+++ /dev/null
-#ifndef PAIRWISESEQSCOMMAND_H
-#define PAIRWISESEQSCOMMAND_H
-
-/*
- * pairwiseseqscommand.h
- * Mothur
- *
- * Created by westcott on 10/20/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "database.hpp"
-#include "alignment.hpp"
-#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 {
-
-public:
- PairwiseSeqsCommand(string);
- PairwiseSeqsCommand();
- ~PairwiseSeqsCommand() {}
-
- vector<string> setParameters();
- string getCommandName() { return "pairwise.seqs"; }
- string getCommandCategory() { return "Sequence Processing"; }
- string getHelpString();
- 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"; }
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-
-private:
- struct distlinePair {
- int start;
- int end;
- };
-
- vector<int> processIDS; //end line, processid
- vector<distlinePair> lines;
-
- SequenceDB alignDB;
-
- void createProcesses(string);
- int driver(int, int, string, float);
- int driver(int, int, string, string);
-
- #ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, float);
- 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, 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, 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;
- 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 = pDataArray->end;
-
- 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++){
-
- 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();
-
- outFile << dist << '\t';
- }
-
- outFile << endl;
-
- if(i % 100 == 0){
- pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
- }
-
- }
- pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
-
- 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);
-
- pDataArray->count = pDataArray->end;
-
- 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; }
-
- for(int i=pDataArray->start;i<pDataArray->end;i++){
-
- 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(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->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
- }
-
- }
- pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
-
- outFile.close();
- delete alignment;
- delete distCalculator;
-
-
- }
- catch(exception& e) {
- pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseThreadFunction");
- exit(1);
- }
-}
-
-#endif
-
-
-#endif
-
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