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#ifndef Mothur_makecontigscommand_h
#define Mothur_makecontigscommand_h
//
// makecontigscommand.h
// Mothur
//
// Created by Sarah Westcott on 5/15/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "sequence.hpp"
#include "qualityscores.h"
#include "alignment.hpp"
#include "gotohoverlap.hpp"
#include "needlemanoverlap.hpp"
#include "blastalign.hpp"
#include "noalign.hpp"
#include "trimoligos.h"
struct fastqRead {
vector<int> scores;
string name;
string sequence;
fastqRead() { name = ""; sequence = ""; scores.clear(); };
fastqRead(string n, string s, vector<int> sc) : name(n), sequence(s), scores(sc) {};
~fastqRead() {};
};
struct pairFastqRead {
fastqRead forward;
fastqRead reverse;
fastqRead findex;
fastqRead rindex;
pairFastqRead() {};
pairFastqRead(fastqRead f, fastqRead r) : forward(f), reverse(r){};
pairFastqRead(fastqRead f, fastqRead r, fastqRead fi, fastqRead ri) : forward(f), reverse(r), findex(fi), rindex(ri) {};
~pairFastqRead() {};
};
/**************************************************************************************************/
class MakeContigsCommand : public Command {
public:
MakeContigsCommand(string);
MakeContigsCommand();
~MakeContigsCommand(){}
vector<string> setParameters();
string getCommandName() { return "make.contigs"; }
string getCommandCategory() { return "Sequence Processing"; }
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
string getDescription() { return "description"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allFiles, trimOverlap, createFileGroup, createOligosGroup, makeCount, noneOk;
string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, findexfile, rindexfile, file, format;
float match, misMatch, gapOpen, gapExtend;
int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq;
vector<string> outputNames;
map<int, oligosPair> barcodes;
map<int, oligosPair> primers;
vector<string> linker;
vector<string> spacer;
vector<string> primerNameVector;
vector<string> barcodeNameVector;
vector<char> convertTable;
map<string, int> groupCounts;
map<string, string> groupMap;
map<int, string> file2Group;
vector<int> convertQual(string);
fastqRead readFastq(ifstream&, bool&);
vector< vector< vector<string> > > preProcessData(unsigned long int&);
vector< vector<string> > readFileNames(string);
vector< vector<string> > readFastqFiles(unsigned long int&, string, string, string, string);
vector< vector<string> > readFastaFiles(unsigned long int&, string, string);
//bool checkReads(fastqRead&, fastqRead&, string, string);
int createProcesses(vector< vector<string> >, string, string, string, vector<vector<string> >, int);
int driver(vector<string>, string, string, string, vector<vector<string> >, int, string);
bool getOligos(vector<vector<string> >&, string);
string reverseOligo(string);
vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques, bool);
vector<pairFastqRead> mergeReads(vector<pairFastqRead> frReads, vector<pairFastqRead> friReads, map<string, pairFastqRead>& pairUniques);
};
/**************************************************************************************************/
/**************************************************************************************************/
//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 contigsData {
string outputFasta;
string outputScrapFasta;
string outputMisMatches;
string align, group;
vector<string> files;
vector<vector<string> > fastaFileNames;
MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq;
bool allFiles, createOligosGroup, createFileGroup, done, trimOverlap;
map<string, int> groupCounts;
map<string, string> groupMap;
vector<string> primerNameVector;
vector<string> barcodeNameVector;
map<int, oligosPair> barcodes;
map<int, oligosPair> primers;
contigsData(){}
contigsData(string g, vector<string> f, string of, string osf, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, map<int, oligosPair> br, map<int, oligosPair> pr, vector<vector<string> > ffn, vector<string>bnv, vector<string> pnv, int pdf, int bdf, int tdf, bool cg, bool cfg, bool all, bool to, int tid) {
files = f;
outputFasta = of;
outputMisMatches = om;
m = mout;
match = ma;
misMatch = misMa;
gapOpen = gapO;
gapExtend = gapE;
insert = thr;
align = al;
group = g;
count = 0;
outputScrapFasta = osf;
fastaFileNames = ffn;
barcodes = br;
primers = pr;
barcodeNameVector = bnv;
primerNameVector = pnv;
pdiffs = pdf;
bdiffs = bdf;
tdiffs = tdf;
allFiles = all;
trimOverlap = to;
createOligosGroup = cg;
createFileGroup = cfg;
threadID = tid;
deltaq = delt;
done=false;
}
};
/**************************************************************************************************/
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
contigsData* pDataArray;
pDataArray = (contigsData*)lpParam;
try {
int longestBase = 1000;
Alignment* alignment;
if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); }
else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, longestBase); }
pDataArray->count = 0;
string thisffastafile = pDataArray->files[0];
string thisfqualfile = pDataArray->files[1];
string thisrfastafile = pDataArray->files[2];
string thisrqualfile = pDataArray->files[3];
string thisfindexfile = pDataArray->files[4];
string thisrindexfile = pDataArray->files[5];
if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n[DEBUG]: findex = " + thisfindexfile + ".\n[DEBUG]: rindex = " + thisrindexfile + ".\n"); }
if(pDataArray->allFiles){
for (int i = 0; i < pDataArray->fastaFileNames.size(); i++) { //clears old file
for (int j = 0; j < pDataArray->fastaFileNames[i].size(); j++) { //clears old file
if (pDataArray->fastaFileNames[i][j] != "") {
ofstream temp;
pDataArray->m->openOutputFile(pDataArray->fastaFileNames[i][j], temp); temp.close();
}
}
}
}
ifstream inFFasta, inRFasta, inFQual, inRQual, inFIndex, inRIndex;
ofstream outFasta, outMisMatch, outScrapFasta;
pDataArray->m->openInputFile(thisffastafile, inFFasta);
pDataArray->m->openInputFile(thisrfastafile, inRFasta);
if (thisfqualfile != "") {
pDataArray->m->openInputFile(thisfqualfile, inFQual);
pDataArray->m->openInputFile(thisrqualfile, inRQual);
}
if (thisfindexfile != "") { pDataArray->m->openInputFile(thisfindexfile, inFIndex); }
if (thisrindexfile != "") { pDataArray->m->openInputFile(thisrindexfile, inRIndex); }
pDataArray->m->openOutputFile(pDataArray->outputFasta, outFasta);
pDataArray->m->openOutputFile(pDataArray->outputMisMatches, outMisMatch);
pDataArray->m->openOutputFile(pDataArray->outputScrapFasta, outScrapFasta);
outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";
TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->primers, pDataArray->barcodes);
while ((!inFFasta.eof()) && (!inRFasta.eof())) {
if (pDataArray->m->control_pressed) { break; }
int success = 1;
string trashCode = "";
int currentSeqsDiffs = 0;
//read seqs and quality info
Sequence fSeq(inFFasta); pDataArray->m->gobble(inFFasta);
Sequence rSeq(inRFasta); pDataArray->m->gobble(inRFasta);
QualityScores* fQual = NULL; QualityScores* rQual = NULL;
if (thisfqualfile != "") {
fQual = new QualityScores(inFQual); pDataArray->m->gobble(inFQual);
rQual = new QualityScores(inRQual); pDataArray->m->gobble(inRQual);
}
Sequence findexBarcode("findex", "NONE"); Sequence rindexBarcode("rindex", "NONE");
if (thisfindexfile != "") {
Sequence temp(inFIndex); pDataArray->m->gobble(inFIndex);
findexBarcode.setAligned(temp.getAligned());
}
if (thisrindexfile != "") {
Sequence temp(inRIndex); pDataArray->m->gobble(inRIndex);
rindexBarcode.setAligned(temp.getAligned());
}
int barcodeIndex = 0;
int primerIndex = 0;
if(pDataArray->barcodes.size() != 0){
if (thisfqualfile != "") {
if ((thisfindexfile != "") || (thisrindexfile != "")) {
success = trimOligos.stripBarcode(findexBarcode, rindexBarcode, *fQual, *rQual, barcodeIndex);
}else {
success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
}
}else {
success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
}
if(success > pDataArray->bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(pDataArray->primers.size() != 0){
if (thisfqualfile != "") {
success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
}else {
success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
}
if(success > pDataArray->pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
if (currentSeqsDiffs > pDataArray->tdiffs) { trashCode += 't'; }
//flip the reverse reads
rSeq.reverseComplement();
if (thisfqualfile != "") { rQual->flipQScores(); }
//pairwise align
alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
fSeq.setAligned(alignment->getSeqAAln());
rSeq.setAligned(alignment->getSeqBAln());
int length = fSeq.getAligned().length();
//traverse alignments merging into one contiguous seq
string contig = "";
int numMismatches = 0;
string seq1 = fSeq.getAligned();
string seq2 = rSeq.getAligned();
vector<int> scores1, scores2;
if (thisfqualfile != "") {
scores1 = fQual->getQualityScores();
scores2 = rQual->getQualityScores();
delete fQual; delete rQual;
}
int overlapStart = fSeq.getStartPos();
int seq2Start = rSeq.getStartPos();
//bigger of the 2 starting positions is the location of the overlapping start
if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
overlapStart = seq2Start;
for (int i = 0; i < overlapStart; i++) { contig += seq1[i]; }
}else { //seq1 starts later so take from 0 to overlapStart from seq2
for (int i = 0; i < overlapStart; i++) { contig += seq2[i]; }
}
int seq1End = fSeq.getEndPos();
int seq2End = rSeq.getEndPos();
int overlapEnd = seq1End;
if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
int oStart = contig.length();
for (int i = overlapStart; i < overlapEnd; i++) {
if (seq1[i] == seq2[i]) { //match, add base and choose highest score
contig += seq1[i];
}else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base
if (thisfqualfile != "") {
if (scores2[BBaseMap[i]] < pDataArray->insert) { } //
else { contig += seq2[i]; }
}else { contig += seq2[i]; } //with no quality info, then we keep it?
}else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below insert. In that case eliminate base
if (thisfqualfile != "") {
if (scores1[ABaseMap[i]] < pDataArray->insert) { } //
else { contig += seq1[i]; }
}else { contig += seq1[i]; } //with no quality info, then we keep it?
}else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
if (thisfqualfile != "") {
if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= pDataArray->deltaq) { //is the difference in qual scores >= deltaq, if yes choose base with higher score
char c = seq1[i];
if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; }
contig += c;
}else { //if no, base becomes n
contig += 'N';
}
numMismatches++;
}else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
}else { //should never get here
pDataArray->m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
}
}
int oend = contig.length();
if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
for (int i = overlapEnd; i < length; i++) { contig += seq2[i]; }
}else { //seq2 ends before seq1 so take from overlap to length from seq1
for (int i = overlapEnd; i < length; i++) { contig += seq1[i]; }
}
if (pDataArray->trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart); if (contig.length() == 0) { trashCode += "l"; } }
if(trashCode.length() == 0){
bool ignore = false;
if (pDataArray->createOligosGroup) {
if(pDataArray->barcodes.size() != 0){
string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
if (pDataArray->primers.size() != 0) {
if (pDataArray->primerNameVector[primerIndex] != "") {
if(thisGroup != "") {
thisGroup += "." + pDataArray->primerNameVector[primerIndex];
}else {
thisGroup = pDataArray->primerNameVector[primerIndex];
}
}
}
if (pDataArray->m->debug) { pDataArray->m->mothurOut(", group= " + thisGroup + "\n"); }
int pos = thisGroup.find("ignore");
if (pos == string::npos) {
pDataArray->groupMap[fSeq.getName()] = thisGroup;
map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1; }
else { pDataArray->groupCounts[it->first] ++; }
}else { ignore = true; }
}
}else if (pDataArray->createFileGroup) {
int pos = pDataArray->group.find("ignore");
if (pos == string::npos) {
pDataArray->groupMap[fSeq.getName()] = pDataArray->group;
map<string, int>::iterator it = pDataArray->groupCounts.find(pDataArray->group);
if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[pDataArray->group] = 1; }
else { pDataArray->groupCounts[it->first]++; }
}else { ignore = true; }
}
if(pDataArray->allFiles && !ignore){
ofstream output;
pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
output << ">" << fSeq.getName() << endl << contig << endl;
output.close();
}
//output
outFasta << ">" << fSeq.getName() << endl << contig << endl;
int numNs = 0;
for (int i = 0; i < contig.length(); i++) { if (contig[i] == 'N') { numNs++; } }
outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << (oend-oStart) << '\t' << oStart << '\t' << oend << '\t' << numMismatches << '\t' << numNs << endl;
}else {
//output
outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
}
pDataArray->count++;
//report progress
if((pDataArray->count) % 1000 == 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
}
//report progress
if((pDataArray->count) % 1000 != 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
inFFasta.close();
inRFasta.close();
outFasta.close();
outMisMatch.close();
outScrapFasta.close();
if (thisfqualfile != "") {
inFQual.close();
inRQual.close();
}
delete alignment;
pDataArray->done = true;
if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches); pDataArray->m->mothurRemove(pDataArray->outputScrapFasta); }
return 0;
}
catch(exception& e) {
pDataArray->m->errorOut(e, "AlignCommand", "MyContigsThreadFunction");
exit(1);
}
}
#endif
#endif
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