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; }
104 vector<string> myArray = setParameters();
106 OptionParser parser(option);
107 map<string, string> parameters = parser.getParameters();
109 ValidParameters validParameter("pairwise.seqs");
110 map<string, string>::iterator it;
112 //check to make sure all parameters are valid for command
113 for (it = parameters.begin(); it != parameters.end(); it++) {
114 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
117 //initialize outputTypes
118 vector<string> tempOutNames;
119 outputTypes["phylip"] = tempOutNames;
120 outputTypes["column"] = tempOutNames;
122 //if the user changes the output directory command factory will send this info to us in the output parameter
123 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
126 //if the user changes the input directory command factory will send this info to us in the output parameter
127 string inputDir = validParameter.validFile(parameters, "inputdir", false);
129 if (inputDir == "not found"){ inputDir = ""; }
131 fastaFileName = validParameter.validFile(parameters, "fasta", false);
132 if (fastaFileName == "not found") {
133 //if there is a current fasta file, use it
134 string filename = m->getFastaFile();
135 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
136 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
139 m->splitAtDash(fastaFileName, fastaFileNames);
141 //go through files and make sure they are good, if not, then disregard them
142 for (int i = 0; i < fastaFileNames.size(); i++) {
144 if (inputDir != "") {
145 string path = m->hasPath(fastaFileNames[i]);
146 //if the user has not given a path then, add inputdir. else leave path alone.
147 if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
153 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
155 //if you can't open it, try default location
156 if (ableToOpen == 1) {
157 if (m->getDefaultPath() != "") { //default path is set
158 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
159 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
161 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
163 fastaFileNames[i] = tryPath;
167 //if you can't open it, try output location
168 if (ableToOpen == 1) {
169 if (m->getOutputDir() != "") { //default path is set
170 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
171 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
173 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
175 fastaFileNames[i] = tryPath;
181 if (ableToOpen == 1) {
182 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
183 //erase from file list
184 fastaFileNames.erase(fastaFileNames.begin()+i);
189 //make sure there is at least one valid file left
190 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
193 //check for optional parameter and set defaults
194 // ...at some point should added some additional type checking...
196 temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
197 convert(temp, match);
199 temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
200 convert(temp, misMatch);
202 temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
203 convert(temp, gapOpen);
205 temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
206 convert(temp, gapExtend);
208 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
209 m->setProcessors(temp);
210 convert(temp, processors);
212 temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
213 convert(temp, cutoff);
215 temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
216 countends = m->isTrue(temp);
218 temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
219 compress = m->isTrue(temp);
221 align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
223 output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
224 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"; }
226 calc = validParameter.validFile(parameters, "calc", false);
227 if (calc == "not found") { calc = "onegap"; }
229 if (calc == "default") { calc = "onegap"; }
231 m->splitAtDash(calc, Estimators);
233 ValidCalculators validCalculator;
235 for (int i=0; i<Estimators.size(); i++) {
236 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
237 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
238 else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
239 else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
243 for (int i=0; i<Estimators.size(); i++) {
244 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
245 if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
246 else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
247 else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
254 catch(exception& e) {
255 m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
259 //**********************************************************************************************************************
261 int PairwiseSeqsCommand::execute(){
263 if (abort == true) { if (calledHelp) { return 0; } return 2; }
265 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.
267 if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
268 else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
269 else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
270 else if(align == "noalign") { alignment = new NoAlign(); }
272 m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
273 m->mothurOutEndLine();
274 alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
279 for (int s = 0; s < fastaFileNames.size(); s++) {
280 if (m->control_pressed) { outputTypes.clear(); return 0; }
282 m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
284 if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
287 m->openInputFile(fastaFileNames[s], inFASTA);
288 alignDB = SequenceDB(inFASTA);
291 int numSeqs = alignDB.getNumSeqs();
292 int startTime = time(NULL);
293 string outputFile = "";
295 if (output == "lt") { //does the user want lower triangle phylip formatted file
296 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
297 remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
298 }else if (output == "column") { //user wants column format
299 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
300 outputTypes["column"].push_back(outputFile);
301 remove(outputFile.c_str());
302 }else { //assume square
303 outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
304 remove(outputFile.c_str());
305 outputTypes["phylip"].push_back(outputFile);
314 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
315 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
317 //each process gets where it should start and stop in the file
318 if (output != "square") {
319 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
320 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
322 start = int ((float(pid)/float(processors)) * numSeqs);
323 end = int ((float(pid+1)/float(processors)) * numSeqs);
326 if (output == "column") {
328 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
331 strcpy(filename, outputFile.c_str());
333 MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
335 if (pid == 0) { //you are the root process
340 driverMPI(start, end, outMPI, cutoff);
342 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
345 for(int i = 1; i < processors; i++) {
346 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
349 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
351 }else { //you are a child process
353 driverMPI(start, end, outMPI, cutoff);
355 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
359 //tell parent you are done.
360 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
363 MPI_File_close(&outMPI);
365 }else { //lower triangle format
366 if (pid == 0) { //you are the root process
370 unsigned long int mySize;
372 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
373 else { driverMPI(start, end, outputFile, mySize, output); }
375 if (m->control_pressed) { outputTypes.clear(); remove(outputFile.c_str()); delete distCalculator; return 0; }
377 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
382 strcpy(filename, outputFile.c_str());
384 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
387 for(int b = 1; b < processors; b++) {
388 unsigned long int fileSize;
390 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
392 MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
394 string outTemp = outputFile + toString(b) + ".temp";
396 char* buf = new char[outTemp.length()];
397 memcpy(buf, outTemp.c_str(), outTemp.length());
399 MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
403 while (count < fileSize) {
405 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
406 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
410 MPI_File_close(&inMPI); //deleted on close
413 MPI_File_close(&outMPI);
414 }else { //you are a child process
416 unsigned long int size;
417 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
418 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
420 if (m->control_pressed) { delete distCalculator; return 0; }
422 //tell parent you are done.
423 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
426 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
429 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
430 //if you don't need to fork anything
432 if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
433 else { driver(0, numSeqs, outputFile, "square"); }
434 }else{ //you have multiple processors
436 for (int i = 0; i < processors; i++) {
437 distlinePair tempLine;
438 lines.push_back(tempLine);
439 if (output != "square") {
440 lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
441 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
443 lines[i].start = int ((float(i)/float(processors)) * numSeqs);
444 lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
448 createProcesses(outputFile);
452 if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
453 else { driver(0, numSeqs, outputFile, "square"); }
457 if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
460 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
462 if (pid == 0) { //only one process should output to screen
466 fileHandle.open(outputFile.c_str());
468 m->gobble(fileHandle);
469 if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
473 m->mothurOut("Compressing..."); m->mothurOutEndLine();
474 m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
475 system(("gzip -v " + outputFile).c_str());
476 outputNames.push_back(outputFile + ".gz");
477 }else { outputNames.push_back(outputFile); }
483 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
485 if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
488 delete distCalculator;
490 //set phylip file as new current phylipfile
492 itTypes = outputTypes.find("phylip");
493 if (itTypes != outputTypes.end()) {
494 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
497 //set column file as new current columnfile
498 itTypes = outputTypes.find("column");
499 if (itTypes != outputTypes.end()) {
500 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
503 m->mothurOutEndLine();
504 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
505 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
506 m->mothurOutEndLine();
511 catch(exception& e) {
512 m->errorOut(e, "PairwiseSeqsCommand", "execute");
517 /**************************************************************************************************/
518 void PairwiseSeqsCommand::createProcesses(string filename) {
520 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
524 //loop through and create all the processes you want
525 while (process != processors) {
529 processIDS.push_back(pid);
532 if (output != "square") { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
533 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
536 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
537 for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
543 if (output != "square") { driver(lines[0].start, lines[0].end, filename, cutoff); }
544 else { driver(lines[0].start, lines[0].end, filename, "square"); }
547 //force parent to wait until all the processes are done
548 for (int i=0;i<processIDS.size();i++) {
549 int temp = processIDS[i];
553 //append and remove temp files
554 for (int i=0;i<processIDS.size();i++) {
555 m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
556 remove((filename + toString(processIDS[i]) + ".temp").c_str());
560 catch(exception& e) {
561 m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
566 /**************************************************************************************************/
567 /////// need to fix to work with calcs and sequencedb
568 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
571 int startTime = time(NULL);
574 ofstream outFile(dFileName.c_str(), ios::trunc);
575 outFile.setf(ios::fixed, ios::showpoint);
576 outFile << setprecision(4);
578 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
580 for(int i=startLine;i<endLine;i++){
582 string name = alignDB.get(i).getName();
583 if (name.length() < 10) { //pad with spaces to make compatible
584 while (name.length() < 10) { name += " "; }
586 outFile << name << '\t';
589 for(int j=0;j<i;j++){
591 if (m->control_pressed) { outFile.close(); return 0; }
593 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
594 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
597 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
598 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
601 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
602 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
604 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
605 seqI.setAligned(alignment->getSeqAAln());
606 seqJ.setAligned(alignment->getSeqBAln());
609 distCalculator->calcDist(seqI, seqJ);
610 double dist = distCalculator->getDist();
613 if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
615 if (output == "lt") { outFile << dist << '\t'; }
618 if (output == "lt") { outFile << endl; }
621 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
625 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
631 catch(exception& e) {
632 m->errorOut(e, "PairwiseSeqsCommand", "driver");
636 /**************************************************************************************************/
637 /////// need to fix to work with calcs and sequencedb
638 int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
641 int startTime = time(NULL);
644 ofstream outFile(dFileName.c_str(), ios::trunc);
645 outFile.setf(ios::fixed, ios::showpoint);
646 outFile << setprecision(4);
648 if(startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
650 for(int i=startLine;i<endLine;i++){
652 string name = alignDB.get(i).getName();
653 //pad with spaces to make compatible
654 if (name.length() < 10) { while (name.length() < 10) { name += " "; } }
656 outFile << name << '\t';
658 for(int j=0;j<alignDB.getNumSeqs();j++){
660 if (m->control_pressed) { outFile.close(); return 0; }
662 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
663 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
666 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
667 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
670 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
671 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
673 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
674 seqI.setAligned(alignment->getSeqAAln());
675 seqJ.setAligned(alignment->getSeqBAln());
677 distCalculator->calcDist(seqI, seqJ);
678 double dist = distCalculator->getDist();
680 outFile << dist << '\t';
686 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
690 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
696 catch(exception& e) {
697 m->errorOut(e, "PairwiseSeqsCommand", "driver");
702 /**************************************************************************************************/
703 /////// need to fix to work with calcs and sequencedb
704 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
707 int startTime = time(NULL);
709 string outputString = "";
711 for(int i=startLine;i<endLine;i++){
713 for(int j=0;j<i;j++){
715 if (m->control_pressed) { return 0; }
717 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
718 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
721 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
722 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
725 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
726 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
728 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
729 seqI.setAligned(alignment->getSeqAAln());
730 seqJ.setAligned(alignment->getSeqBAln());
732 distCalculator->calcDist(seqI, seqJ);
733 double dist = distCalculator->getDist();
736 outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
741 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
742 cout << i << '\t' << (time(NULL) - startTime) << endl;
746 //send results to parent
747 int length = outputString.length();
749 char* buf = new char[length];
750 memcpy(buf, outputString.c_str(), length);
752 MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
760 catch(exception& e) {
761 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
765 /**************************************************************************************************/
766 /////// need to fix to work with calcs and sequencedb
767 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
772 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
775 strcpy(filename, file.c_str());
777 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
781 string outputString = "";
784 if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
786 for(int i=startLine;i<endLine;i++){
788 string name = alignDB.get(i).getName();
789 if (name.length() < 10) { //pad with spaces to make compatible
790 while (name.length() < 10) { name += " "; }
792 outputString += name + "\t";
794 for(int j=0;j<i;j++){
796 if (m->control_pressed) { return 0; }
798 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
799 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
802 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
803 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
806 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
807 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
809 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
810 seqI.setAligned(alignment->getSeqAAln());
811 seqJ.setAligned(alignment->getSeqBAln());
813 distCalculator->calcDist(seqI, seqJ);
814 double dist = distCalculator->getDist();
816 outputString += toString(dist) + "\t";
819 outputString += "\n";
821 //send results to parent
822 int length = outputString.length();
823 char* buf = new char[length];
824 memcpy(buf, outputString.c_str(), length);
826 MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
827 size += outputString.length();
832 MPI_File_close(&outMPI);
836 catch(exception& e) {
837 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
841 /**************************************************************************************************/
842 /////// need to fix to work with calcs and sequencedb
843 int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
848 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
851 strcpy(filename, file.c_str());
853 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
857 string outputString = "";
860 if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
862 for(int i=startLine;i<endLine;i++){
864 string name = alignDB.get(i).getName();
865 if (name.length() < 10) { //pad with spaces to make compatible
866 while (name.length() < 10) { name += " "; }
868 outputString += name + "\t";
870 for(int j=0;j<alignDB.getNumSeqs();j++){
872 if (m->control_pressed) { return 0; }
874 if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
875 alignment->resize(alignDB.get(i).getUnaligned().length()+1);
878 if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
879 alignment->resize(alignDB.get(j).getUnaligned().length()+1);
882 Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
883 Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
885 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
886 seqI.setAligned(alignment->getSeqAAln());
887 seqJ.setAligned(alignment->getSeqBAln());
889 distCalculator->calcDist(seqI, seqJ);
890 double dist = distCalculator->getDist();
892 outputString += toString(dist) + "\t";
895 outputString += "\n";
897 //send results to parent
898 int length = outputString.length();
899 char* buf = new char[length];
900 memcpy(buf, outputString.c_str(), length);
902 MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
903 size += outputString.length();
908 MPI_File_close(&outMPI);
912 catch(exception& e) {
913 m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
918 /**************************************************************************************************/