if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ int start = time(NULL);
+
readFasta();
if (m->control_pressed) { return 0; }
if (namefile != "") { readNames(); }
- if (countfile != "") { ct.readTable(countfile); }
+ if (countfile != "") { ct.readTable(countfile, true); }
if (m->control_pressed) { return 0; }
}else {
-
+
InputData* input = new InputData(listfile, "list");
ListVector* list = input->getListVector();
delete input;
}
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the consensus sequences.");
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
+ string snumBins = toString(list->getNumBins());
for (int i = 0; i < list->getNumBins(); i++) {
if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
string bin = list->get(i);
string consSeq = getConsSeq(bin, outSummary, i);
+
+ string seqName = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { seqName += "0"; }
+ }
+ seqName += sbinNumber;
- outFasta << ">seq" << (i+1) << endl << consSeq << endl;
- outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << bin << endl;
+ outFasta << ">" << seqName << endl << consSeq << endl;
+ outName << seqName << '\t' << seqName << "," << bin << endl;
}
outSummary.close(); outName.close(); outFasta.close();