else {
//valid paramters for this command
- string AlignArray[] = {"template","fasta","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters"};
+ string AlignArray[] = {"template","fasta","name","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
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 (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //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 = ""; }
+
+ //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("template");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["template"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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; }
+ }
+ }
+
//check for required parameters
templateFileName = validParameter.validFile(parameters, "template", true);
if (templateFileName == "not found") {
}
else if (templateFileName == "not open") { abort = true; }
- fastaFileName = validParameter.validFile(parameters, "fasta", true);
- if (fastaFileName == "not found") {
- mothurOut("fasta is a required parameter for the classify.seqs command.");
- mothurOutEndLine();
- abort = true;
+ fastaFileName = validParameter.validFile(parameters, "fasta", false);
+ if (fastaFileName == "not found") { mothurOut("fasta is a required parameter for the classify.seqs command."); mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(fastaFileName, fastaFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+ ableToOpen = openInputFile(fastaFileNames[i], in);
+ if (ableToOpen == 1) {
+ mothurOut(fastaFileNames[i] + " will be disregarded."); mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }
+ in.close();
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
}
- else if (fastaFileName == "not open") { abort = true; }
+
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
if (taxonomyFileName == "not found") {
abort = true;
}
else if (taxonomyFileName == "not open") { abort = true; }
+
+
+ namefile = validParameter.validFile(parameters, "name", false);
+ if (namefile == "not found") { namefile = ""; }
+
+ else {
+ splitAtDash(namefile, namefileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < namefileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(namefileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { namefileNames[i] = inputDir + namefileNames[i]; }
+ }
+ int ableToOpen;
+ ifstream in;
+ ableToOpen = openInputFile(namefileNames[i], in);
+ if (ableToOpen == 1) { mothurOut("Unable to match name file with fasta file."); mothurOutEndLine(); abort = true; }
+ in.close();
+ }
+ }
+
+ if (namefile != "") {
+ if (namefileNames.size() != fastaFileNames.size()) { abort = true; mothurOut("If you provide a name file, you must have one for each fasta file."); mothurOutEndLine(); }
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
void ClassifySeqsCommand::help(){
try {
mothurOut("The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n");
- mothurOut("The classify.seqs command parameters are template, fasta, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n");
- mothurOut("The template, fasta and taxonomy parameters are required.\n");
- mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
+ mothurOut("The classify.seqs command parameters are template, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n");
+ mothurOut("The template, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
+ mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is kmer.\n");
+ mothurOut("The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n");
mothurOut("The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n");
mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
try {
if (abort == true) { return 0; }
- if(method == "bayesian") { classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters); }
- else if(method == "knn") { classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted); }
+ if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters); }
+ else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted); }
else {
mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
mothurOutEndLine();
classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);
}
- int numFastaSeqs = 0;
+
+ for (int s = 0; s < fastaFileNames.size(); s++) {
- string newTaxonomyFile = getRootName(fastaFileName) + getRootName(taxonomyFileName) + "taxonomy";
- string tempTaxonomyFile = getRootName(fastaFileName) + "taxonomy.temp";
- string taxSummary = getRootName(fastaFileName) + getRootName(taxonomyFileName) + "tax.summary";
+ //read namefile
+ if(namefile != "") {
+ nameMap.clear(); //remove old names
+
+ ifstream inNames;
+ openInputFile(namefileNames[s], inNames);
+
+ string firstCol, secondCol;
+ while(!inNames.eof()) {
+ inNames >> firstCol >> secondCol; gobble(inNames);
+ nameMap[firstCol] = getNumNames(secondCol); //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
+ }
+ inNames.close();
+ }
- int start = time(NULL);
+ mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); mothurOutEndLine();
+
+ if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
+ string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
+ string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
+ string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
+
+ int start = time(NULL);
+ int numFastaSeqs = 0;
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[s], inFASTA);
+ numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
+ }
+ else{
+ vector<int> positions;
+ processIDS.resize(0);
+
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[s], inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ }
+ }
+ inFASTA.close();
+
+ numFastaSeqs = positions.size();
+
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+ createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
+
+ rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str());
+ rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str());
+
+ for(int i=1;i<processors;i++){
+ appendTaxFiles((newTaxonomyFile + toString(processIDS[i]) + ".temp"), newTaxonomyFile);
+ appendTaxFiles((tempTaxonomyFile + toString(processIDS[i]) + ".temp"), tempTaxonomyFile);
+ remove((newTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
+ remove((tempTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
+ }
+
+ }
+#else
ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
+ openInputFile(fastaFileNames[s], inFASTA);
numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
inFASTA.close();
lines.push_back(new linePair(0, numFastaSeqs));
-
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile);
- }
- else{
- vector<int> positions;
- processIDS.resize(0);
-
- ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
- string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
- if (input.length() != 0) {
- if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
- }
+ driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
+#endif
+ //make taxonomy tree from new taxonomy file
+ PhyloTree taxaBrowser;
+
+ ifstream in;
+ openInputFile(tempTaxonomyFile, in);
+
+ //read in users taxonomy file and add sequences to tree
+ string name, taxon;
+ while(!in.eof()){
+ in >> name >> taxon; gobble(in);
+
+ if (namefile != "") {
+ itNames = nameMap.find(name);
+
+ if (itNames == nameMap.end()) {
+ mothurOut(name + " is not in your name file please correct."); mothurOutEndLine(); exit(1);
+ }else{
+ for (int i = 0; i < itNames->second; i++) {
+ taxaBrowser.addSeqToTree(name+toString(i), taxon); //add it as many times as there are identical seqs
+ }
+ }
+ }else { taxaBrowser.addSeqToTree(name, taxon); } //add it once
}
- inFASTA.close();
+ in.close();
+
+ taxaBrowser.assignHeirarchyIDs(0);
+
+ taxaBrowser.binUnclassified();
- numFastaSeqs = positions.size();
+ remove(tempTaxonomyFile.c_str());
- int numSeqsPerProcessor = numFastaSeqs / processors;
+ //print summary file
+ ofstream outTaxTree;
+ openOutputFile(taxSummary, outTaxTree);
+ taxaBrowser.print(outTaxTree);
+ outTaxTree.close();
- for (int i = 0; i < processors; i++) {
- int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
- createProcesses(newTaxonomyFile, tempTaxonomyFile);
+ //output taxonomy with the unclassified bins added
+ ifstream inTax;
+ openInputFile(newTaxonomyFile, inTax);
- rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str());
- rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str());
+ ofstream outTax;
+ string unclass = newTaxonomyFile + ".unclass.temp";
+ openOutputFile(unclass, outTax);
- for(int i=1;i<processors;i++){
- appendTaxFiles((newTaxonomyFile + toString(processIDS[i]) + ".temp"), newTaxonomyFile);
- appendTaxFiles((tempTaxonomyFile + toString(processIDS[i]) + ".temp"), tempTaxonomyFile);
- remove((newTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
- remove((tempTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
+ //get maxLevel from phylotree so you know how many 'unclassified's to add
+ int maxLevel = taxaBrowser.getMaxLevel();
+
+ //read taxfile - this reading and rewriting is done to preserve the confidence sscores.
+ while (!inTax.eof()) {
+ inTax >> name >> taxon; gobble(inTax);
+
+ string newTax = addUnclassifieds(taxon, maxLevel);
+
+ outTax << name << '\t' << newTax << endl;
}
+ inTax.close();
+ outTax.close();
+ remove(newTaxonomyFile.c_str());
+ rename(unclass.c_str(), newTaxonomyFile.c_str());
+
+ mothurOutEndLine();
+ mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); mothurOutEndLine(); mothurOutEndLine();
}
-#else
- ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
- driver(lines[0], newTaxonomyFile, tempTaxonomyFile);
-#endif
delete classify;
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "ClassifySeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
+ try{
+ string newTax, taxon;
+ int level = 0;
- //make taxonomy tree from new taxonomy file
- ifstream inTaxonomy;
- openInputFile(tempTaxonomyFile, inTaxonomy);
-
- string accession, taxaList;
- PhyloTree taxaBrowser;
-
- //read in users taxonomy file and add sequences to tree
- while(!inTaxonomy.eof()){
- inTaxonomy >> accession >> taxaList;
-
- taxaBrowser.addSeqToTree(accession, taxaList);
-
- gobble(inTaxonomy);
+ //keep what you have counting the levels
+ while (tax.find_first_of(';') != -1) {
+ //get taxon
+ taxon = tax.substr(0,tax.find_first_of(';'))+';';
+ tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+ newTax += taxon;
+ level++;
}
- inTaxonomy.close();
- remove(tempTaxonomyFile.c_str());
-
- taxaBrowser.assignHeirarchyIDs(0);
-
- ofstream outTaxTree;
- openOutputFile(taxSummary, outTaxTree);
-
- taxaBrowser.print(outTaxTree);
- mothurOutEndLine();
- mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences.");
- mothurOutEndLine();
- mothurOutEndLine();
+ //add "unclassified" until you reach maxLevel
+ while (level < maxlevel) {
+ newTax += "unclassified;";
+ level++;
+ }
- return 0;
+ return newTax;
}
catch(exception& e) {
- errorOut(e, "ClassifySeqsCommand", "execute");
+ errorOut(e, "ClassifySeqsCommand", "addUnclassifieds");
exit(1);
}
}
+
/**************************************************************************************************/
-void ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile) {
+void ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp");
+ driver(lines[process], taxFileName + toString(getpid()) + ".temp", tempTaxFile + toString(getpid()) + ".temp", filename);
exit(0);
}else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
}
//**********************************************************************************************************************
-int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFName){
+int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFName, string filename){
try {
ofstream outTax;
openOutputFile(taxFName, outTax);
openOutputFile(tempTFName, outTaxSimple);
ifstream inFASTA;
- openInputFile(fastaFileName, inFASTA);
+ openInputFile(filename, inFASTA);
inFASTA.seekg(line->start);
if (candidateSeq->getName() != "") {
taxonomy = classify->getTaxonomy(candidateSeq);
-
+
if (taxonomy != "bad seq") {
//output confidence scores or not
if (probs) {
outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
}else{
outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
+ cout << classify->getSimpleTax() << endl;
}
outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
projects / mothur.git / blobdiff