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primerdesigncommand.h
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primerdesigncommand.h
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//
// primerdesigncommand.h
// Mothur
//
// Created by Sarah Westcott on 1/18/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_primerdesigncommand_h
#define Mothur_primerdesigncommand_h
#include "command.hpp"
#include "listvector.hpp"
#include "inputdata.h"
#include "sequence.hpp"
#include "alignment.hpp"
#include "needlemanoverlap.hpp"
/**************************************************************************************************/
class PrimerDesignCommand : public Command {
public:
PrimerDesignCommand(string);
PrimerDesignCommand();
~PrimerDesignCommand(){}
vector<string> setParameters();
string getCommandName() { return "primer.design"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getOutputPattern(string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Primer.design"; }
string getDescription() { return "identify sequence fragments that are specific to particular OTUs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
struct linePair {
int start;
int end;
linePair(int i, int j) : start(i), end(j) {}
};
struct fastaLinePair {
unsigned long long start;
unsigned long long end;
fastaLinePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
bool abort, allLines, large;
int cutoff, pdiffs, length, otunumber, processors, alignedLength;
string outputDir, listfile, namefile, countfile, fastafile, label;
double minTM, maxTM;
ListVector* list;
vector<string> outputNames;
int initializeCounts(vector< vector< vector<unsigned int> > >& counts, int length, map<string, int>&, map<string, int>&, vector<unsigned int>&);
map<string, int> readCount(unsigned long int&);
char getBase(vector<unsigned int> counts, int size);
int getListVector();
int countDiffs(string, string);
set<string> getPrimer(Sequence);
bool findPrimer(string, string, vector<int>&, vector<int>&, vector<int>&);
int findMeltingPoint(string primer, double&, double&);
set<int> createProcesses(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&);
set<int> driver(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&, int, int, int&);
vector< vector< vector<unsigned int> > > driverGetCounts(map<string, int>&, unsigned long int&, vector<unsigned int>&, unsigned long long&, unsigned long long&);
vector<Sequence> createProcessesConSeqs(map<string, int>&, unsigned long int&);
};
/**************************************************************************************************/
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct primerDesignData {
string summaryFileName;
MothurOut* m;
int start;
int end;
int pdiffs, threadID, otunumber, length;
set<string> primers;
vector<double> minTms, maxTms;
set<int> otusToRemove;
vector<Sequence> consSeqs;
int numBinsProcessed;
primerDesignData(){}
primerDesignData(string sf, MothurOut* mout, int st, int en, vector<double> min, vector<double> max, set<string> pri, vector<Sequence> seqs, int d, int otun, int l, int tid) {
summaryFileName = sf;
m = mout;
start = st;
end = en;
pdiffs = d;
minTms = min;
maxTms = max;
primers = pri;
consSeqs = seqs;
otunumber = otun;
length = l;
threadID = tid;
numBinsProcessed = 0;
}
};
/**************************************************************************************************/
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MyPrimerThreadFunction(LPVOID lpParam){
primerDesignData* pDataArray;
pDataArray = (primerDesignData*)lpParam;
try {
ofstream outSum;
pDataArray->m->openOutputFileAppend(pDataArray->summaryFileName, outSum);
for (int i = pDataArray->start; i < pDataArray->end; i++) {
if (pDataArray->m->control_pressed) { break; }
if (i != (pDataArray->otunumber-1)) {
int primerIndex = 0;
for (set<string>::iterator it = pDataArray->primers.begin(); it != pDataArray->primers.end(); it++) {
vector<int> primerStarts;
vector<int> primerEnds;
vector<int> mismatches;
//bool found = findPrimer(conSeqs[i].getUnaligned(), (*it), primerStarts, primerEnds, mismatches);
///////////////////////////////////////////////////////////////////////////////////////////////////
bool found = false; //innocent til proven guilty
string rawSequence = pDataArray->consSeqs[i].getUnaligned();
string primer = *it;
//look for exact match
if(rawSequence.length() < primer.length()) { found = false; }
else {
//search for primer
for (int j = 0; j < rawSequence.length()-pDataArray->length; j++){
if (pDataArray->m->control_pressed) { found = false; break; }
string rawChunk = rawSequence.substr(j, pDataArray->length);
//int numDiff = countDiffs(primer, rawchuck);
///////////////////////////////////////////////////////////////////////
int numDiff = 0;
string oligo = primer;
string seq = rawChunk;
for(int k=0;k<pDataArray->length;k++){
oligo[k] = toupper(oligo[k]);
seq[k] = toupper(seq[k]);
if(oligo[k] != seq[k]){
if((oligo[k] == 'N' || oligo[k] == 'I') && (seq[k] == 'N')) { numDiff++; }
else if(oligo[k] == 'R' && (seq[k] != 'A' && seq[k] != 'G')) { numDiff++; }
else if(oligo[k] == 'Y' && (seq[k] != 'C' && seq[k] != 'T')) { numDiff++; }
else if(oligo[k] == 'M' && (seq[k] != 'C' && seq[k] != 'A')) { numDiff++; }
else if(oligo[k] == 'K' && (seq[k] != 'T' && seq[k] != 'G')) { numDiff++; }
else if(oligo[k] == 'W' && (seq[k] != 'T' && seq[k] != 'A')) { numDiff++; }
else if(oligo[k] == 'S' && (seq[k] != 'C' && seq[k] != 'G')) { numDiff++; }
else if(oligo[k] == 'B' && (seq[k] != 'C' && seq[k] != 'T' && seq[k] != 'G')) { numDiff++; }
else if(oligo[k] == 'D' && (seq[k] != 'A' && seq[k] != 'T' && seq[k] != 'G')) { numDiff++; }
else if(oligo[k] == 'H' && (seq[k] != 'A' && seq[k] != 'T' && seq[k] != 'C')) { numDiff++; }
else if(oligo[k] == 'V' && (seq[k] != 'A' && seq[k] != 'C' && seq[k] != 'G')) { numDiff++; }
else if(oligo[k] == 'A' && (seq[k] != 'A' && seq[k] != 'M' && seq[k] != 'R' && seq[k] != 'W' && seq[k] != 'D' && seq[k] != 'H' && seq[k] != 'V')) { numDiff++; }
else if(oligo[k] == 'C' && (seq[k] != 'C' && seq[k] != 'Y' && seq[k] != 'M' && seq[k] != 'S' && seq[k] != 'B' && seq[k] != 'H' && seq[k] != 'V')) { numDiff++; }
else if(oligo[k] == 'G' && (seq[k] != 'G' && seq[k] != 'R' && seq[k] != 'K' && seq[k] != 'S' && seq[k] != 'B' && seq[k] != 'D' && seq[k] != 'V')) { numDiff++; }
else if(oligo[k] == 'T' && (seq[k] != 'T' && seq[k] != 'Y' && seq[k] != 'K' && seq[k] != 'W' && seq[k] != 'B' && seq[k] != 'D' && seq[k] != 'H')) { numDiff++; }
else if((oligo[k] == '.' || oligo[k] == '-')) { numDiff++; }
}
}
///////////////////////////////////////////////////////////////////////
if(numDiff <= pDataArray->pdiffs){
primerStarts.push_back(j);
primerEnds.push_back(j+pDataArray->length);
mismatches.push_back(numDiff);
found = true;
}
}
}
///////////////////////////////////////////////////////////////////////////////////////////////////
//if we found it report to the table
if (found) {
for (int j = 0; j < primerStarts.size(); j++) {
outSum << (i+1) << '\t' << *it << '\t' << primerStarts[j] << '\t' << primerEnds[j] << '\t' << pDataArray->length << '\t' << mismatches[j] << '\t' << pDataArray->minTms[primerIndex] << '\t' << pDataArray->maxTms[primerIndex] << endl;
}
pDataArray->otusToRemove.insert(i);
}
primerIndex++;
}
}
pDataArray->numBinsProcessed++;
}
outSum.close();
}
catch(exception& e) {
pDataArray->m->errorOut(e, "PrimerDesignCommand", "MyPrimerThreadFunction");
exit(1);
}
}
#endif
/**************************************************************************************************/
#endif