X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=45d1176f9ddafeee56b219529efed45ea3d19d02;hb=8c8acb6218f58f662466e4111ab8aa4da0caf93c;hp=0c25f2a62ed8961cfc8c29080ae37cd2f2d6b77a;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 0c25f2a..45d1176 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -39,6 +39,8 @@ void MothurOut::printCurrentFiles() { if (sharedfile != "") { mothurOut("shared=" + sharedfile); mothurOutEndLine(); } if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); } if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); } + if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); } + if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); } } catch(exception& e) { @@ -46,6 +48,42 @@ void MothurOut::printCurrentFiles() { exit(1); } } +/*********************************************************************************************/ +bool MothurOut::hasCurrentFiles() { + try { + bool hasCurrent = false; + + if (accnosfile != "") { return true; } + if (columnfile != "") { return true; } + if (designfile != "") { return true; } + if (fastafile != "") { return true; } + if (groupfile != "") { return true; } + if (listfile != "") { return true; } + if (namefile != "") { return true; } + if (oligosfile != "") { return true; } + if (orderfile != "") { return true; } + if (ordergroupfile != "") { return true; } + if (phylipfile != "") { return true; } + if (qualfile != "") { return true; } + if (rabundfile != "") { return true; } + if (relabundfile != "") { return true; } + if (sabundfile != "") { return true; } + if (sfffile != "") { return true; } + if (sharedfile != "") { return true; } + if (taxonomyfile != "") { return true; } + if (treefile != "") { return true; } + if (flowfile != "") { return true; } + if (processors != "1") { return true; } + + return hasCurrent; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "hasCurrentFiles"); + exit(1); + } +} + /*********************************************************************************************/ void MothurOut::clearCurrentFiles() { try { @@ -67,7 +105,9 @@ void MothurOut::clearCurrentFiles() { sfffile = ""; oligosfile = ""; accnosfile = ""; - taxonomyfile = ""; + taxonomyfile = ""; + flowfile = ""; + processors = "1"; } catch(exception& e) { errorOut(e, "MothurOut", "clearCurrentFiles"); @@ -207,6 +247,53 @@ 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 + + cout << output; + out << output; + outputFile << 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 + + cout << endl; + out << endl; + outputFile << endl; + +#ifdef USE_MPI + } +#endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOutEndLine"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::mothurOutJustToLog(string output) { try { #ifdef USE_MPI @@ -398,12 +485,12 @@ string MothurOut::getline(ifstream& fileHandle) { string line = ""; - while (!fileHandle.eof()) { + while (fileHandle) { //get next character char c = fileHandle.get(); //are you at the end of the line - if ((c == '\n') || (c == '\r') || (c == '\f')){ break; } + if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){ break; } else { line += c; } } @@ -475,6 +562,21 @@ 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; @@ -709,7 +811,7 @@ 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"; @@ -755,7 +857,7 @@ 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"; @@ -800,7 +902,7 @@ 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; @@ -856,7 +958,7 @@ 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; @@ -866,15 +968,18 @@ 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()){ 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"); @@ -936,8 +1041,8 @@ 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; @@ -948,19 +1053,27 @@ 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(); @@ -978,7 +1091,7 @@ 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); @@ -991,6 +1104,7 @@ vector MothurOut::setFilePosFasta(string filename, int& num) in.close(); positions.push_back(size); + positions[0] = 0; return positions; } @@ -1000,31 +1114,51 @@ 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"); @@ -1035,7 +1169,7 @@ vector MothurOut::setFilePosEachLine(string filename, int& nu fclose (pFile); } - positions.push_back(size); + positions[(positions.size()-1)] = size; return positions; } @@ -1046,14 +1180,14 @@ 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); @@ -1067,7 +1201,7 @@ vector MothurOut::divideFile(string filename, int& proc) { } //estimate file breaks - unsigned long int chunkSize = 0; + unsigned long long chunkSize = 0; chunkSize = size / proc; //file to small to divide by processors @@ -1075,21 +1209,21 @@ 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; } } //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); } @@ -1114,7 +1248,43 @@ vector MothurOut::divideFile(string filename, int& proc) { exit(1); } } - +/**************************************************************************************************/ +int MothurOut::divideFile(string filename, int& proc, vector& files) { + try{ + + vector filePos = divideFile(filename, proc); + + for (int i = 0; i < (filePos.size()-1); i++) { + + //read file chunk + ifstream in; + openInputFile(filename, in); + in.seekg(filePos[i]); + unsigned long long size = filePos[(i+1)] - filePos[i]; + char* chunk = new char[size]; + in.read(chunk, size); + in.close(); + + //open new file + string fileChunkName = filename + "." + toString(i) + ".tmp"; + ofstream out; + openOutputFile(fileChunkName, out); + + out << chunk << endl; + out.close(); + delete[] chunk; + + //save name + files.push_back(fileChunkName); + } + + return 0; + } + catch(exception& e) { + errorOut(e, "MothurOut", "divideFile"); + exit(1); + } +} /***********************************************************************/ bool MothurOut::isTrue(string f){ @@ -1153,6 +1323,33 @@ float MothurOut::ceilDist(float dist, int precision){ 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); + + nameMap[firstCol] = secondCol; + } + in.close(); + + return 0; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} + /**********************************************************************************************************************/ map MothurOut::readNames(string namefile) { try { @@ -1183,6 +1380,42 @@ map MothurOut::readNames(string namefile) { exit(1); } } +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, vector& nameVector, map& fastamap) { + try { + int error = 0; + + //open input file + ifstream in; + openInputFile(namefile, in); + + while (!in.eof()) { + if (control_pressed) { break; } + + string firstCol, secondCol; + in >> firstCol >> secondCol; gobble(in); + + int num = getNumNames(secondCol); + + map::iterator it = fastamap.find(firstCol); + if (it == fastamap.end()) { + error = 1; + mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine(); + }else { + seqPriorityNode temp(num, it->second, firstCol); + nameVector.push_back(temp); + } + } + in.close(); + + return error; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} /***********************************************************************/ @@ -1206,7 +1439,18 @@ int MothurOut::getNumNames(string names){ exit(1); } } +/***********************************************************************/ +void MothurOut::mothurRemove(string filename){ + try { + filename = getFullPathName(filename); + remove(filename.c_str()); + } + catch(exception& e) { + errorOut(e, "MothurOut", "mothurRemove"); + exit(1); + } +} /**************************************************************************************************/ vector > MothurOut::binomial(int maxOrder){ @@ -1730,7 +1974,23 @@ bool MothurOut::checkReleaseVersion(ifstream& file, string version) { exit(1); } } - +/**************************************************************************************************/ +bool MothurOut::isContainingOnlyDigits(string input) { + try{ + + //are you a digit in ascii code + for (int i = 0;i < input.length(); i++){ + if( input[i]>47 && input[i]<58){} + else { return false; } + } + + return true; + } + catch(exception& e) { + errorOut(e, "MothurOut", "isContainingOnlyDigits"); + exit(1); + } +} /**************************************************************************************************/