X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.cpp;h=a462bc7df80d0a0543c6cf9722daeabf4159ca40;hb=4169642e8a8d45f71a4a7241ee02f1b1aae29520;hp=efe99b007d6cd37e823ccca91937f4c38cd26c1b;hpb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a;p=mothur.git diff --git a/catchallcommand.cpp b/catchallcommand.cpp index efe99b0..a462bc7 100644 --- a/catchallcommand.cpp +++ b/catchallcommand.cpp @@ -13,7 +13,7 @@ //********************************************************************************************************************** vector CatchAllCommand::getValidParameters(){ try { - string AlignArray[] = {"sabund","label","inputdir","outputdir"}; + string AlignArray[] = {"sabund","shared","label","inputdir","outputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); return myArray; } @@ -25,6 +25,7 @@ vector CatchAllCommand::getValidParameters(){ //********************************************************************************************************************** CatchAllCommand::CatchAllCommand(){ try { + abort = true; calledHelp = true; //initialize outputTypes vector tempOutNames; outputTypes["csv"] = tempOutNames; @@ -38,7 +39,7 @@ CatchAllCommand::CatchAllCommand(){ //********************************************************************************************************************** vector CatchAllCommand::getRequiredParameters(){ try { - string AlignArray[] = {"sabund"}; + string AlignArray[] = {"sabund","shared","or"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); return myArray; } @@ -62,15 +63,15 @@ vector CatchAllCommand::getRequiredFiles(){ CatchAllCommand::CatchAllCommand(string option) { try { globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string Array[] = {"sabund","label","inputdir","outputdir"}; + string Array[] = {"shared","sabund","label","inputdir","outputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -101,14 +102,31 @@ CatchAllCommand::CatchAllCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["sabund"] = inputDir + it->second; } } + + it = parameters.find("shared"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["shared"] = inputDir + it->second; } + } } //check for required parameters sabundfile = validParameter.validFile(parameters, "sabund", true); if (sabundfile == "not open") { sabundfile = ""; abort = true; } - else if (sabundfile == "not found") { sabundfile = ""; m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; } + else if (sabundfile == "not found") { sabundfile = ""; } else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); } + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + + //check for shared file loaded during read.otu + if (sharedfile == "") { + if (globaldata->getSharedFile() != "") { sharedfile = globaldata->getSharedFile(); } + } + string label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { @@ -116,9 +134,14 @@ CatchAllCommand::CatchAllCommand(string option) { else { allLines = 1; } } + if ((sharedfile == "") && (sabundfile == "")) { m->mothurOut("You must provide a sabund or shared file for the catchall command."); m->mothurOutEndLine(); abort=true; } //if the user changes the output directory command factory will send this info to us in the output parameter - outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sabundfile); } + outputDir = validParameter.validFile(parameters, "outputdir", false); + if (outputDir == "not found"){ + if (sabundfile != "") { outputDir = m->hasPath(sabundfile); } + else { outputDir = m->hasPath(sharedfile); } + } } } @@ -133,9 +156,9 @@ void CatchAllCommand::help(){ try { m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n"); m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n"); - m->mothurOut("The catchall executable must be in a folder called catchall in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n"); + m->mothurOut("The catchall executable must be in the same folder as your mothur executable. \n"); m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n"); - m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n"); + m->mothurOut("The catchall command parameters are shared, sabund and label. shared or sabund is required. \n"); m->mothurOut("The label parameter is used to analyze specific labels in your input.\n"); m->mothurOut("The catchall command should be in the following format: \n"); m->mothurOut("catchall(sabund=yourSabundFile) \n"); @@ -151,7 +174,7 @@ void CatchAllCommand::help(){ int CatchAllCommand::execute() { try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } //prepare full output directory outputDir = m->getFullPathName(outputDir); @@ -164,150 +187,200 @@ int CatchAllCommand::execute() { string catchAllCommandExe = ""; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe "; + catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe "; #else - catchAllCommandExe += path + "catchall/CatchAllcmdW.exe "; + catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " "; #endif - read = new ReadOTUFile(sabundfile); - read->read(&*globaldata); - - SAbundVector* sabund = globaldata->sabund; - string lastLabel = sabund->getLabel(); - input = globaldata->ginput; - - set processedLabels; - set userLabels = labels; + vector inputFileNames; + if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); globaldata->setFormat("sabund"); } + else { inputFileNames.push_back(sabundfile); } - //for each label the user selected - while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + for (int p = 0; p < inputFileNames.size(); p++) { + if (inputFileNames.size() > 1) { + m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine(); + } + + InputData* input = new InputData(inputFileNames[p], "sabund"); + SAbundVector* sabund = input->getSAbundVector(); + string lastLabel = sabund->getLabel(); + + set processedLabels; + set userLabels = labels; + + string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary"; + summaryfilename = m->getFullPathName(summaryfilename); + + ofstream out; + m->openOutputFile(summaryfilename, out); + + out << "label\tmodel\testimate\tlci\tuci" << endl; + + //for each label the user selected + while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if(allLines == 1 || labels.count(sabund->getLabel()) == 1){ + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + + //create catchall input file from mothur's inputfile + string filename = process(sabund, inputFileNames[p]); + string outputPath = m->getPathName(filename); - if(allLines == 1 || labels.count(sabund->getLabel()) == 1){ - m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + //create system command + string catchAllCommand = ""; + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1"; + #else + if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); } + catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1"; + //wrap entire string in "" + catchAllCommand = "\"" + catchAllCommand + "\""; + #endif + //run catchall + system(catchAllCommand.c_str()); - //create catchall input file from mothur's inputfile - string filename = process(sabund); - string outputPath = m->getPathName(filename); - - //create system command - string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1"; - - //run catchall - system(catchAllCommand.c_str()); - - remove(filename.c_str()); - - filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . - - outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv"); - outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv"); - outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv"); - outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv"); + remove(filename.c_str()); + + filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . + + outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv"); + outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv"); + outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv"); + outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv"); + + createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out); + + if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; } + + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); + } - createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel()); - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; } + if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = sabund->getLabel(); + + delete sabund; + sabund = (input->getSAbundVector(lastLabel)); + + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + - processedLabels.insert(sabund->getLabel()); - userLabels.erase(sabund->getLabel()); - } - - if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - string saveLabel = sabund->getLabel(); + //create catchall input file from mothur's inputfile + string filename = process(sabund, inputFileNames[p]); + string outputPath = m->getPathName(filename); + + //create system command + string catchAllCommand = ""; + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1"; + #else + if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); } + catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1"; + catchAllCommand = "\"" + catchAllCommand + "\""; + #endif + + //run catchall + system(catchAllCommand.c_str()); - delete sabund; - sabund = (input->getSAbundVector(lastLabel)); + remove(filename.c_str()); - m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); + filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . - - //create catchall input file from mothur's inputfile - string filename = process(sabund); - string outputPath = m->getPathName(filename); + outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv"); + outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv"); + outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv"); + outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv"); - //create system command - string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1"; + createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out); + + if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; } - //run catchall - system(catchAllCommand.c_str()); + processedLabels.insert(sabund->getLabel()); + userLabels.erase(sabund->getLabel()); + + //restore real lastlabel to save below + sabund->setLabel(saveLabel); + } + + + lastLabel = sabund->getLabel(); + + delete sabund; + sabund = (input->getSAbundVector()); + } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; + }else { + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + } + } + + //run last label if you need to + if (needToRun == true) { + if (sabund != NULL) { delete sabund; } + sabund = (input->getSAbundVector(lastLabel)); - remove(filename.c_str()); + m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); - filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . + //create catchall input file from mothur's inputfile + string filename = process(sabund, inputFileNames[p]); + string outputPath = m->getPathName(filename); - outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv"); - outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv"); - outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv"); - outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv"); + //create system command + string catchAllCommand = ""; + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1"; + #else + if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); } + catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1"; + catchAllCommand = "\"" + catchAllCommand + "\""; + #endif - createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel()); + //run catchall + system(catchAllCommand.c_str()); - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read; delete input; globaldata->ginput = NULL; delete sabund; return 0; } - - processedLabels.insert(sabund->getLabel()); - userLabels.erase(sabund->getLabel()); - - //restore real lastlabel to save below - sabund->setLabel(saveLabel); + remove(filename.c_str()); + + filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . + + outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv"); + outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv"); + outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv"); + outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv"); + + createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out); + + delete sabund; } + out.close(); + delete input; - lastLabel = sabund->getLabel(); - - delete sabund; - sabund = (input->getSAbundVector()); + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; } + } - //output error messages about any remaining user labels - set::iterator it; - bool needToRun = false; - for (it = userLabels.begin(); it != userLabels.end(); it++) { - m->mothurOut("Your file does not include the label " + *it); - if (processedLabels.count(lastLabel) != 1) { - m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); - needToRun = true; - }else { - m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + if (sharedfile == "") { + string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary"; + summaryfilename = m->getFullPathName(summaryfilename); + outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename); + }else { //combine summaries + vector sumNames; + for (int i = 0; i < inputFileNames.size(); i++) { + sumNames.push_back(m->getFullPathName(outputDir + m->getRootName(m->getSimpleName(inputFileNames[i])) + "catchall.summary")); } + string summaryfilename = combineSummmary(sumNames); + outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename); } - //run last label if you need to - if (needToRun == true) { - if (sabund != NULL) { delete sabund; } - sabund = (input->getSAbundVector(lastLabel)); - - m->mothurOut(sabund->getLabel()); m->mothurOutEndLine(); - - //create catchall input file from mothur's inputfile - string filename = process(sabund); - string outputPath = m->getPathName(filename); - - //create system command - string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1"; - - //run catchall - system(catchAllCommand.c_str()); - - remove(filename.c_str()); - - filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . - - outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv"); - outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv"); - outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv"); - outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv"); - - createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel()); - - delete sabund; - } - - delete read; - delete input; globaldata->ginput = NULL; - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; } - m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -322,9 +395,9 @@ int CatchAllCommand::execute() { } } //********************************************************************************************************************** -string CatchAllCommand::process(SAbundVector* sabund) { +string CatchAllCommand::process(SAbundVector* sabund, string file1) { try { - string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv"; + string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv"; filename = m->getFullPathName(filename); ofstream out; @@ -347,48 +420,146 @@ string CatchAllCommand::process(SAbundVector* sabund) { exit(1); } } -//********************************************************************************************************************** -string CatchAllCommand::createSummaryFile(string file1, string label) { +//********************************************************************************************************************* +string CatchAllCommand::combineSummmary(vector& outputNames) { try { - string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + label + ".catchall.summary"; - filename = m->getFullPathName(filename); - outputNames.push_back(filename); outputTypes["summary"].push_back(filename); ofstream out; - m->openOutputFile(filename, out); + string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary"; + + //open combined file + m->openOutputFile(combineFileName, out); + + out << "label\tgroup\tmodel\testimate\tlci\tuci" << endl; - out << "group\tmodel\testimate\tlci\tuci" << endl; + //open each groups summary file + string newLabel = ""; + int numLines = 0; + map > files; + for (int i=0; i thisFilesLines; + + ifstream temp; + m->openInputFile(outputNames[i], temp); + + //read through first line - labels + m->getline(temp); + m->gobble(temp); + + //for each label + while (!temp.eof()) { + + string thisLine = ""; + string tempLabel; + + for (int j = 0; j < 5; j++) { + temp >> tempLabel; + + //save for later + if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; } + else{ thisLine += tempLabel + "\t"; } + } + + thisLine += "\n"; + + thisFilesLines.push_back(thisLine); + + m->gobble(temp); + } + + files[outputNames[i]] = thisFilesLines; + + numLines = thisFilesLines.size(); + + temp.close(); + remove(outputNames[i].c_str()); + } + + //for each label + for (int k = 0; k < numLines; k++) { + + //grab summary data for each group + for (int i=0; ierrorOut(e, "CatchAllCommand", "combineSummmary"); + exit(1); + } +} +//********************************************************************************************************************** +int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) { + try { ifstream in; - m->openInputFile(file1, in); + int able = m->openInputFile(file1, in, "noerror"); + if (able == 1) { m->mothurOut("[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.");m->mothurOutEndLine(); m->control_pressed = true; return 0; } + if (!in.eof()) { string header = m->getline(in); m->gobble(in); int pos = header.find("Total Number of Observed Species ="); - cout << pos << '\t' << header.length() << endl; exit(1); + string numString = ""; + + if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); } else { //pos will be the position of the T in total, so we want to count to the position of = pos += 34; char c=header[pos]; - string numString = ""; while (c != ','){ if (c != ' ') { numString += c; } + pos++; + c=header[pos]; + + //sanity check + if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; } } + } + + string firstline = m->getline(in); m->gobble(in); + vector values; + m->splitAtComma(firstline, values); + + values.pop_back(); //last value is always a blank string since the last character in the line is always a ',' + + if (values.size() == 1) { //grab next line if firstline didn't have what you wanted + string secondline = m->getline(in); m->gobble(in); + values.clear(); + m->splitAtComma(secondline, values); - int numOtus; convert(numString, numOtus); - cout << numOtus << endl; + values.pop_back(); //last value is always a blank string since the last character in the line is always a ',' + } + + if (values.size() == 1) { //still not what we wanted fill values with numOTUs + values.resize(8, ""); + values[1] = "Sobs"; + values[4] = numString; + values[6] = numString; + values[7] = numString; } + + if (values.size() < 8) { values.resize(8, ""); } + + out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl; } in.close(); - out.close(); - return filename; + return 0; } catch(exception& e) { @@ -396,7 +567,45 @@ string CatchAllCommand::createSummaryFile(string file1, string label) { exit(1); } } +//********************************************************************************************************************** +vector CatchAllCommand::parseSharedFile(string filename) { + try { + vector filenames; + + //read first line + InputData* input = new InputData(filename, "sharedfile"); + vector lookup = input->getSharedRAbundVectors(); + + string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename)); + + //clears file before we start to write to it below + for (int i=0; igetGroup() + ".sabund").c_str()); + filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund")); + groups.push_back(lookup[i]->getGroup()); + } + + while(lookup[0] != NULL) { + + for (int i = 0; i < lookup.size(); i++) { + SAbundVector sav = lookup[i]->getSAbundVector(); + ofstream out; + m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out); + sav.print(out); + out.close(); + } + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(); + } + + delete input; + + return filenames; + } + catch(exception& e) { + m->errorOut(e, "CatchAllCommand", "parseSharedFile"); + exit(1); + } +} /**************************************************************************************/ - - -