CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
+ CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);
CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
try {
string helpString = "";
helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
- helpString += "The classify.seqs command parameters are reference, fasta, name, group, count, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n";
+ helpString += "The classify.seqs command parameters are reference, fasta, name, group, count, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted, relabund and probs.\n";
helpString += "The reference, 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";
helpString += "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast, align and distance. The default is kmer.\n";
helpString += "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";
helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n";
helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n";
helpString += "The probs parameter shuts off the bootstrapping results for the wang and zap method. The default is true, meaning you want the bootstrapping to be shown.\n";
+ helpString += "The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F. \n";
helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the wang method. The default is 100.\n";
//helpString += "The flip parameter allows you shut off mothur's The default is T.\n";
helpString += "The classify.seqs command should be in the following format: \n";
namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") { namefile = ""; }
-
else {
m->splitAtDash(namefile, namefileNames);
temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
probs = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "relabund", false); if (temp == "not found"){ temp = "false"; }
+ relabund = m->isTrue(temp);
+
temp = validParameter.validFile(parameters, "shortcuts", false); if (temp == "not found"){ temp = "true"; }
writeShortcuts = m->isTrue(temp);
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputMethodTag = method + ".";
+ string outputMethodTag = method;
if(method == "wang"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts); }
else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand()); }
else if(method == "zap"){
}
#endif
- if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine();
+ if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur reversed some your sequences for a better classification. If you would like to take a closer look, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine();
outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
}else { m->mothurRemove(newaccnosFile); }
PhyloSummary* taxaSum;
if (hasCount) {
ct = new CountTable();
- ct->readTable(countfileNames[s]);
- taxaSum = new PhyloSummary(taxonomyFileName, ct);
+ ct->readTable(countfileNames[s], true, false);
+ taxaSum = new PhyloSummary(taxonomyFileName, ct, relabund);
taxaSum->summarize(tempTaxonomyFile);
}else {
if (groupfile != "") { group = groupfileNames[s]; groupMap = new GroupMap(group); groupMap->readMap(); }
- taxaSum = new PhyloSummary(taxonomyFileName, groupMap);
+ taxaSum = new PhyloSummary(taxonomyFileName, groupMap, relabund);
if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ if (pDataArray[i]->count != pDataArray[i]->end) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) +"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); }
inFASTA.close();
outTax.close();
projects / mothur.git / blobdiff