- //open input file
- ifstream in;
- m->openInputFile(fastafile, in);
-
- while (!in.eof()) {
- if (m->control_pressed) { break; }
-
- Sequence seq(in); m->gobble(in);
-
- if (seq.getName() != "") {
-
- itNames = nameMap.find(seq.getName());
-
- if (itNames == nameMap.end()) {
- if (namefile != "") { m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine(); }
- else { //no names file given
- string group = groupMap->getGroup(seq.getName());
-
- if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
- seq.printSequence(*(filehandles[group+"fasta"]));
- }else if(group == "not found") {
- m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
- }
- }
- }else{
- vector<string> names = itNames->second;
- map<string, string> group2Names;
- map<string, string>::iterator it;
-
- for (int i = 0; i < names.size(); i++) { //build strings for new group names file, will select rep below
- string group = groupMap->getGroup(names[i]);
-
- if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
- it = group2Names.find(group);
- if (it == group2Names.end()) {
- group2Names[group] = names[i] + ",";
- }else{
- group2Names[group] += names[i] + ",";
- }
- }else if(group == "not found") {
- m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
- }
- }
-
- for (map<string, string>::iterator itGroups = group2Names.begin(); itGroups != group2Names.end(); itGroups++) {
- //edit names string, by grabbing the first guy as the rep and removing the last comma
- string newNames = itGroups->second;
- newNames = newNames.substr(0, newNames.length()-1);
- string repName = "";
-
- int pos = newNames.find_first_of(',');
- if (pos == newNames.npos) { //only one sequence so it represents itself
- repName = newNames;
- }else{
- repName = newNames.substr(0, pos);
- }
-
- *(filehandles[itGroups->first+"name"]) << repName << '\t' << newNames << endl;
- *(filehandles[itGroups->first+"fasta"]) << ">" << repName << endl << seq.getAligned() << endl;
- }
- }
- }