X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.cpp;h=1f1c96b6f203e4f1fa8b1dca2e018c735caa6b9f;hp=f7b0d86bf93ff1c3f1ff6ec4ad62d21d66fc382b;hb=b25ede2ad307ae76f8a610443e0ec3ec69621ce7;hpb=8d341208b0cd0c7a4ff8b77c6b164e06f2f39610 diff --git a/mothurout.cpp b/mothurout.cpp index f7b0d86..1f1c96b 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -23,6 +23,7 @@ set MothurOut::getCurrentTypes() { set types; types.insert("fasta"); + types.insert("summary"); types.insert("accnos"); types.insert("column"); types.insert("design"); @@ -81,6 +82,7 @@ void MothurOut::printCurrentFiles() { if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); } if (counttablefile != "") { mothurOut("count=" + counttablefile); mothurOutEndLine(); } if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); } + if (summaryfile != "") { mothurOut("summary=" + summaryfile); mothurOutEndLine(); } } catch(exception& e) { @@ -115,6 +117,7 @@ bool MothurOut::hasCurrentFiles() { if (flowfile != "") { return true; } if (biomfile != "") { return true; } if (counttablefile != "") { return true; } + if (summaryfile != "") { return true; } if (processors != "1") { return true; } return hasCurrent; @@ -151,6 +154,7 @@ void MothurOut::clearCurrentFiles() { flowfile = ""; biomfile = ""; counttablefile = ""; + summaryfile = ""; processors = "1"; } catch(exception& e) { @@ -344,6 +348,27 @@ void MothurOut::mothurOut(string output) { } } /*********************************************************************************************/ +void MothurOut::mothurOutJustToScreen(string output) { + try { + +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should output to screen +#endif + logger() << output; + +#ifdef USE_MPI + } +#endif + } + catch(exception& e) { + errorOut(e, "MothurOut", "MothurOut"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::mothurOutEndLine() { try { #ifdef USE_MPI @@ -771,6 +796,39 @@ bool MothurOut::dirCheck(string& dirName){ } } +//********************************************************************************************************************** + +map > MothurOut::parseClasses(string classes){ + try { + map > parts; + + //treatment-age + vector pieces; splitAtDash(classes, pieces); // -> treatment, age + + for (int i = 0; i < pieces.size(); i++) { + string category = ""; string value = ""; + bool foundOpen = false; + for (int j = 0; j < pieces[i].length(); j++) { + if (control_pressed) { return parts; } + + if (pieces[i][j] == '<') { foundOpen = true; } + else if (pieces[i][j] == '>') { j += pieces[i].length(); } + else { + if (!foundOpen) { category += pieces[i][j]; } + else { value += pieces[i][j]; } + } + } + vector values; splitAtChar(value, values, '|'); + parts[category] = values; + } + + return parts; + } + catch(exception& e) { + errorOut(e, "MothurOut", "parseClasses"); + exit(1); + } +} /***********************************************************************/ string MothurOut::hasPath(string longName){ @@ -1170,7 +1228,42 @@ int MothurOut::appendFiles(string temp, string filename) { exit(1); } } - +/**************************************************************************************************/ +int MothurOut::appendFilesWithoutHeaders(string temp, string filename) { + try{ + ofstream output; + ifstream input; + + //open output file in append mode + openOutputFileAppend(filename, output); + int ableToOpen = openInputFile(temp, input, "no error"); + //int ableToOpen = openInputFile(temp, input); + + int numLines = 0; + if (ableToOpen == 0) { //you opened it + + string headers = getline(input); gobble(input); + if (debug) { mothurOut("[DEBUG]: skipping headers " + headers +'\n'); } + + char buffer[4096]; + while (!input.eof()) { + input.read(buffer, 4096); + output.write(buffer, input.gcount()); + //count number of lines + for (int i = 0; i < input.gcount(); i++) { if (buffer[i] == '\n') {numLines++;} } + } + input.close(); + } + + output.close(); + + return numLines; + } + catch(exception& e) { + errorOut(e, "MothurOut", "appendFiles"); + exit(1); + } +} /**************************************************************************************************/ string MothurOut::sortFile(string distFile, string outputDir){ try { @@ -1257,15 +1350,15 @@ vector MothurOut::setFilePosFasta(string filename, int& num) char c = inFASTA.get(); count++; if (c == '>') { positions.push_back(count-1); - //cout << count << endl; + if (debug) { mothurOut("[DEBUG]: numSeqs = " + toString(positions.size()) + " count = " + toString(count) + ".\n"); } } } inFASTA.close(); num = positions.size(); - - /*FILE * pFile; - long size; + if (debug) { mothurOut("[DEBUG]: num = " + toString(num) + ".\n"); } + FILE * pFile; + unsigned long long size; //get num bytes in file pFile = fopen (filename.c_str(),"rb"); @@ -1274,9 +1367,9 @@ vector MothurOut::setFilePosFasta(string filename, int& num) fseek (pFile, 0, SEEK_END); size=ftell (pFile); fclose (pFile); - }*/ + } - unsigned long long size = positions[(positions.size()-1)]; + /*unsigned long long size = positions[(positions.size()-1)]; ifstream in; openInputFile(filename, in); @@ -1286,8 +1379,10 @@ vector MothurOut::setFilePosFasta(string filename, int& num) if(in.eof()) { break; } else { size++; } } - in.close(); - + in.close();*/ + + if (debug) { mothurOut("[DEBUG]: size = " + toString(size) + ".\n"); } + positions.push_back(size); positions[0] = 0; @@ -1298,6 +1393,67 @@ vector MothurOut::setFilePosFasta(string filename, int& num) exit(1); } } +//********************************************************************************************************************** +vector MothurOut::readConsTax(string inputfile){ + try { + + vector taxes; + + ifstream in; + openInputFile(inputfile, in); + + //read headers + getline(in); + + while (!in.eof()) { + + if (control_pressed) { break; } + + string otu = ""; string tax = "unknown"; + int size = 0; + + in >> otu >> size >> tax; gobble(in); + consTax temp(otu, tax, size); + taxes.push_back(temp); + } + in.close(); + + return taxes; + } + catch(exception& e) { + errorOut(e, "MothurOut", "readConsTax"); + exit(1); + } +} +//********************************************************************************************************************** +int MothurOut::readConsTax(string inputfile, map& taxes){ + try { + ifstream in; + openInputFile(inputfile, in); + + //read headers + getline(in); + + while (!in.eof()) { + + if (control_pressed) { break; } + + string otu = ""; string tax = "unknown"; + int size = 0; + + in >> otu >> size >> tax; gobble(in); + consTax2 temp(tax, size); + taxes[otu] = temp; + } + in.close(); + + return 0; + } + catch(exception& e) { + errorOut(e, "MothurOut", "readConsTax"); + exit(1); + } +} /**************************************************************************************************/ vector MothurOut::setFilePosEachLine(string filename, int& num) { try { @@ -2180,9 +2336,11 @@ map MothurOut::readNames(string namefile, unsigned long int& numSeq /************************************************************/ int MothurOut::checkName(string& name) { try { - for (int i = 0; i < name.length(); i++) { - if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; } - } + if (modifyNames) { + for (int i = 0; i < name.length(); i++) { + if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; } + } + } return 0; } catch(exception& e) { @@ -2284,7 +2442,9 @@ set MothurOut::readAccnos(string accnosfile){ in.read(buffer, 4096); vector pieces = splitWhiteSpace(rest, buffer, in.gcount()); - for (int i = 0; i < pieces.size(); i++) { checkName(pieces[i]); names.insert(pieces[i]); } + for (int i = 0; i < pieces.size(); i++) { checkName(pieces[i]); + names.insert(pieces[i]); + } } in.close(); @@ -3208,6 +3368,26 @@ vector MothurOut::getAverages(vector< vector >& dists) { exit(1); } } +/**************************************************************************************************/ +double MothurOut::getAverage(vector dists) { + try{ + double average = 0; + + for (int i = 0; i < dists.size(); i++) { + average += dists[i]; + } + + //finds average. + average /= (double) dists.size(); + + return average; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getAverage"); + exit(1); + } +} + /**************************************************************************************************/ vector MothurOut::getStandardDeviation(vector< vector >& dists) { try{