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 pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pconstaxonomy);
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);
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, 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 create.database command parameters are repfasta, list, shared, repname, constaxonomy, group, count and label. List, repfasta, repnames or count, and constaxonomy 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 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 constaxonomy 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";
if (path == "") { parameters["repname"] = inputDir + it->second; }
}
- it = parameters.find("contaxonomy");
+ it = parameters.find("constaxonomy");
//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; }
+ if (path == "") { parameters["constaxonomy"] = inputDir + it->second; }
}
it = parameters.find("repfasta");
if (sharedfile != "") { if (outputDir == "") { outputDir = m->hasPath(sharedfile); } }
else { if (outputDir == "") { outputDir = m->hasPath(listfile); } }
- contaxonomyfile = validParameter.validFile(parameters, "contaxonomy", true);
+ contaxonomyfile = validParameter.validFile(parameters, "constaxonomy", 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;
+ contaxonomyfile = ""; m->mothurOut("The constaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
}
else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
}
repNames = tempRepNames;
}else {
- ct.readTable(countfile, true);
+ ct.readTable(countfile, true, false);
numUniqueNamesFile = ct.getNumUniqueSeqs();
nameMap = ct.getNameMap();
}
header += "repSeqName\trepSeq\tOTUConTaxonomy";
out << header << endl;
+ vector<string> binLabels = list->getLabels();
for (int i = 0; i < list->getNumBins(); i++) {
+ int index = findIndex(otuLabels, binLabels[i]);
+ if (index == -1) { m->mothurOut("[ERROR]: " + binLabels[i] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
+
if (m->control_pressed) { break; }
- out << otuLabels[i] << '\t';
+ out << otuLabels[index] << '\t';
vector<string> binNames;
string bin = list->get(i);
if (countfile == "") {
sort(binNames.begin(), binNames.end());
bin = "";
- for (int i = 0; i < binNames.size()-1; i++) {
- bin += binNames[i] + ',';
+ for (int j = 0; j < binNames.size()-1; j++) {
+ bin += binNames[j] + ',';
}
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;
+ m->mothurOut("[ERROR: OTU " + otuLabels[index] + " 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;
+ if (binNames.size() != classifyOtuSizes[index]) {
+ m->mothurOut("[ERROR: OTU " + otuLabels[index] + " contains " + toString(binNames.size()) + " 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;
}
}else {
//find rep sequence in bin
}
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;
+ m->mothurOut("[ERROR: OTU " + otuLabels[index] + " 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;
+ m->mothurOut("[ERROR: OTU " + otuLabels[index] + " contains " + toString(numSeqsRep) + " 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;
}
}
}else { out << numSeqsRep << '\t'; }
//output repSeq
- out << seqRepName << '\t' << seqs[i].getAligned() << '\t' << taxonomies[i] << endl;
+ out << seqRepName << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
}
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; }
+ int index = findIndex(otuLabels, m->currentSharedBinLabels[h]);
+ if (index == -1) { m->mothurOut("[ERROR]: " + m->currentSharedBinLabels[h] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
if (m->control_pressed) { break; }
//sanity check
if (totalAbund != classifyOtuSizes[index]) {
- 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;
+ m->mothurOut("[WARNING]: OTU " + m->currentSharedBinLabels[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
try {
int index = -1;
for (int i = 0; i < otuLabels.size(); i++) {
- if (otuLabels[i] == label) { index = i; break; }
+ if (m->isLabelEquivalent(otuLabels[i],label)) { index = i; break; }
}
return index;
}
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);
+ m->mothurConvert(m->getSimpleLabel(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;
return lookup;
}
catch(exception& e) {
- m->errorOut(e, "CreateDatabaseCommand", "getList");
+ m->errorOut(e, "CreateDatabaseCommand", "getShared");
exit(1);
}
}
projects / mothur.git / blobdiff