//
#include "createdatabasecommand.h"
-#include "sequence.hpp"
#include "inputdata.h"
//**********************************************************************************************************************
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 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";
+ helpString += "The group file is optional and will just give you the abundance breakdown by group.\n";
+ helpString += "The label parameter allows you to specify a label to be used from your listfile.\n";
+ helpString += "NOTE: Make SURE the repfasta, repnames and contaxonomy are for the same label as the listfile.\n";
helpString += "The create.database command should be in the following format: \n";
helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, name=final.an.0.03.rep.names, list=fina.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
}
}
//**********************************************************************************************************************
+CreateDatabaseCommand::CreateDatabaseCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["database"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+CreateDatabaseCommand::CreateDatabaseCommand(string option) {
+ try{
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if (option == "help") {
+ help(); abort = true; calledHelp = true;
+ }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["database"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("list");
+ //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["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("repname");
+ //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["repname"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("contaxonomy");
+ //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["contaxonomy"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("repfasta");
+ //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["repfasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+ }
+
+
+ //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 = ""; }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not found") {
+ //if there is a current list file, use it
+ 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 if (listfile == "not open") { abort = true; }
+ else { m->setListFile(listfile); }
+
+ contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
+ if (contaxonomyfile == "not found") { //if there is a current list file, use it
+ contaxonomyfile = ""; m->mothurOut("The contaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
+ }
+ else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
+
+ repfastafile = validParameter.validFile(parameters, "repfasta", true);
+ if (repfastafile == "not found") { //if there is a current list file, use it
+ repfastafile = ""; m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
+ }
+ else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
+
+ repnamesfile = validParameter.validFile(parameters, "repname", true);
+ if (repnamesfile == "not found") { //if there is a current list file, use it
+ repnamesfile = ""; m->mothurOut("The repnames parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
+ }
+ else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your listfile.\n");}
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int CreateDatabaseCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //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);
+
+ if (m->control_pressed) { return 0; }
+
+ vector<Sequence> seqs;
+ vector<int> repOtusSizes = readFasta(seqs);
+
+ 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 = readNames(repNames);
+
+ //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; }
+
+ //are there the same number of OTUs in the tax and fasta file
+ if (classifyOtuSizes.size() != repOtusSizes.size()) { m->mothurOut("[ERROR]: you have " + toString(classifyOtuSizes.size()) + " taxonomies in your contaxonomy 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 have the same number of OTUs. Are the sizes we have found so far accurate?
+ for (int i = 0; i < classifyOtuSizes.size(); i++) {
+ if (classifyOtuSizes[i] != repOtusSizes[i]) {
+ m->mothurOut("[ERROR]: OTU size info does not match for bin " + toString(i+1) + ". The contaxonomy file indicated the OTU represented " + toString(classifyOtuSizes[i]) + " sequences, but the repfasta file had " + toString(repOtusSizes[i]) + ". These should match. Make sure you are using files for the same distance.\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)) + "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 (m->control_pressed) { break; }
+
+ out << (i+1) << '\t';
+
+ 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;
+ }
+
+ m->splitAtComma(bin, binNames);
+
+ //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;
+ }
+
+ //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;
+ }
+ out.close();
+
+ delete list;
+ if (groupfile != "") { delete groupmap; }
+
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies){
+ try {
+
+ vector<int> sizes;
+
+ ifstream in;
+ m->openInputFile(contaxonomyfile, in);
+
+ //read headers
+ m->getline(in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string otu = ""; string tax = "unknown";
+ int size = 0;
+
+ in >> otu >> size >> tax; m->gobble(in);
+
+ sizes.push_back(size);
+ taxonomies.push_back(tax);
+ }
+ in.close();
+
+ return sizes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "readTax");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
+ try {
+
+ vector<int> sizes;
+
+ ifstream in;
+ m->openInputFile(repfastafile, in);
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string binInfo;
+ Sequence seq(in, binInfo, true); m->gobble(in);
+
+ //the binInfo should look like - binNumber|size ie. 1|200 if it is binNumber|size|group then the user gave us the wrong repfasta file
+ vector<string> info;
+ m->splitAtChar(binInfo, info, '|');
+ if (info.size() != 2) { m->mothurOut("[ERROR]: your repfasta file is not the right format. The create database command is designed to be used with the output from get.oturep. When running get.oturep you can not use a group file, because mothur is only expecting one representative sequence per OTU and when you use a group file with get.oturep a representative is found for each group.\n"); m->control_pressed = true; break;}
+
+ int size = 0;
+ m->mothurConvert(info[1], size);
+
+ sizes.push_back(size);
+ seqs.push_back(seq);
+ }
+ in.close();
+
+ return sizes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "readFasta");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int CreateDatabaseCommand::readNames(map<string, string>& nameMap) {
+ try {
+
+ //open input file
+ ifstream in;
+ m->openInputFile(repnamesfile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; m->gobble(in);
+
+ nameMap[secondCol] = firstCol;
+ }
+ in.close();
+
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "readNames");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ListVector* CreateDatabaseCommand::getList(){
+ try {
+ InputData* input = new InputData(listfile, "list");
+ ListVector* list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ if (label == "") { label = lastLabel; delete input; return list; }
+
+ //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((list != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { delete input; return list; }
+
+ if(labels.count(list->getLabel()) == 1){
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = list->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ delete list;
+ list = input->getListVector();
+ }
+
+
+ if (m->control_pressed) { delete input; return list; }
+
+ //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) {
+ delete list;
+ list = input->getListVector(lastLabel);
+ }
+
+ delete input;
+
+ return list;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "getList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
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