2 // primerdesigncommand.h
5 // Created by Sarah Westcott on 1/18/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef Mothur_primerdesigncommand_h
10 #define Mothur_primerdesigncommand_h
12 #include "command.hpp"
13 #include "listvector.hpp"
14 #include "inputdata.h"
15 #include "sequence.hpp"
16 #include "alignment.hpp"
17 #include "needlemanoverlap.hpp"
19 /**************************************************************************************************/
21 class PrimerDesignCommand : public Command {
23 PrimerDesignCommand(string);
24 PrimerDesignCommand();
25 ~PrimerDesignCommand(){}
27 vector<string> setParameters();
28 string getCommandName() { return "primer.design"; }
29 string getCommandCategory() { return "OTU-Based Approaches"; }
31 string getOutputPattern(string);
32 string getHelpString();
33 string getCitation() { return "http://www.mothur.org/wiki/Primer.design"; }
34 string getDescription() { return "identify sequence fragments that are specific to particular OTUs"; }
37 void help() { m->mothurOut(getHelpString()); }
44 linePair(int i, int j) : start(i), end(j) {}
46 struct fastaLinePair {
47 unsigned long long start;
48 unsigned long long end;
49 fastaLinePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
52 bool abort, allLines, large;
53 int cutoff, pdiffs, length, otunumber, processors, alignedLength;
54 string outputDir, listfile, namefile, countfile, fastafile, label;
57 vector<string> outputNames;
59 int initializeCounts(vector< vector< vector<unsigned int> > >& counts, int length, map<string, int>&, map<string, int>&, vector<unsigned int>&);
60 map<string, int> readCount(unsigned long int&);
61 char getBase(vector<unsigned int> counts, int size);
63 int countDiffs(string, string);
64 set<string> getPrimer(Sequence);
65 bool findPrimer(string, string, vector<int>&, vector<int>&, vector<int>&);
66 int findMeltingPoint(string primer, double&, double&);
68 set<int> createProcesses(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&);
69 set<int> driver(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&, int, int, int&);
70 vector< vector< vector<unsigned int> > > driverGetCounts(map<string, int>&, unsigned long int&, vector<unsigned int>&, unsigned long long&, unsigned long long&);
71 vector<Sequence> createProcessesConSeqs(map<string, int>&, unsigned long int&);
75 /**************************************************************************************************/
76 //custom data structure for threads to use.
77 // This is passed by void pointer so it can be any data type
78 // that can be passed using a single void pointer (LPVOID).
79 struct primerDesignData {
80 string summaryFileName;
84 int pdiffs, threadID, otunumber, length;
86 vector<double> minTms, maxTms;
87 set<int> otusToRemove;
88 vector<Sequence> consSeqs;
92 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) {
105 numBinsProcessed = 0;
109 /**************************************************************************************************/
110 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
112 static DWORD WINAPI MyPrimerThreadFunction(LPVOID lpParam){
113 primerDesignData* pDataArray;
114 pDataArray = (primerDesignData*)lpParam;
118 pDataArray->m->openOutputFileAppend(pDataArray->summaryFileName, outSum);
120 for (int i = pDataArray->start; i < pDataArray->end; i++) {
122 if (pDataArray->m->control_pressed) { break; }
124 if (i != (pDataArray->otunumber-1)) {
126 for (set<string>::iterator it = pDataArray->primers.begin(); it != pDataArray->primers.end(); it++) {
127 vector<int> primerStarts;
128 vector<int> primerEnds;
129 vector<int> mismatches;
131 //bool found = findPrimer(conSeqs[i].getUnaligned(), (*it), primerStarts, primerEnds, mismatches);
132 ///////////////////////////////////////////////////////////////////////////////////////////////////
133 bool found = false; //innocent til proven guilty
135 string rawSequence = pDataArray->consSeqs[i].getUnaligned();
138 //look for exact match
139 if(rawSequence.length() < primer.length()) { found = false; }
142 for (int j = 0; j < rawSequence.length()-pDataArray->length; j++){
144 if (pDataArray->m->control_pressed) { found = false; break; }
146 string rawChunk = rawSequence.substr(j, pDataArray->length);
148 //int numDiff = countDiffs(primer, rawchuck);
149 ///////////////////////////////////////////////////////////////////////
151 string oligo = primer;
152 string seq = rawChunk;
154 for(int k=0;k<pDataArray->length;k++){
156 oligo[k] = toupper(oligo[k]);
157 seq[k] = toupper(seq[k]);
159 if(oligo[k] != seq[k]){
161 if((oligo[k] == 'N' || oligo[k] == 'I') && (seq[k] == 'N')) { numDiff++; }
162 else if(oligo[k] == 'R' && (seq[k] != 'A' && seq[k] != 'G')) { numDiff++; }
163 else if(oligo[k] == 'Y' && (seq[k] != 'C' && seq[k] != 'T')) { numDiff++; }
164 else if(oligo[k] == 'M' && (seq[k] != 'C' && seq[k] != 'A')) { numDiff++; }
165 else if(oligo[k] == 'K' && (seq[k] != 'T' && seq[k] != 'G')) { numDiff++; }
166 else if(oligo[k] == 'W' && (seq[k] != 'T' && seq[k] != 'A')) { numDiff++; }
167 else if(oligo[k] == 'S' && (seq[k] != 'C' && seq[k] != 'G')) { numDiff++; }
168 else if(oligo[k] == 'B' && (seq[k] != 'C' && seq[k] != 'T' && seq[k] != 'G')) { numDiff++; }
169 else if(oligo[k] == 'D' && (seq[k] != 'A' && seq[k] != 'T' && seq[k] != 'G')) { numDiff++; }
170 else if(oligo[k] == 'H' && (seq[k] != 'A' && seq[k] != 'T' && seq[k] != 'C')) { numDiff++; }
171 else if(oligo[k] == 'V' && (seq[k] != 'A' && seq[k] != 'C' && seq[k] != 'G')) { numDiff++; }
172 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++; }
173 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++; }
174 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++; }
175 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++; }
176 else if((oligo[k] == '.' || oligo[k] == '-')) { numDiff++; }
179 ///////////////////////////////////////////////////////////////////////
181 if(numDiff <= pDataArray->pdiffs){
182 primerStarts.push_back(j);
183 primerEnds.push_back(j+pDataArray->length);
184 mismatches.push_back(numDiff);
189 ///////////////////////////////////////////////////////////////////////////////////////////////////
191 //if we found it report to the table
193 for (int j = 0; j < primerStarts.size(); j++) {
194 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;
196 pDataArray->otusToRemove.insert(i);
201 pDataArray->numBinsProcessed++;
206 catch(exception& e) {
207 pDataArray->m->errorOut(e, "PrimerDesignCommand", "MyPrimerThreadFunction");
213 /**************************************************************************************************/