+ ifstream in;
+ m->openInputFile(inFastaName, in);
+
+ ofstream outFasta;
+ m->openOutputFile(outFastaFile, outFasta);
+
+ map<string, string> sequenceStrings; //sequenceString -> list of names. "atgc...." -> seq1,seq2,seq3.
+ map<string, string>::iterator itStrings;
+ set<string> nameInFastaFile; //for sanity checking
+ set<string>::iterator itname;
+ int count = 0;
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); outFasta.close(); remove(outFastaFile.c_str()); return 0; }
+
+ Sequence seq(in);
+
+ if (seq.getName() != "") {
+
+ //sanity checks
+ itname = nameInFastaFile.find(seq.getName());
+ if (itname == nameInFastaFile.end()) { nameInFastaFile.insert(seq.getName()); }
+ else { m->mothurOut("[ERROR]: You already have a sequence named " + seq.getName() + " in your fasta file, sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+
+ itStrings = sequenceStrings.find(seq.getAligned());
+
+ if (itStrings == sequenceStrings.end()) { //this is a new unique sequence
+ //output to unique fasta file
+ seq.printSequence(outFasta);
+
+ if (oldNameMapFName != "") {
+ itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) { //namefile and fastafile do not match
+ m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
+ }else {
+ sequenceStrings[seq.getAligned()] = itNames->second;
+ }
+ }else { sequenceStrings[seq.getAligned()] = seq.getName(); }
+ }else { //this is a dup
+ if (oldNameMapFName != "") {
+ itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) { //namefile and fastafile do not match
+ m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
+ }else {
+ sequenceStrings[seq.getAligned()] += "," + itNames->second;
+ }
+ }else { sequenceStrings[seq.getAligned()] += "," + seq.getName(); }
+ }
+
+ count++;
+ }
+
+ m->gobble(in);
+
+ if(count % 1000 == 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
+ }
+
+ if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
+
+ in.close();
+ outFasta.close();
+
+ if (m->control_pressed) { remove(outFastaFile.c_str()); return 0; }
+
+ //print new names file
+ ofstream outNames;
+ m->openOutputFile(outNameFile, outNames);
+
+ for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
+ if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); outNames.close(); remove(outNameFile.c_str()); return 0; }
+
+ //get rep name
+ int pos = (itStrings->second).find_first_of(',');
+
+ if (pos == string::npos) { // only reps itself
+ outNames << itStrings->second << '\t' << itStrings->second << endl;
+ }else {
+ outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
+ }
+ }
+ outNames.close();