+++ /dev/null
-//
-// createdatabasecommand.cpp
-// Mothur
-//
-// Created by Sarah Westcott on 3/28/12.
-// Copyright (c) 2012 Schloss Lab. All rights reserved.
-//
-
-#include "createdatabasecommand.h"
-#include "inputdata.h"
-
-//**********************************************************************************************************************
-vector<string> CreateDatabaseCommand::setParameters(){
- try {
- 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 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);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "CreateDatabaseCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-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 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";
- helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-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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