it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
it = parameters.find("taxonomy");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; allLines = 1; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
convert(temp, cutoff);
temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
- probs = isTrue(temp);
+ probs = m->isTrue(temp);
if ((cutoff < 51) || (cutoff > 100)) { m->mothurOut("cutoff must be above 50, and no greater than 100."); m->mothurOutEndLine(); abort = true; }
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
try {
ifstream inNames;
- openInputFile(namefile, inNames);
+ m->openInputFile(namefile, inNames);
string name, names;
while(inNames){
inNames >> name; //read from first column A
inNames >> names; //read from second column A,B,C,D
- gobble(inNames);
+ m->gobble(inNames);
- nameMap[name] = names;
+ //parse names into vector
+ vector<string> theseNames;
+ m->splitAtComma(names, theseNames);
+
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = name; }
if (m->control_pressed) { inNames.close(); nameMap.clear(); return 0; }
}
try {
ifstream in;
- openInputFile(taxfile, in);
+ m->openInputFile(taxfile, in);
string name, tax;
while(!in.eof()){
in >> name >> tax;
- gobble(in);
+ m->gobble(in);
//are there confidence scores, if so remove them
if (tax.find_first_of('(') != -1) { removeConfidences(tax); }
//parse names into vector
string binnames = thisList->get(bin);
- splitAtComma(binnames, names);
+ m->splitAtComma(binnames, names);
//create a tree containing sequences from this bin
PhyloTree* phylo = new PhyloTree();
size = 0;
for (int i = 0; i < names.size(); i++) {
-
- if (m->control_pressed) { delete phylo; return conTax; }
-
- //is this sequence in the taxonomy file
- it = taxMap.find(names[i]);
-
- if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
- m->mothurOut(names[i] + " is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine();
- }else{
+
+ //if namesfile include the names
+ if (namefile != "") {
+ //is this sequence in the name file - namemap maps seqName -> repSeqName
+ it2 = nameMap.find(names[i]);
- //if namesfile include the names
- if (namefile != "") {
- //is this sequence in the name file
- it2 = nameMap.find(names[i]);
+ if (it2 == nameMap.end()) { //this name is not in name file, skip it
+ m->mothurOut(names[i] + " is not in your name file. I will not include it in the consensus."); m->mothurOutEndLine();
+ }else{
- if (it2 == nameMap.end()) { //this name is not in name file, skip it
- m->mothurOut(names[i] + " is not in your name file. I will not include it in the consensus."); m->mothurOutEndLine();
+ //is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
+ it = taxMap.find(it2->second);
+
+ if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
+ if (names[i] != it->second) { m->mothurOut(names[i] + " is represented by " + it2->second + " and is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine(); }
+ else { m->mothurOut(names[i] + " is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine(); }
}else{
-
- vector<string> nameFileNames;
- splitAtComma(it2->second, nameFileNames);
-
- for (int j = 0; j < nameFileNames.size(); j++) {
- //add seq to tree
- phylo->addSeqToTree(nameFileNames[j], it->second);
- size++;
- }
+
+ //add seq to tree
+ phylo->addSeqToTree(names[i], it->second);
+ size++;
}
-
+ }
+
+ }else{
+ //is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
+ it = taxMap.find(names[i]);
+
+ if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
+ m->mothurOut(names[i] + " is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine();
}else{
//add seq to tree
phylo->addSeqToTree(names[i], it->second);
size++;
}
}
+
+
+ if (m->control_pressed) { delete phylo; return conTax; }
+
}
//build tree
int size;
//create output file
- if (outputDir == "") { outputDir += hasPath(listfile); }
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
ofstream out;
- string outputFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".cons.taxonomy";
- openOutputFile(outputFile, out);
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".cons.taxonomy";
+ m->openOutputFile(outputFile, out);
outputNames.push_back(outputFile);
//for each bin in the list vector
projects / mothur.git / blobdiff