void ShhherCommand::writeSequences(vector<int> otuCounts){
try {
- flowOrder = "TACG";
string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
ofstream fastaFile;
if(otuCounts[i] > 0){
fastaFile << '>' << seqNameVector[aaI[i][0]] << endl;
- for(int j=8;j<numFlowCells;j++){
+ string newSeq = "";
+
+ for(int j=0;j<numFlowCells;j++){
char base = flowOrder[j % 4];
for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
- fastaFile << base;
+ newSeq += base;
}
}
- fastaFile << endl;
+
+ fastaFile << newSeq.substr(4) << endl;
}
}
fastaFile.close();
ofstream otuCountsFile;
m->openOutputFile(otuCountsFileName, otuCountsFile);
- string bases = "TACG";
+ string bases = flowOrder;
for(int i=0;i<numOTUs;i++){
//output the translated version of the centroid sequence for the otu
int sequence = aaI[i][j];
otuCountsFile << seqNameVector[sequence] << '\t';
- for(int k=8;k<lengths[sequence];k++){
+ string newSeq = "";
+
+ for(int k=0;k<lengths[sequence];k++){
char base = bases[k % 4];
int freq = int(0.01 * (double)flowDataIntI[sequence * numFlowCells + k] + 0.5);
-
+
for(int s=0;s<freq;s++){
- otuCountsFile << base;
+ newSeq += base;
+ //otuCountsFile << base;
}
}
- otuCountsFile << endl;
+ otuCountsFile << newSeq.substr(4) << endl;
}
otuCountsFile << endl;
}