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Merge pull request #273 from mothur/Rep_32 

Rep 32
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2 parents ee7be1e + 2ff2527 commit 3f9606aa717d651dc12ab6a0df984c47679bcf03 @mothur-westcott mothur-westcott committed on GitHub Sep 15, 2016
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99 source/commands/createdatabasecommand.cpp
@@ -12,9 +12,9 @@
//**********************************************************************************************************************
vector<string> CreateDatabaseCommand::setParameters(){
try {
- 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 pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("repname", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
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);
@@ -37,8 +37,8 @@ vector<string> CreateDatabaseCommand::setParameters(){
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, or count file and creates a database file.\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 create.database command reads a list file or a shared file, *.cons.taxonomy, and optional *.rep.fasta, *.rep.names, groupfile, or count file and creates a database file.\n";
+ helpString += "The create.database command parameters are repfasta, list, shared, repname, constaxonomy, group, count and label. List or shared 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";
@@ -199,7 +199,7 @@ CreateDatabaseCommand::CreateDatabaseCommand(string option) {
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();
+ m->mothurOut("[ERROR]: No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
abort = true;
}
}
@@ -216,30 +216,20 @@ CreateDatabaseCommand::CreateDatabaseCommand(string option) {
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;
- }
+ if (repfastafile == "not found") { repfastafile = ""; }
else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
repnamesfile = validParameter.validFile(parameters, "repname", true);
if (repnamesfile == "not found") { repnamesfile = ""; }
else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
+ if ((repnamesfile != "") && (repfastafile == "")) { m->mothurOut("[ERROR]: You must provide a repfasta file if you are using a repnames file."); m->mothurOutEndLine();
+ 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; }
else if (groupfile == "not found") { groupfile = ""; }
@@ -271,7 +261,8 @@ int CreateDatabaseCommand::execute(){
if (m->control_pressed) { return 0; }
vector<Sequence> seqs;
- vector<int> repOtusSizes = readFasta(seqs);
+ vector<int> repOtusSizes;
+ if (repfastafile != "") { repOtusSizes = readFasta(seqs); }
if (m->control_pressed) { return 0; }
@@ -280,7 +271,7 @@ int CreateDatabaseCommand::execute(){
map<string, int> nameMap;
int numUniqueNamesFile = 0;
CountTable ct;
- if (countfile == "") {
+ if (repnamesfile != "") {
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;
@@ -298,26 +289,29 @@ int CreateDatabaseCommand::execute(){
repNames.erase(it++);
}
repNames = tempRepNames;
- }else {
+ }else if (countfile != ""){
ct.readTable(countfile, true, false);
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; }
-
- //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 (repfastafile != "") {
+
+ //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; }
+
+ //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;
+ }
}
}
@@ -362,7 +356,9 @@ int CreateDatabaseCommand::execute(){
for (int i = 0; i < ct.getNamesOfGroups().size(); i++) { header += '\t' + (ct.getNamesOfGroups())[i]; }
}
}
- header += "\trepSeqName\trepSeq\tOTUConTaxonomy";
+
+ if (repfastafile != "") { header += "\trepSeqName\trepSeq"; }
+ header += "\tOTUConTaxonomy";
out << header << endl;
vector<string> binLabels = list->getLabels();
@@ -380,9 +376,9 @@ int CreateDatabaseCommand::execute(){
m->splitAtComma(bin, binNames);
string seqRepName = "";
- int numSeqsRep = 0;
+ int numSeqsRep = binNames.size();
- if (countfile == "") {
+ if (repnamesfile != "") {
sort(binNames.begin(), binNames.end());
bin = "";
for (int j = 0; j < binNames.size()-1; j++) {
@@ -399,14 +395,14 @@ int CreateDatabaseCommand::execute(){
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 {
+ }else if ((countfile != "") && (repfastafile != "")) {
//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();
+ j += binNames.size(); //exit loop
}
}
@@ -440,15 +436,25 @@ int CreateDatabaseCommand::execute(){
for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << '\t' << counts[(groupmap->getNamesOfGroups())[j]]; }
if (error) { m->control_pressed = true; }
- }else if (countfile != "") {
+ }else if ((countfile != "") && (repfastafile != "")) {
if (ct.hasGroupInfo()) {
vector<int> groupCounts = ct.getGroupCounts(seqRepName);
for (int j = 0; j < groupCounts.size(); j++) { out << '\t' << groupCounts[j]; }
}else { out << '\t' << numSeqsRep; }
+ }else if ((countfile != "") && (repfastafile == "")) {
+ if (ct.hasGroupInfo()) {
+ vector<int> groupTotals; groupTotals.resize(ct.getNumGroups(), 0);
+ for (int j = 0; j < binNames.size(); j++) {
+ vector<int> groupCounts = ct.getGroupCounts(binNames[j]);
+ for (int k = 0; k < groupCounts.size(); k++) { groupTotals[k] += groupCounts[k]; }
+ }
+ for (int j = 0; j < groupTotals.size(); j++) { out << '\t' << groupTotals[j]; }
+ }else { out << '\t' << numSeqsRep; }
}else { out << '\t' << numSeqsRep; }
//output repSeq
- out << '\t' << seqRepName << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
+ if (repfastafile != "") { out << '\t' << seqRepName << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl; }
+ else { out << '\t' << taxonomies[index] << endl; }
}
@@ -460,7 +466,8 @@ int CreateDatabaseCommand::execute(){
header = "OTUNumber";
for (int i = 0; i < lookup.size(); i++) { header += '\t' + lookup[i]->getGroup(); }
- header += "\trepSeqName\trepSeq\tOTUConTaxonomy";
+ if (repfastafile != "") { header += "\trepSeqName\trepSeq"; }
+ header += "\tOTUConTaxonomy";
out << header << endl;
for (int h = 0; h < lookup[0]->getNumBins(); h++) {
@@ -487,7 +494,8 @@ int CreateDatabaseCommand::execute(){
}
//output repSeq
- out << '\t' << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
+ if (repfastafile != "") { out << '\t' << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl; }
+ else { out << '\t' << taxonomies[index] << endl; }
}
}
out.close();
@@ -539,7 +547,8 @@ vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies, vector<st
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; m->gobble(in);
+ in >> otu >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
sizes.push_back(size);
taxonomies.push_back(tax);
View
3 source/commands/getotulabelscommand.cpp
@@ -305,7 +305,8 @@ int GetOtuLabelsCommand::readClassifyOtu(){
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; m->gobble(in);
+ in >> otu >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (m->debug) { m->mothurOut("Otu=" + otu + ", size=" + toString(size) + ", tax=" + tax + "\n"); }
View
3 source/commands/removeotulabelscommand.cpp
@@ -306,7 +306,8 @@ int RemoveOtuLabelsCommand::readClassifyOtu(){
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; m->gobble(in);
+ in >> otu >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (m->debug) { m->mothurOut("[DEBUG]: " + otu + toString(size) + tax + "\n"); }

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