CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcontaxonomy);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none",false,false); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none",false,false); parameters.push_back(pshared);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
string CreateDatabaseCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The create.database command reads a listfile, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, and creates a database file.\n";
- helpString += "The create.database command parameters are repfasta, list, repname, contaxonomy, group and label. List, repfasta, repnames, and contaxonomy are required.\n";
+ helpString += "The create.database command reads a list file or a shared file, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, and creates a database file.\n";
+ helpString += "The create.database command parameters are repfasta, list, shared, repname, contaxonomy, group and label. List, repfasta, repnames, and contaxonomy are required.\n";
helpString += "The repfasta file is fasta file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
helpString += "The repname file is the name file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile).\n";
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = 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
listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not found") {
- //if there is a current list file, use it
+ if (listfile == "not found") { listfile = ""; }
+ else if (listfile == "not open") { listfile = ""; abort = true; }
+ else { m->setListFile(listfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not found") { sharedfile = ""; }
+ else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else { m->setSharedFile(sharedfile); }
+
+ if ((sharedfile == "") && (listfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to list, then shared
listfile = m->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ else {
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
}
- else if (listfile == "not open") { abort = true; }
- else { m->setListFile(listfile); }
+ else if ((sharedfile != "") && (listfile != "")) { m->mothurOut("When executing a create.database command you must enter ONLY ONE of the following: shared or list."); m->mothurOutEndLine(); abort = true; }
+
+ if (sharedfile != "") { if (outputDir == "") { outputDir = m->hasPath(sharedfile); } }
+ else { if (outputDir == "") { outputDir = m->hasPath(listfile); } }
contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
if (contaxonomyfile == "not found") { //if there is a current list file, use it
//taxonomies holds the taxonomy info for each Otu
//classifyOtuSizes holds the size info of each Otu to help with error checking
vector<string> taxonomies;
- vector<int> classifyOtuSizes = readTax(taxonomies);
+ vector<string> otuLabels;
+ vector<int> classifyOtuSizes = readTax(taxonomies, otuLabels);
if (m->control_pressed) { return 0; }
//names redundants to uniques. backwards to how we normally do it, but each bin is the list file will be a key entry in the map.
map<string, string> repNames;
- int numUniqueNamesFile = m->readNames(repnamesfile, repNames);
+ int numUniqueNamesFile = m->readNames(repnamesfile, repNames, 1);
//are there the same number of otus in the fasta and name files
if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
if (m->control_pressed) { return 0; }
- //at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
- ListVector* list = getList();
-
- if (m->control_pressed) { delete list; return 0; }
- GroupMap* groupmap = NULL;
- if (groupfile != "") {
- groupmap = new GroupMap(groupfile);
- groupmap->readMap();
- }
-
- if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
-
- if (outputDir == "") { outputDir += m->hasPath(listfile); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("database");
+ string outputFileName = "";
+ if (listfile != "") { outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("database"); }
+ else { outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("database"); }
outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
string header = "OTUNumber\tAbundance\t";
- if (groupfile != "") {
- header = "OTUNumber\t";
- for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
- }
- header += "repSeqName\trepSeq\tOTUConTaxonomy";
- out << header << endl;
+
- for (int i = 0; i < list->getNumBins(); i++) {
+ if (listfile != "") {
+ //at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
+ ListVector* list = getList();
- if (m->control_pressed) { break; }
+ if (otuLabels.size() != list->getNumBins()) {
+ m->mothurOut("[ERROR]: you have " + toString(otuLabels.size()) + " otus in your contaxonomy file, but your list file has " + toString(list->getNumBins()) + " otus. These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true; }
- out << (i+1) << '\t';
+ if (m->control_pressed) { delete list; return 0; }
- vector<string> binNames;
- string bin = list->get(i);
-
- map<string, string>::iterator it = repNames.find(bin);
- if (it == repNames.end()) {
- m->mothurOut("[ERROR: OTU " + toString(i+1) + " is not in the repnames file. Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
+ GroupMap* groupmap = NULL;
+ if (groupfile != "") {
+ groupmap = new GroupMap(groupfile);
+ groupmap->readMap();
}
- m->splitAtComma(bin, binNames);
+ if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
- //sanity check
- if (binNames.size() != classifyOtuSizes[i]) {
- m->mothurOut("[ERROR: OTU " + toString(i+1) + " contains " + toString(binNames.size()) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[i]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
+ if (groupfile != "") {
+ header = "OTUNumber\t";
+ for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
}
+ header += "repSeqName\trepSeq\tOTUConTaxonomy";
+ out << header << endl;
- //output abundances
- if (groupfile != "") {
- string groupAbunds = "";
- map<string, int> counts;
- //initialize counts to 0
- for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
+ for (int i = 0; i < list->getNumBins(); i++) {
+
+ if (m->control_pressed) { break; }
+
+ out << otuLabels[i] << '\t';
+
+ vector<string> binNames;
+ string bin = list->get(i);
- //find abundances by group
- bool error = false;
- for (int j = 0; j < binNames.size(); j++) {
- string group = groupmap->getGroup(binNames[j]);
- if (group == "not found") {
- m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
- error = true;
- }else { counts[group]++; }
+ map<string, string>::iterator it = repNames.find(bin);
+ if (it == repNames.end()) {
+ m->mothurOut("[ERROR: OTU " + otuLabels[i] + " is not in the repnames file. Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
}
- //output counts
- for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t'; }
+ m->splitAtComma(bin, binNames);
- if (error) { m->control_pressed = true; }
- }else { out << binNames.size() << '\t'; }
+ //sanity check
+ if (binNames.size() != classifyOtuSizes[i]) {
+ m->mothurOut("[ERROR: OTU " + otuLabels[i] + " contains " + toString(binNames.size()) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[i]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
+ }
+
+ //output abundances
+ if (groupfile != "") {
+ string groupAbunds = "";
+ map<string, int> counts;
+ //initialize counts to 0
+ for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
+
+ //find abundances by group
+ bool error = false;
+ for (int j = 0; j < binNames.size(); j++) {
+ string group = groupmap->getGroup(binNames[j]);
+ if (group == "not found") {
+ m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
+ error = true;
+ }else { counts[group]++; }
+ }
+
+ //output counts
+ for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t'; }
+
+ if (error) { m->control_pressed = true; }
+ }else { out << binNames.size() << '\t'; }
+
+ //output repSeq
+ out << it->second << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
+ }
+
+
+ delete list;
+ if (groupfile != "") { delete groupmap; }
+
+ }else {
+ vector<SharedRAbundVector*> lookup = getShared();
+
+ header = "OTUNumber\t";
+ for (int i = 0; i < lookup.size(); i++) { header += lookup[i]->getGroup() + '\t'; }
+ header += "repSeqName\trepSeq\tOTUConTaxonomy";
+ out << header << endl;
- //output repSeq
- out << it->second << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
+ for (int h = 0; h < lookup[0]->getNumBins(); h++) {
+
+ if (m->control_pressed) { break; }
+
+ int index = findIndex(otuLabels, m->currentBinLabels[h]);
+ if (index == -1) { m->mothurOut("[ERROR]: " + m->currentBinLabels[h] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
+
+ if (m->control_pressed) { break; }
+
+ out << otuLabels[index] << '\t';
+
+ int totalAbund = 0;
+ for (int i = 0; i < lookup.size(); i++) {
+ int abund = lookup[i]->getAbundance(h);
+ totalAbund += abund;
+ out << abund << '\t';
+ }
+
+ //sanity check
+ if (totalAbund != classifyOtuSizes[index]) {
+ m->mothurOut("[ERROR: OTU " + m->currentBinLabels[h] + " contains " + toString(totalAbund) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
+ }
+
+ //output repSeq
+ out << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
+ }
}
out.close();
-
- delete list;
- if (groupfile != "") { delete groupmap; }
-
if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
-vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies){
+int CreateDatabaseCommand::findIndex(vector<string>& otuLabels, string label){
+ try {
+ int index = -1;
+ for (int i = 0; i < otuLabels.size(); i++) {
+ if (otuLabels[i] == label) { index = i; break; }
+ }
+ return index;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "findIndex");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies, vector<string>& otuLabels){
try {
vector<int> sizes;
sizes.push_back(size);
taxonomies.push_back(tax);
+ otuLabels.push_back(otu);
}
in.close();
}
}
//**********************************************************************************************************************
+vector<SharedRAbundVector*> CreateDatabaseCommand::getShared(){
+ try {
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ if (label == "") { label = lastLabel; return lookup; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return lookup; }
+
+ if(labels.count(lookup[0]->getLabel()) == 1){
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ break;
+ }
+
+ 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]; }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors();
+ }
+
+
+ if (m->control_pressed) { return lookup; }
+
+ //output error messages about any remaining user labels
+ set<string>::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) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+ }
+
+ return lookup;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "getList");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
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