else {
//valid paramters for this command
- string AlignArray[] = {"template","fasta","name","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") {
//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);
namefile = validParameter.validFile(parameters, "name", false);
- if (fastaFileName == "not found") { namefile = ""; }
+ 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);
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 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 and blast. The default is kmer.\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();
}
mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); mothurOutEndLine();
- string newTaxonomyFile = getRootName(fastaFileNames[s]) + getRootName(taxonomyFileName) + "taxonomy";
- string tempTaxonomyFile = getRootName(fastaFileNames[s]) + "taxonomy.temp";
- string taxSummary = getRootName(fastaFileNames[s]) + getRootName(taxonomyFileName) + "tax.summary";
+
+ 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;
#endif
//make taxonomy tree from new taxonomy file
PhyloTree taxaBrowser;
-
+
ifstream in;
openInputFile(tempTaxonomyFile, in);
//keep what you have counting the levels
while (tax.find_first_of(';') != -1) {
//get taxon
- taxon = tax.substr(0,tax.find_first_of(';'));
+ taxon = tax.substr(0,tax.find_first_of(';'))+';';
tax = tax.substr(tax.find_first_of(';')+1, tax.length());
newTax += taxon;
level++;
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