2 * pairwiseseqscommand.cpp
5 * Created by westcott on 10/20/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "pairwiseseqscommand.h"
11 #include "sequence.hpp"
13 #include "gotohoverlap.hpp"
14 #include "needlemanoverlap.hpp"
15 #include "blastalign.hpp"
16 #include "noalign.hpp"
18 #include "ignoregaps.h"
19 #include "eachgapdist.h"
20 #include "eachgapignore.h"
21 #include "onegapdist.h"
22 #include "onegapignore.h"
25 //**********************************************************************************************************************
26 vector<string> PairwiseSeqsCommand::setParameters(){
28 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
29 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
30 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
31 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
32 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
33 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
34 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
35 CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
36 CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
37 CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
38 CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
39 CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
40 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
41 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
43 vector<string> myArray;
44 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
48 m->errorOut(e, "PairwiseSeqsCommand", "setParameters");
52 //**********************************************************************************************************************
53 string PairwiseSeqsCommand::getHelpString(){
55 string helpString = "";
56 helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n";
57 helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n";
58 helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
59 helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
60 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
61 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
62 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
63 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
64 helpString += "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n";
65 helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n";
66 helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
67 helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
68 helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
69 helpString += "The pairwise.seqs command should be in the following format: \n";
70 helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
71 helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n";
72 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
76 m->errorOut(e, "PairwiseSeqsCommand", "getHelpString");
81 //**********************************************************************************************************************
82 PairwiseSeqsCommand::PairwiseSeqsCommand(){
84 abort = true; calledHelp = true;
86 vector<string> tempOutNames;
87 outputTypes["phylip"] = tempOutNames;
88 outputTypes["column"] = tempOutNames;
91 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
95 //**********************************************************************************************************************
96 PairwiseSeqsCommand::PairwiseSeqsCommand(string option) {
98 abort = false; calledHelp = false;
100 //allow user to run help
101 if(option == "help") { help(); abort = true; calledHelp = true; }
102 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
105 vector<string> myArray = setParameters();
107 OptionParser parser(option);
108 map<string, string> parameters = parser.getParameters();
110 ValidParameters validParameter("pairwise.seqs");
111 map<string, string>::iterator it;
113 //check to make sure all parameters are valid for command
114 for (it = parameters.begin(); it != parameters.end(); it++) {
115 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
118 //initialize outputTypes
119 vector<string> tempOutNames;
120 outputTypes["phylip"] = tempOutNames;
121 outputTypes["column"] = tempOutNames;
123 //if the user changes the output directory command factory will send this info to us in the output parameter
124 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
127 //if the user changes the input directory command factory will send this info to us in the output parameter
128 string inputDir = validParameter.validFile(parameters, "inputdir", false);
130 if (inputDir == "not found"){ inputDir = ""; }
132 fastaFileName = validParameter.validFile(parameters, "fasta", false);
133 if (fastaFileName == "not found") {
134 //if there is a current fasta file, use it
135 string filename = m->getFastaFile();
136 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
137 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
140 m->splitAtDash(fastaFileName, fastaFileNames);
142 //go through files and make sure they are good, if not, then disregard them
143 for (int i = 0; i < fastaFileNames.size(); i++) {
146 if (fastaFileNames[i] == "current") {
147 fastaFileNames[i] = m->getFastaFile();
148 if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
150 m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
151 //erase from file list
152 fastaFileNames.erase(fastaFileNames.begin()+i);
159 if (inputDir != "") {
160 string path = m->hasPath(fastaFileNames[i]);
161 //if the user has not given a path then, add inputdir. else leave path alone.
162 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
168 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
170 //if you can't open it, try default location
171 if (ableToOpen == 1) {
172 if (m->getDefaultPath() != "") { //default path is set
173 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
174 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
176 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
178 fastaFileNames[i] = tryPath;
182 //if you can't open it, try output location
183 if (ableToOpen == 1) {
184 if (m->getOutputDir() != "") { //default path is set
185 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
186 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
188 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
190 fastaFileNames[i] = tryPath;
196 if (ableToOpen == 1) {
197 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
198 //erase from file list
199 fastaFileNames.erase(fastaFileNames.begin()+i);
205 //make sure there is at least one valid file left
206 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
209 //check for optional parameter and set defaults
210 // ...at some point should added some additional type checking...
212 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
213 convert(temp, match);
215 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
216 convert(temp, misMatch);
218 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
219 convert(temp, gapOpen);
221 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
222 convert(temp, gapExtend);
224 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
225 m->setProcessors(temp);
226 convert(temp, processors);
228 temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
229 convert(temp, cutoff);
231 temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
232 countends = m->isTrue(temp);
234 temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
235 compress = m->isTrue(temp);
237 align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
239 output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
240 if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
242 calc = validParameter.validFile(parameters, "calc", false);
243 if (calc == "not found") { calc = "onegap"; }
245 if (calc == "default") { calc = "onegap"; }
247 m->splitAtDash(calc, Estimators);
249 ValidCalculators validCalculator;
251 for (int i=0; i<Estimators.size(); i++) {
252 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
253 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
254 else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
255 else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
259 for (int i=0; i<Estimators.size(); i++) {
260 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
261 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
262 else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
263 else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
270 catch(exception& e) {
271 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
275 //**********************************************************************************************************************
277 int PairwiseSeqsCommand::execute(){
279 if (abort == true) { if (calledHelp) { return 0; } return 2; }
281 int longestBase = 2000; //will need to update this in driver if we find sequences with more bases. hardcoded so we don't have the pre-read user fasta file.
283 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
284 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
285 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
286 else if(align == "noalign") { alignment = new NoAlign(); }
288 m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
289 m->mothurOutEndLine();
290 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
295 for (int s = 0; s < fastaFileNames.size(); s++) {
296 if (m->control_pressed) { outputTypes.clear(); return 0; }
298 m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
300 if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
303 m->openInputFile(fastaFileNames[s], inFASTA);
304 alignDB = SequenceDB(inFASTA);
307 int numSeqs = alignDB.getNumSeqs();
308 int startTime = time(NULL);
309 string outputFile = "";
311 if (output == "lt") { //does the user want lower triangle phylip formatted file
312 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
313 remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
314 }else if (output == "column") { //user wants column format
315 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
316 outputTypes["column"].push_back(outputFile);
317 remove(outputFile.c_str());
318 }else { //assume square
319 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
320 remove(outputFile.c_str());
321 outputTypes["phylip"].push_back(outputFile);
330 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
331 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
333 //each process gets where it should start and stop in the file
334 if (output != "square") {
335 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
336 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
338 start = int ((float(pid)/float(processors)) * numSeqs);
339 end = int ((float(pid+1)/float(processors)) * numSeqs);
342 if (output == "column") {
344 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
347 strcpy(filename, outputFile.c_str());
349 MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
351 if (pid == 0) { //you are the root process
356 driverMPI(start, end, outMPI, cutoff);
358 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
361 for(int i = 1; i < processors; i++) {
362 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
365 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
367 }else { //you are a child process
369 driverMPI(start, end, outMPI, cutoff);
371 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
375 //tell parent you are done.
376 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
379 MPI_File_close(&outMPI);
381 }else { //lower triangle format
382 if (pid == 0) { //you are the root process
386 unsigned long int mySize;
388 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
389 else { driverMPI(start, end, outputFile, mySize, output); }
391 if (m->control_pressed) { outputTypes.clear(); remove(outputFile.c_str()); delete distCalculator; return 0; }
393 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
398 strcpy(filename, outputFile.c_str());
400 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
403 for(int b = 1; b < processors; b++) {
404 unsigned long int fileSize;
406 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
408 MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
410 string outTemp = outputFile + toString(b) + ".temp";
412 char* buf = new char[outTemp.length()];
413 memcpy(buf, outTemp.c_str(), outTemp.length());
415 MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
419 while (count < fileSize) {
421 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
422 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
426 MPI_File_close(&inMPI); //deleted on close
429 MPI_File_close(&outMPI);
430 }else { //you are a child process
432 unsigned long int size;
433 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
434 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
436 if (m->control_pressed) { delete distCalculator; return 0; }
438 //tell parent you are done.
439 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
442 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
445 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
446 //if you don't need to fork anything
448 if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
449 else { driver(0, numSeqs, outputFile, "square"); }
450 }else{ //you have multiple processors
452 for (int i = 0; i < processors; i++) {
453 distlinePair tempLine;
454 lines.push_back(tempLine);
455 if (output != "square") {
456 lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
457 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
459 lines[i].start = int ((float(i)/float(processors)) * numSeqs);
460 lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
464 createProcesses(outputFile);
468 if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
469 else { driver(0, numSeqs, outputFile, "square"); }
473 if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
476 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
478 if (pid == 0) { //only one process should output to screen
482 fileHandle.open(outputFile.c_str());
484 m->gobble(fileHandle);
485 if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
489 m->mothurOut("Compressing..."); m->mothurOutEndLine();
490 m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
491 system(("gzip -v " + outputFile).c_str());
492 outputNames.push_back(outputFile + ".gz");
493 }else { outputNames.push_back(outputFile); }
499 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
501 if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
504 delete distCalculator;
506 //set phylip file as new current phylipfile
508 itTypes = outputTypes.find("phylip");
509 if (itTypes != outputTypes.end()) {
510 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
513 //set column file as new current columnfile
514 itTypes = outputTypes.find("column");
515 if (itTypes != outputTypes.end()) {
516 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
519 m->mothurOutEndLine();
520 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
521 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
522 m->mothurOutEndLine();
527 catch(exception& e) {
528 m->errorOut(e, "PairwiseSeqsCommand", "execute");
533 /**************************************************************************************************/
534 void PairwiseSeqsCommand::createProcesses(string filename) {
536 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
540 //loop through and create all the processes you want
541 while (process != processors) {
545 processIDS.push_back(pid);
548 if (output != "square") { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
549 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
552 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
553 for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
559 if (output != "square") { driver(lines[0].start, lines[0].end, filename, cutoff); }
560 else { driver(lines[0].start, lines[0].end, filename, "square"); }
563 //force parent to wait until all the processes are done
564 for (int i=0;i<processIDS.size();i++) {
565 int temp = processIDS[i];
569 //append and remove temp files
570 for (int i=0;i<processIDS.size();i++) {
571 m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
572 remove((filename + toString(processIDS[i]) + ".temp").c_str());
576 catch(exception& e) {
577 m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
582 /**************************************************************************************************/
583 /////// need to fix to work with calcs and sequencedb
584 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
587 int startTime = time(NULL);
590 ofstream outFile(dFileName.c_str(), ios::trunc);
591 outFile.setf(ios::fixed, ios::showpoint);
592 outFile << setprecision(4);
594 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
596 for(int i=startLine;i<endLine;i++){
598 string name = alignDB.get(i).getName();
599 if (name.length() < 10) { //pad with spaces to make compatible
600 while (name.length() < 10) { name += " "; }
602 outFile << name << '\t';
605 for(int j=0;j<i;j++){
607 if (m->control_pressed) { outFile.close(); return 0; }
609 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
610 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
613 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
614 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
617 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
618 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
620 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
621 seqI.setAligned(alignment->getSeqAAln());
622 seqJ.setAligned(alignment->getSeqBAln());
625 distCalculator->calcDist(seqI, seqJ);
626 double dist = distCalculator->getDist();
629 if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
631 if (output == "lt") { outFile << dist << '\t'; }
634 if (output == "lt") { outFile << endl; }
637 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
641 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
647 catch(exception& e) {
648 m->errorOut(e, "PairwiseSeqsCommand", "driver");
652 /**************************************************************************************************/
653 /////// need to fix to work with calcs and sequencedb
654 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
657 int startTime = time(NULL);
660 ofstream outFile(dFileName.c_str(), ios::trunc);
661 outFile.setf(ios::fixed, ios::showpoint);
662 outFile << setprecision(4);
664 if(startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
666 for(int i=startLine;i<endLine;i++){
668 string name = alignDB.get(i).getName();
669 //pad with spaces to make compatible
670 if (name.length() < 10) { while (name.length() < 10) { name += " "; } }
672 outFile << name << '\t';
674 for(int j=0;j<alignDB.getNumSeqs();j++){
676 if (m->control_pressed) { outFile.close(); return 0; }
678 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
679 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
682 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
683 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
686 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
687 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
689 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
690 seqI.setAligned(alignment->getSeqAAln());
691 seqJ.setAligned(alignment->getSeqBAln());
693 distCalculator->calcDist(seqI, seqJ);
694 double dist = distCalculator->getDist();
696 outFile << dist << '\t';
702 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
706 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
712 catch(exception& e) {
713 m->errorOut(e, "PairwiseSeqsCommand", "driver");
718 /**************************************************************************************************/
719 /////// need to fix to work with calcs and sequencedb
720 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
723 int startTime = time(NULL);
725 string outputString = "";
727 for(int i=startLine;i<endLine;i++){
729 for(int j=0;j<i;j++){
731 if (m->control_pressed) { return 0; }
733 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
734 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
737 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
738 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
741 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
742 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
744 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
745 seqI.setAligned(alignment->getSeqAAln());
746 seqJ.setAligned(alignment->getSeqBAln());
748 distCalculator->calcDist(seqI, seqJ);
749 double dist = distCalculator->getDist();
752 outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
757 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
758 cout << i << '\t' << (time(NULL) - startTime) << endl;
762 //send results to parent
763 int length = outputString.length();
765 char* buf = new char[length];
766 memcpy(buf, outputString.c_str(), length);
768 MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
776 catch(exception& e) {
777 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
781 /**************************************************************************************************/
782 /////// need to fix to work with calcs and sequencedb
783 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
788 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
791 strcpy(filename, file.c_str());
793 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
797 string outputString = "";
800 if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
802 for(int i=startLine;i<endLine;i++){
804 string name = alignDB.get(i).getName();
805 if (name.length() < 10) { //pad with spaces to make compatible
806 while (name.length() < 10) { name += " "; }
808 outputString += name + "\t";
810 for(int j=0;j<i;j++){
812 if (m->control_pressed) { return 0; }
814 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
815 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
818 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
819 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
822 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
823 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
825 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
826 seqI.setAligned(alignment->getSeqAAln());
827 seqJ.setAligned(alignment->getSeqBAln());
829 distCalculator->calcDist(seqI, seqJ);
830 double dist = distCalculator->getDist();
832 outputString += toString(dist) + "\t";
835 outputString += "\n";
837 //send results to parent
838 int length = outputString.length();
839 char* buf = new char[length];
840 memcpy(buf, outputString.c_str(), length);
842 MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
843 size += outputString.length();
848 MPI_File_close(&outMPI);
852 catch(exception& e) {
853 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
857 /**************************************************************************************************/
858 /////// need to fix to work with calcs and sequencedb
859 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
864 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
867 strcpy(filename, file.c_str());
869 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
873 string outputString = "";
876 if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
878 for(int i=startLine;i<endLine;i++){
880 string name = alignDB.get(i).getName();
881 if (name.length() < 10) { //pad with spaces to make compatible
882 while (name.length() < 10) { name += " "; }
884 outputString += name + "\t";
886 for(int j=0;j<alignDB.getNumSeqs();j++){
888 if (m->control_pressed) { return 0; }
890 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
891 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
894 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
895 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
898 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
899 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
901 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
902 seqI.setAligned(alignment->getSeqAAln());
903 seqJ.setAligned(alignment->getSeqBAln());
905 distCalculator->calcDist(seqI, seqJ);
906 double dist = distCalculator->getDist();
908 outputString += toString(dist) + "\t";
911 outputString += "\n";
913 //send results to parent
914 int length = outputString.length();
915 char* buf = new char[length];
916 memcpy(buf, outputString.c_str(), length);
918 MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
919 size += outputString.length();
924 MPI_File_close(&outMPI);
928 catch(exception& e) {
929 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
934 /**************************************************************************************************/