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|
/*
* pairwiseseqscommand.cpp
* Mothur
*
* Created by westcott on 10/20/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "pairwiseseqscommand.h"
//**********************************************************************************************************************
vector<string> PairwiseSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true,true); parameters.push_back(pfasta);
CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "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);
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false,true); parameters.push_back(poutput);
CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false,true); parameters.push_back(pcutoff);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string PairwiseSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n";
helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n";
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";
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";
helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
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";
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";
helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
helpString += "The pairwise.seqs command should be in the following format: \n";
helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string PairwiseSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "phylip") { pattern = "[filename],[outputtag],dist"; }
else if (type == "column") { pattern = "[filename],dist"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(string option) {
try {
abort = false; calledHelp = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter("pairwise.seqs");
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else {
m->splitAtDash(fastaFileName, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
bool ignore = false;
if (fastaFileNames[i] == "current") {
fastaFileNames[i] = m->getFastaFile();
if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
//if you can't open it, try output location
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}else {
m->setFastaFile(fastaFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
m->mothurConvert(temp, misMatch);
if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
m->mothurConvert(temp, gapOpen);
if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
m->mothurConvert(temp, gapExtend);
if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
countends = m->isTrue(temp);
temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
compress = m->isTrue(temp);
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
if (output=="phylip") { output = "lt"; }
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"; }
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "onegap"; }
else {
if (calc == "default") { calc = "onegap"; }
}
m->splitAtDash(calc, Estimators);
}
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int PairwiseSeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
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.
cutoff += 0.005;
for (int s = 0; s < fastaFileNames.size(); s++) {
if (m->control_pressed) { outputTypes.clear(); return 0; }
m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
ifstream inFASTA;
m->openInputFile(fastaFileNames[s], inFASTA);
alignDB = SequenceDB(inFASTA);
inFASTA.close();
int numSeqs = alignDB.getNumSeqs();
int startTime = time(NULL);
string outputFile = "";
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
if (output == "lt") { //does the user want lower triangle phylip formatted file
variables["[outputtag]"] = "phylip";
outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
}else if (output == "column") { //user wants column format
outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
m->mothurRemove(outputFile);
}else { //assume square
variables["[outputtag]"] = "square";
outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
#ifdef USE_MPI
int pid, start, end;
int tag = 2001;
MPI_Status status;
MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
//each process gets where it should start and stop in the file
if (output != "square") {
start = int (sqrt(float(pid)/float(processors)) * numSeqs);
end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
}else{
start = int ((float(pid)/float(processors)) * numSeqs);
end = int ((float(pid+1)/float(processors)) * numSeqs);
}
if (output == "column") {
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
char filename[1024];
strcpy(filename, outputFile.c_str());
MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
if (pid == 0) { //you are the root process
//do your part
string outputMyPart;
driverMPI(start, end, outMPI, cutoff);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
char buf[5];
MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
}
}else { //you are a child process
//do your part
driverMPI(start, end, outMPI, cutoff);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
char buf[5];
strcpy(buf, "done");
//tell parent you are done.
MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
MPI_File_close(&outMPI);
}else { //lower triangle format
if (pid == 0) { //you are the root process
//do your part
string outputMyPart;
unsigned long long mySize;
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
MPI_File inMPI;
char filename[1024];
strcpy(filename, outputFile.c_str());
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
//wait on chidren
for(int b = 1; b < processors; b++) {
unsigned long long fileSize;
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); return 0; }
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
string outTemp = outputFile + toString(b) + ".temp";
char* buf = new char[outTemp.length()];
memcpy(buf, outTemp.c_str(), outTemp.length());
MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
delete buf;
int count = 0;
while (count < fileSize) {
char buf2[1];
MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
count += 1;
}
MPI_File_close(&inMPI); //deleted on close
}
MPI_File_close(&outMPI);
}else { //you are a child process
//do your part
unsigned long long size;
if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
if (m->control_pressed) { return 0; }
//tell parent you are done.
MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
}
}
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//if you don't need to fork anything
if(processors == 1){
if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
else { driver(0, numSeqs, outputFile, "square"); }
}else{ //you have multiple processors
for (int i = 0; i < processors; i++) {
distlinePair tempLine;
lines.push_back(tempLine);
if (output != "square") {
lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
}else{
lines[i].start = int ((float(i)/float(processors)) * numSeqs);
lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
}
}
createProcesses(outputFile);
}
//#else
//ifstream inFASTA;
//if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
//else { driver(0, numSeqs, outputFile, "square"); }
//#endif
#endif
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
if (pid == 0) { //only one process should output to screen
#endif
ifstream fileHandle;
fileHandle.open(outputFile.c_str());
if(fileHandle) {
m->gobble(fileHandle);
if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
}
if (compress) {
m->mothurOut("Compressing..."); m->mothurOutEndLine();
m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
system(("gzip -v " + outputFile).c_str());
outputNames.push_back(outputFile + ".gz");
}else { outputNames.push_back(outputFile); }
#ifdef USE_MPI
}
#endif
m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
}
//set phylip file as new current phylipfile
string current = "";
itTypes = outputTypes.find("phylip");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
}
//set column file as new current columnfile
itTypes = outputTypes.find("column");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************************/
void PairwiseSeqsCommand::createProcesses(string filename) {
try {
int process = 1;
processIDS.clear();
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
if (pid > 0) {
processIDS.push_back(pid);
process++;
}else if (pid == 0){
if (output != "square") { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
exit(0);
}
}
//parent do my part
if (output != "square") { driver(lines[0].start, lines[0].end, filename, cutoff); }
else { driver(lines[0].start, lines[0].end, filename, "square"); }
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
//Windows version shared memory, so be careful when passing variables through the distanceData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
//that's why the distance calculator was moved inside of the driver to make separate copies.
//////////////////////////////////////////////////////////////////////////////////////////////////////
vector<pairwiseData*> pDataArray; //[processors-1];
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
//Create processor-1 worker threads.
for( int i=0; i<processors-1; i++ ){
string extension = toString(i) + ".temp";
// Allocate memory for thread data.
pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, i);
pDataArray.push_back(tempDist);
processIDS.push_back(i);
if (output != "square") { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); }
else { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseSquareThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); }
}
//do your part
if (output != "square") { driver(lines[0].start, lines[0].end, filename, cutoff); }
else { driver(lines[0].start, lines[0].end, filename, "square"); }
//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++){
if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
}
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#endif
//append and remove temp files
for (int i=0;i<processIDS.size();i++) {
m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
}
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
exit(1);
}
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
try {
int startTime = time(NULL);
Alignment* alignment;
if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
else if(align == "noalign") { alignment = new NoAlign(); }
else {
m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
m->mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
ValidCalculators validCalculator;
Dist* distCalculator;
if (countends) {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
}
}else {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
//column file
ofstream outFile(dFileName.c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
for(int i=startLine;i<endLine;i++){
if(output == "lt") {
string name = 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 (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
}
if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
Sequence seqJ(alignDB.get(j).getName(), 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 (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
if(dist <= cutoff){
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}
if (output == "lt") { outFile << dist << '\t'; }
}
if (output == "lt") { outFile << endl; }
if(i % 100 == 0){
m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
outFile.close();
delete alignment;
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "driver");
exit(1);
}
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
try {
int startTime = time(NULL);
Alignment* alignment;
if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
else if(align == "noalign") { alignment = new NoAlign(); }
else {
m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
m->mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
ValidCalculators validCalculator;
Dist* distCalculator;
if (countends) {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
}
}else {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
//column file
ofstream outFile(dFileName.c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
if(startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
for(int i=startLine;i<endLine;i++){
string name = 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<alignDB.getNumSeqs();j++){
if (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
}
if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
Sequence seqJ(alignDB.get(j).getName(), 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';
if (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
}
outFile << endl;
if(i % 100 == 0){
m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
outFile.close();
delete alignment;
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "driver");
exit(1);
}
}
#ifdef USE_MPI
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
try {
MPI_Status status;
int startTime = time(NULL);
Alignment* alignment;
if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
else if(align == "noalign") { alignment = new NoAlign(); }
else {
m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
m->mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
ValidCalculators validCalculator;
Dist* distCalculator;
if (countends) {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
}
}else {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
string outputString = "";
for(int i=startLine;i<endLine;i++){
for(int j=0;j<i;j++){
if (m->control_pressed) { delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
}
if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
Sequence seqJ(alignDB.get(j).getName(), 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 (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
if(dist <= cutoff){
outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
}
}
if(i % 100 == 0){
//m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
cout << i << '\t' << (time(NULL) - startTime) << endl;
}
//send results to parent
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
delete buf;
}
delete alignment;
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
exit(1);
}
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
try {
MPI_Status status;
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
char filename[1024];
strcpy(filename, file.c_str());
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
Alignment* alignment;
if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
else if(align == "noalign") { alignment = new NoAlign(); }
else {
m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
m->mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
ValidCalculators validCalculator;
Dist* distCalculator;
if (countends) {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
}
}else {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
string outputString = "";
size = 0;
if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
for(int i=startLine;i<endLine;i++){
string name = alignDB.get(i).getName();
if (name.length() < 10) { //pad with spaces to make compatible
while (name.length() < 10) { name += " "; }
}
outputString += name + "\t";
for(int j=0;j<i;j++){
if (m->control_pressed) { delete alignment; delete distCalculator; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
}
if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
Sequence seqJ(alignDB.get(j).getName(), 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 (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
outputString += toString(dist) + "\t";
}
outputString += "\n";
//send results to parent
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
size += outputString.length();
outputString = "";
delete buf;
}
MPI_File_close(&outMPI);
delete alignment;
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
exit(1);
}
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
try {
MPI_Status status;
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
char filename[1024];
strcpy(filename, file.c_str());
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
Alignment* alignment;
if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
else if(align == "noalign") { alignment = new NoAlign(); }
else {
m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
m->mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
ValidCalculators validCalculator;
Dist* distCalculator;
if (countends) {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
}
}else {
if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
string outputString = "";
size = 0;
if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
for(int i=startLine;i<endLine;i++){
string name = alignDB.get(i).getName();
if (name.length() < 10) { //pad with spaces to make compatible
while (name.length() < 10) { name += " "; }
}
outputString += name + "\t";
for(int j=0;j<alignDB.getNumSeqs();j++){
if (m->control_pressed) { delete alignment; return 0; }
if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(i).getUnaligned().length()+1);
}
if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
alignment->resize(alignDB.get(j).getUnaligned().length()+1);
}
Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
Sequence seqJ(alignDB.get(j).getName(), 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();
outputString += toString(dist) + "\t";
if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
}
outputString += "\n";
//send results to parent
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
size += outputString.length();
outputString = "";
delete buf;
}
MPI_File_close(&outMPI);
delete alignment;
return 1;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
exit(1);
}
}
#endif
/**************************************************************************************************/
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