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 != "") {
//make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
SharedUtil* util = new SharedUtil();
- util->setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> nameGroups = groupMap->getNamesOfGroups();
+ util->setGroups(Groups, nameGroups);
delete util;
//sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
//open input file
ifstream in;
m->openInputFile(namefile, in);
-
+
+ int total = 0;
while (!in.eof()) {
if (m->control_pressed) { break; }
out << firstCol << '\t' << names.size() << endl;
}
-
+ total += names.size();
}
in.close();
if (groupfile != "") { delete groupMap; }
- if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+ m->mothurOutEndLine();
+ m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine();