From: westcott Date: Mon, 28 Jun 2010 18:32:11 +0000 (+0000) Subject: added groups option to get.oturep command X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=a8367302932de9be5434e77f6e5829d7609e2aec added groups option to get.oturep command --- diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp index a73fdf6..9dfc8bd 100644 --- a/getoturepcommand.cpp +++ b/getoturepcommand.cpp @@ -12,7 +12,7 @@ #include "readcolumn.h" #include "formatphylip.h" #include "formatcolumn.h" - +#include "sharedutilities.h" //******************************************************************************************************************** @@ -48,7 +48,7 @@ GetOTURepCommand::GetOTURepCommand(string option) { help(); abort = true; } else { //valid paramters for this command - string Array[] = {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision","outputdir","inputdir"}; + string Array[] = {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -172,6 +172,18 @@ GetOTURepCommand::GetOTURepCommand(string option) { sorted = ""; } + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + if (groupfile == "") { + m->mothurOut("You must provide a groupfile to use groups."); m->mothurOutEndLine(); + abort = true; + }else { + splitAtDash(groups, Groups); + } + } + globaldata->Groups = Groups; + string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; } large = isTrue(temp); @@ -193,7 +205,7 @@ GetOTURepCommand::GetOTURepCommand(string option) { void GetOTURepCommand::help(){ try { - m->mothurOut("The get.oturep command parameters are phylip, column, list, fasta, name, group, large, cutoff, precision, sorted and label. The fasta and list parameters are required, as well as phylip or column and name.\n"); + m->mothurOut("The get.oturep command parameters are phylip, column, list, fasta, name, group, large, cutoff, precision, groups, sorted and label. The fasta and list parameters are required, as well as phylip or column and name.\n"); m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n"); m->mothurOut("The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. \n"); m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n"); @@ -202,6 +214,7 @@ void GetOTURepCommand::help(){ m->mothurOut("The default value for label is all labels in your inputfile.\n"); m->mothurOut("The sorted parameter allows you to indicate you want the output sorted. You can sort by sequence name, bin number, bin size or group. The default is no sorting, but your options are name, number, size, or group.\n"); m->mothurOut("The large parameter allows you to indicate that your distance matrix is too large to fit in RAM. The default value is false.\n"); + m->mothurOut("The groups parameter allows you to indicate that you want representative sequences for each group specified for each OTU, group name should be separated by dashes. ex. groups=A-B-C.\n"); m->mothurOut("The get.oturep command outputs a .fastarep and .rep.names file for each distance you specify, selecting one OTU representative for each bin.\n"); m->mothurOut("If you provide a groupfile, then it also appends the names of the groups present in that bin.\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); @@ -321,7 +334,20 @@ int GetOTURepCommand::execute(){ if (large) { inRow.close(); remove(distFile.c_str()); } return 0; } - + + if (groupfile != "") { + //read in group map info. + groupMap = new GroupMap(groupfile); + int error = groupMap->readMap(); + if (error == 1) { delete groupMap; m->mothurOut("Error reading your groupfile. Proceeding without groupfile."); m->mothurOutEndLine(); groupfile = ""; } + + if (Groups.size() != 0) { + SharedUtil* util = new SharedUtil(); + util->setGroups(Groups, groupMap->namesOfGroups, "getoturep"); + delete util; + } + } + //set format to list so input can get listvector globaldata->setFormat("list"); @@ -425,13 +451,6 @@ int GetOTURepCommand::execute(){ delete input; globaldata->ginput = NULL; delete read; - if (groupfile != "") { - //read in group map info. - groupMap = new GroupMap(groupfile); - int error = groupMap->readMap(); - if (error == 1) { delete groupMap; m->mothurOut("Error reading your groupfile. Proceeding without groupfile."); m->mothurOutEndLine(); groupfile = ""; } - } - //read fastafile fasta = new FastaMap(); fasta->readFastaFile(fastafile); @@ -499,16 +518,8 @@ void GetOTURepCommand::readNamesFile() { } } //********************************************************************************************************************** -string GetOTURepCommand::findRep(int bin, ListVector* thisList) { +string GetOTURepCommand::findRep(vector names) { try{ - vector names; - map groups; - map::iterator groupIt; - - //parse names into vector - string binnames = thisList->get(bin); - splitAtComma(binnames, names); - // if only 1 sequence in bin or processing the "unique" label, then // the first sequence of the OTU is the representative one if ((names.size() == 1) || (list->getLabel() == "unique")) { @@ -569,7 +580,7 @@ string GetOTURepCommand::findRep(int bin, ListVector* thisList) { } } } - + return(names[minIndex]); } } @@ -582,28 +593,100 @@ string GetOTURepCommand::findRep(int bin, ListVector* thisList) { //********************************************************************************************************************** int GetOTURepCommand::process(ListVector* processList) { try{ - string nameRep, name, sequence; + string name, sequence; + string nameRep; //create output file if (outputDir == "") { outputDir += hasPath(listfile); } ofstream newNamesOutput; - string outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.names"; - openOutputFile(outputNamesFile, newNamesOutput); - outputNames.push_back(outputNamesFile); - outputNameFiles[outputNamesFile] = processList->getLabel(); + string outputNamesFile; + map filehandles; + + if (Groups.size() == 0) { //you don't want to use groups + outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.names"; + openOutputFile(outputNamesFile, newNamesOutput); + outputNames.push_back(outputNamesFile); + outputNameFiles[outputNamesFile] = processList->getLabel(); + }else{ //you want to use groups + ofstream* temp; + for (int i=0; igetLabel() + "." + Groups[i] + ".rep.names"; + + openOutputFile(outputNamesFile, *(temp)); + outputNames.push_back(outputNamesFile); + outputNameFiles[outputNamesFile] = processList->getLabel() + "." + Groups[i]; + } + } //for each bin in the list vector for (int i = 0; i < processList->size(); i++) { - nameRep = findRep(i, processList); - - if (m->control_pressed) { out.close(); newNamesOutput.close(); return 0; } + if (m->control_pressed) { + out.close(); + if (Groups.size() == 0) { //you don't want to use groups + newNamesOutput.close(); + }else{ + for (int j=0; jget(i) << endl; + string temp = processList->get(i); + vector namesInBin; + splitAtComma(temp, namesInBin); + + if (Groups.size() == 0) { + nameRep = findRep(namesInBin); + newNamesOutput << i << '\t' << nameRep << '\t' << processList->get(i) << endl; + }else{ + map > NamesInGroup; + for (int j=0; jgetGroup(namesInBin[j]); + + if (thisgroup == "not found") { m->mothurOut(namesInBin[j] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + + if (inUsersGroups(thisgroup, Groups)) { //add this name to correct group + NamesInGroup[thisgroup].push_back(namesInBin[j]); + } + } + + //get rep for each group in otu + for (int j=0; j reps; outputNames.push_back(outputFileName); + ofstream out2; + string tempNameFile = filename + ".temp"; + openOutputFile(tempNameFile, out2); + ifstream in; openInputFile(filename, in); int i = 0; while (!in.eof()) { string rep, binnames; - in >> rep >> binnames; gobble(in); + in >> i >> rep >> binnames; gobble(in); + out2 << rep << '\t' << binnames << endl; vector names; splitAtComma(binnames, names); @@ -680,7 +768,6 @@ int GetOTURepCommand::processNames(string filename, string label) { }else { m->mothurOut(rep + " is missing from your fasta or name file, ignoring. Please correct."); m->mothurOutEndLine(); } - i++; } @@ -704,6 +791,9 @@ int GetOTURepCommand::processNames(string filename, string label) { } out.close(); + out2.close(); + + rename(tempNameFile.c_str(), filename.c_str()); return 0; diff --git a/getoturepcommand.h b/getoturepcommand.h index 86c5434..8099a39 100644 --- a/getoturepcommand.h +++ b/getoturepcommand.h @@ -53,13 +53,13 @@ private: ReadMatrix* readMatrix; FormatMatrix* formatMatrix; NameAssignment* nameMap; - string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir; + string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups; ofstream out; ifstream in, inNames, inRow; bool abort, allLines, groupError, large; set labels; //holds labels to be used map nameToIndex; //maps sequence name to index in sparsematrix - vector outputNames; + vector outputNames, Groups; map outputNameFiles; float cutoff; int precision; @@ -70,7 +70,7 @@ private: void readNamesFile(); int process(ListVector*); SeqMap getMap(int); - string findRep(int, ListVector*); // returns the name of the "representative" sequence of given bin + string findRep(vector); // returns the name of the "representative" sequence of given bin or subset of a bin, for groups int processNames(string, string); diff --git a/groupmap.cpp b/groupmap.cpp index bc871c8..d57646e 100644 --- a/groupmap.cpp +++ b/groupmap.cpp @@ -27,7 +27,7 @@ int GroupMap::readMap() { int error = 0; while(fileHandle){ - fileHandle >> seqName; //read from first column + fileHandle >> seqName; gobble(fileHandle); //read from first column fileHandle >> seqGroup; //read from second column if (m->control_pressed) { fileHandle.close(); return 1; } diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp index 182e78d..b92927b 100644 --- a/mgclustercommand.cpp +++ b/mgclustercommand.cpp @@ -166,13 +166,6 @@ int MGClusterCommand::execute(){ list = new ListVector(nameMap->getListVector()); RAbundVector* rabund = new RAbundVector(list->getRAbundVector()); -for (int i = 0; i < list->getNumBins(); i++) { -string bin = list->get(i); -if(bin == "") { -cout << "bin " << i << " is blank."<< endl; -} -} -cout << "after outputting blank bins." << endl; if (m->control_pressed) { delete nameMap; delete read; delete list; delete rabund; return 0; } @@ -215,7 +208,7 @@ cout << "after outputting blank bins." << endl; listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); return 0; } - int count = 0; + //cluster using cluster classes while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){ @@ -234,16 +227,13 @@ cout << "after outputting blank bins." << endl; }else{ rndDist = roundDist(dist, precision); } -cout << "here " << count << '\t' << dist << endl; if(previousDist <= 0.0000 && dist != previousDist){ oldList.setLabel("unique"); printData(&oldList); - Seq2Bin = cluster->getSeqtoBin(); } else if(rndDist != rndPreviousDist){ if (merge) { - Seq2Bin = cluster->getSeqtoBin(); ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist); if (m->control_pressed) { @@ -260,22 +250,20 @@ cout << "here " << count << '\t' << dist << endl; printData(&oldList); } } - //cout << "after merge " << count << '\t' << dist << endl; - count++; + previousDist = dist; rndPreviousDist = rndDist; oldList = *list; + Seq2Bin = cluster->getSeqtoBin(); oldSeq2Bin = Seq2Bin; } if(previousDist <= 0.0000){ oldList.setLabel("unique"); printData(&oldList); - Seq2Bin = cluster->getSeqtoBin(); } else if(rndPreviousDistgetSeqtoBin(); ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist); if (m->control_pressed) { @@ -365,11 +353,9 @@ cout << "here " << count << '\t' << dist << endl; if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){ oldList.setLabel("unique"); printData(&oldList); - Seq2Bin = hcluster->getSeqtoBin(); } else if((rndDist != rndPreviousDist)){ if (merge) { - Seq2Bin = hcluster->getSeqtoBin(); ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist); if (m->control_pressed) { @@ -392,6 +378,7 @@ cout << "here " << count << '\t' << dist << endl; previousDist = seqs[i].dist; rndPreviousDist = rndDist; oldList = *list; + Seq2Bin = cluster->getSeqtoBin(); oldSeq2Bin = Seq2Bin; } } @@ -404,7 +391,6 @@ cout << "here " << count << '\t' << dist << endl; } else if(rndPreviousDistgetSeqtoBin(); ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist); if (m->control_pressed) { @@ -485,16 +471,6 @@ ListVector* MGClusterCommand::mergeOPFs(map binInfo, float dist){ try { //create new listvector so you don't overwrite the clustering ListVector* newList = new ListVector(oldList); -for (int i = 0; i < newList->getNumBins(); i++) { -string bin = newList->get(i); -if(bin == "") { -cout << "bin " << i << " is blank."<< endl; -for (map::iterator itBin = binInfo.begin(); itBin != binInfo.end(); itBin++) { - if (itBin->second == i) { cout << itBin->first << " maps to an empty bin." << endl; } -} -} -} -cout << "after outputting blank bins." << endl; bool done = false; ifstream inOverlap; @@ -546,17 +522,16 @@ cout << "after outputting blank bins." << endl; if(itBin1 == binInfo.end()){ cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1); } if(itBin2 == binInfo.end()){ cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1); } -cout << overlapNode.dist << '\t' << dist << endl; + int binKeep = itBin1->second; int binRemove = itBin2->second; //if not merge bins and update binInfo if(binKeep != binRemove) { - cout << "bin keep = " << binKeep << " bin remove = " << binRemove << endl; + //save names in old bin string names = newList->get(binRemove); - cout << names << endl << endl << endl; - cout << newList->get(binKeep) << endl << endl << endl; + //merge bins into name1s bin newList->set(binKeep, newList->get(binRemove)+','+newList->get(binKeep)); newList->set(binRemove, ""); diff --git a/mothur.h b/mothur.h index c3f61b4..2404a84 100644 --- a/mothur.h +++ b/mothur.h @@ -828,7 +828,13 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err //unique is the smallest line if (label == "unique") { return false; } - else { convert(label, labelFloat); } + else { + if (convertTestFloat(label, labelFloat)) { + convert(label, labelFloat); + }else { //cant convert + return false; + } + } //go through users set and make them floats for(it = userLabels.begin(); it != userLabels.end(); ++it) {