#include "validcalculator.h"
#include "dist.h"
#include "sequencedb.h"
+#include "sequence.hpp"
+
+#include "gotohoverlap.hpp"
+#include "needlemanoverlap.hpp"
+#include "blastalign.hpp"
+#include "noalign.hpp"
+
+#include "ignoregaps.h"
+#include "eachgapdist.h"
+#include "eachgapignore.h"
+#include "onegapdist.h"
+#include "onegapignore.h"
class PairwiseSeqsCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "pairwise.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
string getDescription() { return "calculates pairwise distances from an unaligned fasta file"; }
vector<int> processIDS; //end line, processid
vector<distlinePair> lines;
- Alignment* alignment;
- Dist* distCalculator;
SequenceDB alignDB;
void createProcesses(string);
#ifdef USE_MPI
int driverMPI(int, int, MPI_File&, float);
- int driverMPI(int, int, string, unsigned long int&);
- int driverMPI(int, int, string, unsigned long int&, string);
+ int driverMPI(int, int, string, unsigned long long&);
+ int driverMPI(int, int, string, unsigned long long&, string);
#endif
string fastaFileName, align, calc, outputDir, output;
float match, misMatch, gapOpen, gapExtend, cutoff;
- int processors;
+ int processors, longestBase;
vector<string> fastaFileNames, Estimators;
vector<string> outputNames;
bool abort, countends, compress;
};
+/**************************************************************************************************/
+//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 pairwiseData {
+ string outputFileName;
+ string align, square, distcalcType, output;
+ unsigned long long start;
+ unsigned long long end;
+ MothurOut* m;
+ float match, misMatch, gapOpen, gapExtend, cutoff;
+ int count, threadID, longestBase;
+ bool countends;
+ SequenceDB alignDB;
+
+ pairwiseData(){}
+ pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, float cu, int tid) {
+ outputFileName = ofn;
+ m = mout;
+ start = st;
+ end = en;
+ match = ma;
+ misMatch = misMa;
+ gapOpen = gapO;
+ gapExtend = gapE;
+ longestBase = thr;
+ align = al;
+ square = sq;
+ distcalcType = di;
+ countends = co;
+ alignDB = DB;
+ count = 0;
+ output = op;
+ cutoff = cu;
+ threadID = tid;
+ }
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
+ pairwiseData* pDataArray;
+ pDataArray = (pairwiseData*)lpParam;
+
+ try {
+ ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
+
+ pDataArray->count = 0;
+
+ int startTime = time(NULL);
+
+ Alignment* alignment;
+ if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "blast") { alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch); }
+ else if(pDataArray->align == "noalign") { alignment = new NoAlign(); }
+ else {
+ pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
+ pDataArray->m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
+ }
+
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (pDataArray->countends) {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+
+ if(pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
+
+ for(int i=pDataArray->start;i<pDataArray->end;i++){
+ pDataArray->count++;
+
+ string name = pDataArray->alignDB.get(i).getName();
+ //pad with spaces to make compatible
+ if (name.length() < 10) { while (name.length() < 10) { name += " "; } }
+
+ outFile << name << '\t';
+
+ for(int j=0;j<pDataArray->alignDB.getNumSeqs();j++){
+
+ if (pDataArray->m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0; }
+
+ if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
+ }
+
+ if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
+ }
+
+ Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
+ Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
+
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
+
+ distCalculator->calcDist(seqI, seqJ);
+ double dist = distCalculator->getDist();
+
+ if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
+
+ outFile << dist << '\t';
+ }
+
+ outFile << endl;
+
+ if(i % 100 == 0){
+ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }
+
+ }
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
+
+ outFile.close();
+ delete alignment;
+ delete distCalculator;
+
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseSquareThreadFunction");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
+ pairwiseData* pDataArray;
+ pDataArray = (pairwiseData*)lpParam;
+
+ try {
+ ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
+
+ int startTime = time(NULL);
+
+ Alignment* alignment;
+ if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase); }
+ else if(pDataArray->align == "blast") { alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch); }
+ else if(pDataArray->align == "noalign") { alignment = new NoAlign(); }
+ else {
+ pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
+ pDataArray->m->mothurOutEndLine();
+ alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
+ }
+
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (pDataArray->countends) {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }else {
+ if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
+ if (pDataArray->distcalcType == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (pDataArray->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (pDataArray->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+
+ if((pDataArray->output == "lt") && pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
+
+ pDataArray->count = 0;
+ for(int i=pDataArray->start;i<pDataArray->end;i++){
+ pDataArray->count++;
+
+ if(pDataArray->output == "lt") {
+ string name = pDataArray->alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+ outFile << name << '\t';
+ }
+
+
+ for(int j=0;j<i;j++){
+
+ if (pDataArray->m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0; }
+
+ if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
+ }
+
+ if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
+ }
+
+ Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
+ Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
+
+ alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+ seqI.setAligned(alignment->getSeqAAln());
+ seqJ.setAligned(alignment->getSeqBAln());
+
+ distCalculator->calcDist(seqI, seqJ);
+ double dist = distCalculator->getDist();
+
+ if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
+
+ if(dist <= pDataArray->cutoff){
+ if (pDataArray->output == "column") { outFile << pDataArray->alignDB.get(i).getName() << ' ' << pDataArray->alignDB.get(j).getName() << ' ' << dist << endl; }
+ }
+ if (pDataArray->output == "lt") { outFile << dist << '\t'; }
+ }
+
+ if (pDataArray->output == "lt") { outFile << endl; }
+
+ if(i % 100 == 0){
+ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }
+
+ }
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+
+ outFile.close();
+ delete alignment;
+ delete distCalculator;
+
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseThreadFunction");
+ exit(1);
+ }
+}
+
+#endif
+
+
#endif
projects / mothur.git / blobdiff