string CountSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.seqs command reads a name file and outputs a .count.summary file. You may also provide a group file to get the counts broken down by group.\n";
+ helpString += "The count.seqs command reads a name file and outputs a .seq.count file. You may also provide a group file to get the counts broken down by group.\n";
helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "count.summary";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count";
m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
- out << "Representative Sequence\t total\t";
+ out << "Representative_Sequence\ttotal\t";
GroupMap* groupMap;
if (groupfile != "") {