X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrelabundcommand.cpp;h=08e9228b215819f5e19e4d697137384294392422;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=8293c9b31485bad93f1bb8875f2e53fc28a1d746;hpb=1dc7ed939c314b3057dad3a834e9739fb7ecfbe6;p=mothur.git diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp index 8293c9b..08e9228 100644 --- a/getrelabundcommand.cpp +++ b/getrelabundcommand.cpp @@ -10,7 +10,54 @@ #include "getrelabundcommand.h" //********************************************************************************************************************** - +vector GetRelAbundCommand::getValidParameters(){ + try { + string Array[] = {"groups","label","scale","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +GetRelAbundCommand::GetRelAbundCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["relabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetRelAbundCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetRelAbundCommand::getRequiredFiles(){ + try { + string Array[] = {"shared"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** GetRelAbundCommand::GetRelAbundCommand(string option) { try { globaldata = GlobalData::getInstance(); @@ -36,10 +83,14 @@ GetRelAbundCommand::GetRelAbundCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["relabund"] = tempOutNames; + //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 = ""; - outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it } //make sure the user has already run the read.otu command @@ -52,7 +103,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) { label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } @@ -66,7 +117,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) { if (groups == "not found") { groups = ""; pickedGroups = false; } else { pickedGroups = true; - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } @@ -94,7 +145,7 @@ void GetRelAbundCommand::help(){ m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n"); m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n"); m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n"); - m->mothurOut("Example get.relabund(groups=A-B-C, scale=log10).\n"); + m->mothurOut("Example get.relabund(groups=A-B-C, scale=averagegroup).\n"); m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n"); m->mothurOut("The get.relabund command outputs a .relabund file.\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); @@ -118,9 +169,9 @@ int GetRelAbundCommand::execute(){ if (abort == true) { return 0; } - string outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "relabund"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund"; ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); read = new ReadOTUFile(globaldata->inputFileName); @@ -136,7 +187,7 @@ int GetRelAbundCommand::execute(){ //as long as you are not at the end of the file or done wih the lines you want while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; } if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ @@ -147,7 +198,7 @@ int GetRelAbundCommand::execute(){ userLabels.erase(lookup[0]->getLabel()); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = lookup[0]->getLabel(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } @@ -167,13 +218,13 @@ int GetRelAbundCommand::execute(){ //prevent memory leak for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } - if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; } //get next line to process lookup = input->getSharedRAbundVectors(); } - if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; } //output error messages about any remaining user labels set::iterator it; @@ -206,11 +257,11 @@ int GetRelAbundCommand::execute(){ delete read; out.close(); - if (m->control_pressed) { remove(outputFileName.c_str()); return 0;} + if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;} m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); + m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName); m->mothurOutEndLine(); return 0; @@ -224,16 +275,6 @@ int GetRelAbundCommand::execute(){ int GetRelAbundCommand::getRelAbundance(vector& thisLookUp, ofstream& out){ try { - if (pickedGroups) { eliminateZeroOTUS(thisLookUp); } - - int totalNumSeqs = 0; - if ((scale == "totalgroup") || (scale == "averagegroup")) { - for (int i = 0; i < thisLookUp.size(); i++) { - //find total number of sequences in all samples - totalNumSeqs += thisLookUp[i]->getNumSeqs(); - } - } - float averageNumSeqs = totalNumSeqs / (float) thisLookUp.size(); for (int i = 0; i < thisLookUp.size(); i++) { out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t'; @@ -246,16 +287,15 @@ int GetRelAbundCommand::getRelAbundance(vector& thisLookUp, float relabund = 0.0; - if (scale == "totalgroup") { //abund of this otu compared to total number of sequence in my group - relabund = abund / (float) totalNumSeqs; + if (scale == "totalgroup") { + relabund = abund / (float) thisLookUp[i]->getNumSeqs(); }else if (scale == "totalotu") { //calc the total in this otu int totalOtu = 0; for (int l = 0; l < thisLookUp.size(); l++) { totalOtu += thisLookUp[l]->getAbundance(j); } - relabund = abund / (float) totalOtu; }else if (scale == "averagegroup") { - relabund = abund / (float) averageNumSeqs; + relabund = abund / (float) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins()); }else if (scale == "averageotu") { //calc the total in this otu int totalOtu = 0; @@ -278,48 +318,5 @@ int GetRelAbundCommand::getRelAbundance(vector& thisLookUp, } } //********************************************************************************************************************** -int GetRelAbundCommand::eliminateZeroOTUS(vector& thislookup) { - try { - - vector newLookup; - for (int i = 0; i < thislookup.size(); i++) { - SharedRAbundVector* temp = new SharedRAbundVector(); - temp->setLabel(thislookup[i]->getLabel()); - temp->setGroup(thislookup[i]->getGroup()); - newLookup.push_back(temp); - } - - //for each bin - for (int i = 0; i < thislookup[0]->getNumBins(); i++) { - if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; } - - //look at each sharedRabund and make sure they are not all zero - bool allZero = true; - for (int j = 0; j < thislookup.size(); j++) { - if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; } - } - - //if they are not all zero add this bin - if (!allZero) { - for (int j = 0; j < thislookup.size(); j++) { - newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup()); - } - } - } - - for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } - - thislookup = newLookup; - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "GetRelAbundCommand", "eliminateZeroOTUS"); - exit(1); - } -} - -//**********************************************************************************************************************