try {
CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(prfasta);
- CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "",false,false); parameters.push_back(palign);
CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["mismatch"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["mismatch"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
m->mothurConvert(temp, processors);
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
- if ((align != "needleman") && (align != "blast") && (align != "gotoh") && (align != "noalign")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman, blast, gotoh and noalign. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
+ if ((align != "needleman") && (align != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
}
}
//this function will create a forward and reverse, fasta and qual files for each processor.
//files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
int numReads = 0;
- m->mothurOut("Reading fastq data..."); cout.flush();
+ int start = time(NULL);
+ longestBase = 1000;
+ m->mothurOut("Reading fastq data...\n");
vector< vector<string> > files = readFastqFiles(numReads);
m->mothurOut("Done.\n");
+
+ if (m->control_pressed) { return 0; }
+ string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.fasta";
+ string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.qual";
+ string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.mismatches";
+ outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+ outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
+ outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
-
+ m->mothurOut("Making contigs...\n");
+ createProcesses(files, outFastaFile, outQualFile, outMisMatchFile);
+ m->mothurOut("Done.\n");
+
+ //remove temp fasta and qual files
+ for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
string currentFasta = "";
itTypes = outputTypes.find("fasta");
}
}
//**********************************************************************************************************************
+int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputMisMatches) {
+ try {
+ int num = 0;
+ vector<int> processIDS;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int process = 0;
+
+ //loop through and create all the processes you want
+ while (process != processors-1) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driver(files[process], outputFasta + toString(getpid()) + ".temp", outputQual + toString(getpid()) + ".temp", outputMisMatches + toString(getpid()) + ".temp");
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputFasta + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = outputFasta + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); m->mothurRemove(tempFile);
+ }
+ #else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the contigsData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<contigsData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ string extension = toString(i) + ".temp";
+
+ contigsData* tempcontig = new contigsData(files[i], (outputFasta + extension), (outputQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, i);
+ pDataArray.push_back(tempcontig);
+ processIDS.push_back(i);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+ #endif
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
+ m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
+ m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
+ m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
+ }
+
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputMisMatches){
+ try {
+
+ Alignment* alignment;
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
+
+ int num = 0;
+ string thisffastafile = files[0];
+ string thisfqualfile = files[1];
+ string thisrfastafile = files[2];
+ string thisrqualfile = files[3];
+
+ if (m->debug) { m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
+
+ ifstream inFFasta, inRFasta, inFQual, inRQual;
+ m->openInputFile(thisffastafile, inFFasta);
+ m->openInputFile(thisfqualfile, inFQual);
+ m->openInputFile(thisrfastafile, inRFasta);
+ m->openInputFile(thisrqualfile, inRQual);
+
+ ofstream outFasta, outQual, outMisMatch;
+ m->openOutputFile(outputFasta, outFasta);
+ m->openOutputFile(outputQual, outQual);
+ m->openOutputFile(outputMisMatches, outMisMatch);
+ outMisMatch << "Name\tLength\tMisMatches\n";
+
+ while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
+
+ if (m->control_pressed) { break; }
+
+ //read seqs and quality info
+ Sequence fSeq(inFFasta); m->gobble(inFFasta);
+ Sequence rSeq(inRFasta); m->gobble(inRFasta);
+ QualityScores fQual(inFQual); m->gobble(inFQual);
+ QualityScores rQual(inRQual); m->gobble(inRQual);
+
+ //flip the reverse reads
+ rSeq.reverseComplement();
+ 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 = "";
+ vector<int> contigScores;
+ int numMismatches = 0;
+ string seq1 = fSeq.getAligned();
+ string seq2 = rSeq.getAligned();
+
+ vector<int> scores1 = fQual.getQualityScores();
+ vector<int> scores2 = rQual.getQualityScores();
+
+ for (int i = 0; i < length; i++) {
+ if (seq1[i] == seq2[i]) { //match, add base and choose highest score
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; }
+ }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
+ char c = seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; c = seq2[i]; }
+ contig += c;
+ numMismatches++;
+ }else { //should never get here
+ m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
+ }
+ }
+
+ //output
+ outFasta << ">" << fSeq.getName() << endl << contig << endl;
+ outQual << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
+ outQual << endl;
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
+
+ num++;
+
+ //report progress
+ if((num) % 1000 == 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); }
+ }
+
+ //report progress
+ if((num) % 1000 != 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); }
+
+ inFFasta.close();
+ inFQual.close();
+ inRFasta.close();
+ inRQual.close();
+ outFasta.close();
+ outQual.close();
+ outMisMatch.close();
+ delete alignment;
+
+ if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta); m->mothurRemove(outputMisMatches);}
+
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
vector< vector<string> > MakeContigsCommand::readFastqFiles(int& count){
try {
vector< vector<string> > files;
//report progress
if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
+
//close files, delete ofstreams
for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close(); delete (it->second)[i]; } }
exit(1);
}
}
-
//**********************************************************************************************************************
fastqRead MakeContigsCommand::readFastq(ifstream& in){
try {
//
#include "command.hpp"
+#include "sequence.hpp"
+#include "qualityscores.h"
+#include "alignment.hpp"
+#include "gotohoverlap.hpp"
+#include "needlemanoverlap.hpp"
+#include "blastalign.hpp"
+#include "noalign.hpp"
+
struct fastqRead {
vector<int> scores;
fastqRead readFastq(ifstream&);
vector< vector<string> > readFastqFiles(int&);
bool checkReads(fastqRead&, fastqRead&);
+ int createProcesses(vector< vector<string> >, string, string, string);
+ int driver(vector<string>, string, string, string);
};
/**************************************************************************************************/
+/**************************************************************************************************/
+//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 outputQual;
+ string outputMisMatches;
+ string align;
+ vector<string> files;
+ MothurOut* m;
+ float match, misMatch, gapOpen, gapExtend;
+ int count, threadID;
+
+ contigsData(){}
+ contigsData(vector<string> f, string of, string oq, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int tid) {
+ files = f;
+ outputFasta = of;
+ outputQual = oq;
+ outputMisMatches = om;
+ m = mout;
+ match = ma;
+ misMatch = misMa;
+ gapOpen = gapO;
+ gapExtend = gapE;
+ align = al;
+ count = 0;
+ threadID = tid;
+ }
+};
-
-
-
+/**************************************************************************************************/
+#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); }
+
+ int num = 0;
+ string thisffastafile = pDataArray->files[0];
+ string thisfqualfile = pDataArray->files[1];
+ string thisrfastafile = pDataArray->files[2];
+ string thisrqualfile = pDataArray->files[3];
+
+ if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
+
+ ifstream inFFasta, inRFasta, inFQual, inRQual;
+ pDataArray->m->openInputFile(thisffastafile, inFFasta);
+ pDataArray->m->openInputFile(thisfqualfile, inFQual);
+ pDataArray->m->openInputFile(thisrfastafile, inRFasta);
+ pDataArray->m->openInputFile(thisrqualfile, inRQual);
+
+ ofstream outFasta, outQual, outMisMatch;
+ pDataArray->m->openOutputFile(pDataArray->outputFasta, outFasta);
+ pDataArray->m->openOutputFile(pDataArray->outputQual, outQual);
+ pDataArray->m->openOutputFile(pDataArray->outputMisMatches, outMisMatch);
+ outMisMatch << "Name\tLength\tMisMatches\n";
+
+ while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
+
+ if (pDataArray->m->control_pressed) { break; }
+
+ //read seqs and quality info
+ Sequence fSeq(inFFasta); pDataArray->m->gobble(inFFasta);
+ Sequence rSeq(inRFasta); pDataArray->m->gobble(inRFasta);
+ QualityScores fQual(inFQual); pDataArray->m->gobble(inFQual);
+ QualityScores rQual(inRQual); pDataArray->m->gobble(inRQual);
+
+ //flip the reverse reads
+ rSeq.reverseComplement();
+ 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 = "";
+ vector<int> contigScores;
+ int numMismatches = 0;
+ string seq1 = fSeq.getAligned();
+ string seq2 = rSeq.getAligned();
+
+ vector<int> scores1 = fQual.getQualityScores();
+ vector<int> scores2 = rQual.getQualityScores();
+
+ for (int i = 0; i < length; i++) {
+ if (seq1[i] == seq2[i]) { //match, add base and choose highest score
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; }
+ }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
+ char c = seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; c = seq2[i]; }
+ contig += c;
+ numMismatches++;
+ }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");
+ }
+ }
+
+ //output
+ outFasta << ">" << fSeq.getName() << endl << contig << endl;
+ outQual << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
+ outQual << endl;
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
+
+ num++;
+
+ //report progress
+ if((num) % 1000 == 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+ }
+
+ //report progress
+ if((num) % 1000 != 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+
+ inFFasta.close();
+ inFQual.close();
+ inRFasta.close();
+ inRQual.close();
+ outFasta.close();
+ outQual.close();
+ outMisMatch.close();
+ delete alignment;
+
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches);}
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "AlignCommand", "MyContigsThreadFunction");
+ exit(1);
+ }
+}
+#endif
#endif
projects / mothur.git / commitdiff