine(); + return 1; + } + else { + //check for blank file + gobble(fileHandle); + if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine(); } + + return 0; + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "openInputFileBinary"); + exit(1); + } +} +/***********************************************************************/ +int MothurOut::openInputFileBinary(string fileName, ifstream& fileHandle, string noerror){ + try { + + //get full path name + string completeFileName = getFullPathName(fileName); +#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")) { + string tempName = string(tmpnam(0)); + mkfifo(tempName.c_str(), 0666); + int fork_result = fork(); + if (fork_result < 0) { + cerr << "Error forking.\n"; + exit(1); + } else if (fork_result == 0) { + string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName; + cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n"; + system(command.c_str()); + cerr << "Done decompressing " << completeFileName << "\n"; + mothurRemove(tempName); + exit(EXIT_SUCCESS); + } else { + cerr << "waiting on child process " << fork_result << "\n"; + completeFileName = tempName; + } + } +#endif +#endif + + fileHandle.open(completeFileName.c_str(), ios::binary); + if(!fileHandle) { + //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine(); + return 1; + } + else { + //check for blank file + gobble(fileHandle); + //if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine(); } + + return 0; + } + } + catch(exception& e) { + errorOut(e, "MothurOut", "openInputFileBinary - no error"); + exit(1); + } +} + /***********************************************************************/ int MothurOut::renameFile(string oldName, string newName){ @@ -1289,6 +1390,36 @@ int MothurOut::appendFiles(string temp, string filename) { exit(1); } } +/**************************************************************************************************/ +int MothurOut::appendBinaryFiles(string temp, string filename) { + try{ + ofstream output; + ifstream input; + + //open output file in append mode + openOutputFileBinaryAppend(filename, output); + int ableToOpen = openInputFileBinary(temp, input, "no error"); + + if (ableToOpen == 0) { //you opened it + + char buffer[4096]; + while (!input.eof()) { + input.read(buffer, 4096); + output.write(buffer, input.gcount()); + } + input.close(); + } + + output.close(); + + return ableToOpen; + } + catch(exception& e) { + errorOut(e, "MothurOut", "appendBinaryFiles"); + exit(1); + } +} + /**************************************************************************************************/ int MothurOut::appendFilesWithoutHeaders(string temp, string filename) { try{ @@ -2599,6 +2730,65 @@ int MothurOut::getNumChar(string line, char c){ exit(1); } } +/***********************************************************************/ +string MothurOut::getSimpleLabel(string label){ + try { + string simple = ""; + + //remove OTU or phylo tag + string newLabel1 = ""; + for (int i = 0; i < label.length(); i++) { + if(label[i]>47 && label[i]<58) { //is a digit + newLabel1 += label[i]; + } + } + + int num1; + mothurConvert(newLabel1, num1); + + simple = toString(num1); + + return simple; + } + catch(exception& e) { + errorOut(e, "MothurOut", "isLabelEquivalent"); + exit(1); + } +} +/***********************************************************************/ + +bool MothurOut::isLabelEquivalent(string label1, string label2){ + try { + bool same = false; + + //remove OTU or phylo tag + string newLabel1 = ""; + for (int i = 0; i < label1.length(); i++) { + if(label1[i]>47 && label1[i]<58) { //is a digit + newLabel1 += label1[i]; + } + } + + string newLabel2 = ""; + for (int i = 0; i < label2.length(); i++) { + if(label2[i]>47 && label2[i]<58) { //is a digit + newLabel2 += label2[i]; + } + } + + int num1, num2; + mothurConvert(newLabel1, num1); + mothurConvert(newLabel2, num2); + + if (num1 == num2) { same = true; } + + return same; + } + catch(exception& e) { + errorOut(e, "MothurOut", "isLabelEquivalent"); + exit(1); + } +} //********************************************************************************************************************** bool MothurOut::isSubset(vector bigset, vector subset) { try { @@ -2954,6 +3144,64 @@ void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){ } } /***********************************************************************/ +bool MothurOut::checkLocations(string& filename, string inputDir){ + try { + filename = getFullPathName(filename); + + int ableToOpen; + ifstream in; + ableToOpen = openInputFile(filename, in, "noerror"); + in.close(); + + //if you can't open it, try input location + if (ableToOpen == 1) { + if (inputDir != "") { //default path is set + string tryPath = inputDir + getSimpleName(filename); + mothurOut("Unable to open " + filename + ". Trying input directory " + tryPath); mothurOutEndLine(); + ifstream in2; + ableToOpen = openInputFile(tryPath, in2, "noerror"); + in2.close(); + filename = tryPath; + } + } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (getDefaultPath() != "") { //default path is set + string tryPath = getDefaultPath() + getSimpleName(filename); + mothurOut("Unable to open " + filename + ". Trying default " + tryPath); mothurOutEndLine(); + ifstream in2; + ableToOpen = openInputFile(tryPath, in2, "noerror"); + in2.close(); + filename = tryPath; + } + } + + //if you can't open it its not in current working directory or inputDir, try mothur excutable location + if (ableToOpen == 1) { + string exepath = argv; + string tempPath = exepath; + for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); } + exepath = exepath.substr(0, (tempPath.find_last_of('m'))); + + string tryPath = getFullPathName(exepath) + getSimpleName(filename); + mothurOut("Unable to open " + filename + ". Trying mothur's executable location " + tryPath); mothurOutEndLine(); + ifstream in2; + ableToOpen = openInputFile(tryPath, in2, "noerror"); + in2.close(); + filename = tryPath; + } + + if (ableToOpen == 1) { mothurOut("Unable to open " + filename + "."); mothurOutEndLine(); return false; } + + return true; + } + catch(exception& e) { + errorOut(e, "MothurOut", "checkLocations"); + exit(1); + } +} +/***********************************************************************/ //This function parses the estimator options and puts them in a vector void MothurOut::splitAtChar(string& estim, vector& container, char symbol) {