X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=normalizesharedcommand.cpp;h=acd8208ea7ebb20a3d3810d254d0b24f5386d4d3;hp=51c755cc6bdc91d767e56c79771bfe1d81fef2c4;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=8742edef7a51b82834289e570d336f5a81ba1f2b diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp index 51c755c..acd8208 100644 --- a/normalizesharedcommand.cpp +++ b/normalizesharedcommand.cpp @@ -12,15 +12,15 @@ //********************************************************************************************************************** vector NormalizeSharedCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared); - CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "",false,false); parameters.push_back(pmethod); - CommandParameter pnorm("norm", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnorm); - CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pmakerelabund); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(prelabund); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "","",false,false,true); parameters.push_back(pmethod); + CommandParameter pnorm("norm", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnorm); + CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pmakerelabund); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -53,8 +53,21 @@ string NormalizeSharedCommand::getHelpString(){ exit(1); } } - - +//********************************************************************************************************************** +string NormalizeSharedCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "shared") { pattern = "[filename],[distance],norm.shared"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "NormalizeSharedCommand", "getOutputPattern"); + exit(1); + } +} //********************************************************************************************************************** NormalizeSharedCommand::NormalizeSharedCommand(){ try { @@ -166,7 +179,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) { else { pickedGroups = true; m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "totalgroup"; } @@ -176,7 +189,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) { if (temp == "not found") { norm = 0; //once you have read, set norm to smallest group number }else { - convert(temp, norm); + m->mothurConvert(temp, norm); if (norm < 0) { m->mothurOut("norm must be positive."); m->mothurOutEndLine(); abort=true; } } @@ -206,18 +219,20 @@ int NormalizeSharedCommand::execute(){ //look for groups whose numseqs is below norm and remove them, warning the user if (norm != 0) { - m->Groups.clear(); + m->clearGroups(); + vector mGroups; vector temp; for (int i = 0; i < lookup.size(); i++) { if (lookup[i]->getNumSeqs() < norm) { m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine(); delete lookup[i]; }else { - m->Groups.push_back(lookup[i]->getGroup()); + mGroups.push_back(lookup[i]->getGroup()); temp.push_back(lookup[i]); } } lookup = temp; + m->setGroups(mGroups); } //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. @@ -240,7 +255,7 @@ int NormalizeSharedCommand::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 < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; } if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ @@ -271,13 +286,13 @@ int NormalizeSharedCommand::execute(){ //prevent memory leak for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->clearGroups(); return 0; } //get next line to process lookup = input->getSharedRAbundVectors(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->clearGroups(); return 0; } //output error messages about any remaining user labels set::iterator it; @@ -314,18 +329,20 @@ int NormalizeSharedCommand::execute(){ //look for groups whose numseqs is below norm and remove them, warning the user if (norm != 0) { - m->Groups.clear(); + m->clearGroups(); + vector mGroups; vector temp; for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i]->getNumSeqs() < norm) { m->mothurOut(lookupFloat[i]->getGroup() + " contains " + toString(lookupFloat[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine(); delete lookupFloat[i]; }else { - m->Groups.push_back(lookupFloat[i]->getGroup()); + mGroups.push_back(lookupFloat[i]->getGroup()); temp.push_back(lookupFloat[i]); } } lookupFloat = temp; + m->setGroups(mGroups); } //set norm to smallest group number @@ -343,7 +360,7 @@ int NormalizeSharedCommand::execute(){ //as long as you are not at the end of the file or done wih the lines you want while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } m->Groups.clear(); return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } m->clearGroups(); return 0; } if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){ @@ -376,13 +393,13 @@ int NormalizeSharedCommand::execute(){ //prevent memory leak for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->clearGroups(); return 0; } //get next line to process lookupFloat = input->getSharedRAbundFloatVectors(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->Groups.clear(); return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); m->clearGroups(); return 0; } //output error messages about any remaining user labels set::iterator it; @@ -411,7 +428,7 @@ int NormalizeSharedCommand::execute(){ } //reset groups parameter - m->Groups.clear(); + m->clearGroups(); delete input; if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;} @@ -445,7 +462,11 @@ int NormalizeSharedCommand::normalize(vector& thisLookUp){ if (pickedGroups) { eliminateZeroOTUS(thisLookUp); } - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + variables["[distance]"] = thisLookUp[0]->getLabel(); + string outputFileName = getOutputFileName("shared",variables); + ofstream out; m->openOutputFile(outputFileName, out); outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName); @@ -536,7 +557,10 @@ int NormalizeSharedCommand::normalize(vector& thisLook //save mothurOut's binLabels to restore for next label vector saveBinLabels = m->currentBinLabels; - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + variables["[distance]"] = thisLookUp[0]->getLabel(); + string outputFileName = getOutputFileName("shared",variables); ofstream out; m->openOutputFile(outputFileName, out); outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName); @@ -628,6 +652,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector& thisl //for each bin vector newBinLabels; + string snumBins = toString(thislookup[0]->getNumBins()); 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; } @@ -643,7 +668,13 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector& thisl newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup()); } //if there is a bin label use it otherwise make one - string binLabel = "Otu" + toString(i+1); + string binLabel = "Otu"; + string sbinNumber = toString(i+1); + if (sbinNumber.length() < snumBins.length()) { + int diff = snumBins.length() - sbinNumber.length(); + for (int h = 0; h < diff; h++) { binLabel += "0"; } + } + binLabel += sbinNumber; if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } newBinLabels.push_back(binLabel); @@ -677,6 +708,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector& //for each bin vector newBinLabels; + string snumBins = toString(thislookup[0]->getNumBins()); 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; } @@ -692,7 +724,13 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector& newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup()); } //if there is a bin label use it otherwise make one - string binLabel = "Otu" + toString(i+1); + string binLabel = "Otu"; + string sbinNumber = toString(i+1); + if (sbinNumber.length() < snumBins.length()) { + int diff = snumBins.length() - sbinNumber.length(); + for (int h = 0; h < diff; h++) { binLabel += "0"; } + } + binLabel += sbinNumber; if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } newBinLabels.push_back(binLabel);