//**********************************************************************************************************************
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", "", "", "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);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("repname", "InputTypes", "", "", "NameCount", "NameCount", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "NameCount", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pcontaxonomy);
+ CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(pshared);
+ 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); }
string CreateDatabaseCommand::getHelpString(){
try {
string helpString = "";
- 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 create.database command reads a list file or a shared file, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, or count file and creates a database file.\n";
+ helpString += "The create.database command parameters are repfasta, list, shared, repname, contaxonomy, group, count and label. List, repfasta, repnames or count, 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 count file is the count file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, count=yourCountFile). If it includes group info, mothur will give you the abundance breakdown by group. \n";
+ helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile, name=yourNameFile).\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 += "Example: create.database(repfasta=final.an.0.03.rep.fasta, repname=final.an.0.03.rep.names, list=final.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;
}
}
}
//**********************************************************************************************************************
-string CreateDatabaseCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CreateDatabaseCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "database") { outputFileName = "database"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CreateDatabaseCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "database") { pattern = "[filename],database"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
CreateDatabaseCommand::CreateDatabaseCommand(){
try {
if (path == "") { parameters["group"] = inputDir + it->second; }
}
+ it = parameters.find("count");
+ //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["count"] = inputDir + it->second; }
+ }
+
it = parameters.find("shared");
//user has given a template file
if(it != parameters.end()){
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;
- }
+ if (repnamesfile == "not found") { repnamesfile = ""; }
else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not found") { countfile = ""; }
+ else if (countfile == "not open") { countfile = ""; abort = true; }
+
+ if ((countfile == "") && (repnamesfile == "")) {
+ //if there is a current name file, use it, else look for current count file
+ string repnamesfile = m->getNameFile();
+ if (repnamesfile != "") { m->mothurOut("Using " + repnamesfile + " as input file for the repname parameter."); m->mothurOutEndLine(); }
+ else {
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("[ERROR]: You must provide a count or repname file."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
//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, 1);
+ map<string, int> nameMap;
+ int numUniqueNamesFile = 0;
+ CountTable ct;
+ if (countfile == "") {
+ numUniqueNamesFile = m->readNames(repnamesfile, repNames, 1);
+ //the repnames file does not have the same order as the list file bins so we need to sort and reassemble for the search below
+ map<string, string> tempRepNames;
+ for (map<string, string>::iterator it = repNames.begin(); it != repNames.end();) {
+ string bin = it->first;
+ vector<string> temp;
+ m->splitAtChar(bin, temp, ',');
+ sort(temp.begin(), temp.end());
+ bin = "";
+ for (int i = 0; i < temp.size()-1; i++) {
+ bin += temp[i] + ',';
+ }
+ bin += temp[temp.size()-1];
+ tempRepNames[bin] = it->second;
+ repNames.erase(it++);
+ }
+ repNames = tempRepNames;
+ }else {
+ ct.readTable(countfile, true);
+ numUniqueNamesFile = ct.getNumUniqueSeqs();
+ nameMap = ct.getNameMap();
+ }
//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; }
- string outputFileName = "";
- if (listfile != "") { outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("database"); }
- else { outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("database"); }
+ map<string, string> variables;
+ if (listfile != "") { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); }
+ else { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); }
+ string outputFileName = getOutputFileName("database", variables);
outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
ofstream out;
if (groupfile != "") {
header = "OTUNumber\t";
for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
+ }else if (countfile != "") {
+ if (ct.hasGroupInfo()) {
+ header = "OTUNumber\t";
+ for (int i = 0; i < ct.getNamesOfGroups().size(); i++) { header += (ct.getNamesOfGroups())[i] + '\t'; }
+ }
}
header += "repSeqName\trepSeq\tOTUConTaxonomy";
out << header << endl;
vector<string> binNames;
string bin = list->get(i);
-
- 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;
- }
-
m->splitAtComma(bin, binNames);
- //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;
+ string seqRepName = "";
+ int numSeqsRep = 0;
+
+ if (countfile == "") {
+ sort(binNames.begin(), binNames.end());
+ bin = "";
+ for (int i = 0; i < binNames.size()-1; i++) {
+ bin += binNames[i] + ',';
+ }
+ bin += binNames[binNames.size()-1];
+ 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;
+ }else { seqRepName = it->second; numSeqsRep = binNames.size(); }
+
+ //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;
+ }
+ }else {
+ //find rep sequence in bin
+ for (int j = 0; j < binNames.size(); j++) {
+ map<string, int>::iterator itNameMap = nameMap.find(binNames[j]); //if you are in the counttable you must be the rep. because get.oturep with a countfile only includes the rep sequences in the rep.count file.
+ if (itNameMap != nameMap.end()) {
+ seqRepName = itNameMap->first;
+ numSeqsRep = itNameMap->second;
+ j += binNames.size();
+ }
+ }
+
+ if (seqRepName == "") {
+ m->mothurOut("[ERROR: OTU " + otuLabels[i] + " is not in the count file. Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
+ }
+
+ if (numSeqsRep != classifyOtuSizes[i]) {
+ m->mothurOut("[ERROR: OTU " + otuLabels[i] + " contains " + toString(numSeqsRep) + " 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
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'; }
+ }else if (countfile != "") {
+ if (ct.hasGroupInfo()) {
+ vector<int> groupCounts = ct.getGroupCounts(seqRepName);
+ for (int j = 0; j < groupCounts.size(); j++) { out << groupCounts[j] << '\t'; }
+ }else { out << numSeqsRep << '\t'; }
+ }else { out << numSeqsRep << '\t'; }
//output repSeq
- out << it->second << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
+ out << seqRepName << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
}
//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;
+ m->mothurOut("[WARNING]: 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
ifstream in;
m->openInputFile(repfastafile, in);
+ set<int> sanity;
while (!in.eof()) {
if (m->control_pressed) { break; }
//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;}
+ //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);
+ int binNumber = 0;
+ string temp = "";
+ for (int i = 0; i < info[0].size(); i++) { if (isspace(info[0][i])) {;}else{temp +=info[0][i]; } }
+ m->mothurConvert(temp, binNumber);
+ set<int>::iterator it = sanity.find(binNumber);
+ if (it != sanity.end()) {
+ 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;
+ }else { sanity.insert(binNumber); }
+
sizes.push_back(size);
seqs.push_back(seq);
}
projects / mothur.git / blobdiff