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|
/*
* pairwiseseqscommand.cpp
* Mothur
*
* Created by westcott on 10/20/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "pairwiseseqscommand.h"
#include "kmerdist.hpp"
//**********************************************************************************************************************
vector<string> PairwiseSeqsCommand::setParameters(){
try {
CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn","column",false,false); parameters.push_back(pcolumn);
CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn","",false,false); parameters.push_back(poldfasta);
CommandParameter pfitcalc("fitcalc", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfitcalc);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true,true); parameters.push_back(pfasta);
CommandParameter palign("align", "Multiple", "needleman-gotoh-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 pkcutoff("kmercutoff", "Number", "", "-1.0", "", "", "","",false,false,true);
parameters.push_back(pkcutoff);
CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
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, oldfasta, column, processors.\n";
helpString += "The fasta parameter is required.\n";
helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman 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 kmercutoff parameter allows you to specify maximum kmer distance. The kmercutoff is used to reduce the processing time by avoiding the aligning and distance calculations for sequences with a kmer distance above the cutoff. Kmer distance are calculated using methods described here, Edgar, R. C. (2004). Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5:113. The defaults vary based on the cutoff selected. Cutoff <= 0.05 -> kmerCutoff = -1.0, cutoff 0.05 - 0.15 -> kmerCutoff = -0.50, cutoff 0.15-0.25 -> kmerCutoff = -0.25, cutoff > 0.25 -> kmerCutoff = -0.10.\n";
helpString += "The ksize parameter allows you to specify the kmer size for calculating the kmer distance. The default is 7.\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 oldfasta and column parameters allow you to append the distances calculated to the column file.\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=gotoh)\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->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
fastaFileName = validParameter.validFile(parameters, "fasta");
if (fastaFileName == "not found") {
fastaFileName = current->getFastaFile();
if (fastaFileName != "") { m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current fastafile and the fasta parameter is required.\n"); abort = true; }
}else if (fastaFileName == "not open") { abort = true; }
else{ current->setFastaFile(fastaFileName); }
if (outputdir == "") { outputdir += util.hasPath(fastaFileName); }
oldfastafile = validParameter.validFile(parameters, "oldfasta");
if (oldfastafile == "not found") { oldfastafile = ""; }
else if (oldfastafile == "not open") { abort = true; }
column = validParameter.validFile(parameters, "column");
if (column == "not found") { column = ""; }
else if (column == "not open") { abort = true; }
else { current->setColumnFile(column); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.valid(parameters, "match"); if (temp == "not found"){ temp = "1.0"; }
util.mothurConvert(temp, match);
temp = validParameter.valid(parameters, "mismatch"); if (temp == "not found"){ temp = "-1.0"; }
util.mothurConvert(temp, misMatch);
if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
temp = validParameter.valid(parameters, "gapopen"); if (temp == "not found"){ temp = "-2.0"; }
util.mothurConvert(temp, gapOpen);
if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
temp = validParameter.valid(parameters, "gapextend"); if (temp == "not found"){ temp = "-1.0"; }
util.mothurConvert(temp, gapExtend);
if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
temp = validParameter.valid(parameters, "cutoff"); if(temp == "not found"){ temp = "1.0"; }
util.mothurConvert(temp, cutoff);
temp = validParameter.valid(parameters, "kmercutoff");
if(temp == "not found"){
if (cutoff <= 0.05) { kmerCutoff = -1.0; }
else if ((cutoff > 0.05) && (cutoff <= 0.15)) { kmerCutoff = -0.50; }
else if ((cutoff > 0.15) && (cutoff <= 0.25)) { kmerCutoff = -0.25; }
else { kmerCutoff = -0.1; }
}else { util.mothurConvert(temp, kmerCutoff); }
temp = validParameter.valid(parameters, "ksize"); if (temp == "not found"){ temp = "7"; }
util.mothurConvert(temp, kmerSize);
temp = validParameter.valid(parameters, "countends"); if(temp == "not found"){ temp = "T"; }
countends = util.isTrue(temp);
temp = validParameter.valid(parameters, "compress"); if(temp == "not found"){ temp = "F"; }
compress = util.isTrue(temp);
align = validParameter.valid(parameters, "align"); if (align == "not found"){ align = "needleman"; }
temp = validParameter.valid(parameters, "fitcalc"); if(temp == "not found"){ temp = "F"; }
fitCalc = util.isTrue(temp);
output = validParameter.valid(parameters, "output"); 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.\n"); output = "column"; }
calc = validParameter.valid(parameters, "calc");
if (calc == "not found") { calc = "onegap"; }
else {
if (calc == "default") { calc = "onegap"; }
}
if ((calc != "nogaps") && (calc != "eachgap") && (calc != "onegap")) { m->mothurOut(calc + " is not a valid calculator for pairwise.seqs. Options are onegap, eachgap and nogaps. I will use onegap.\n"); calc = "onegap"; }
}
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(StorageDatabase*& storageDB, vector< vector< int > > kDB, vector< int > lths, string outputFileRoot, double cut, string outputformat, int proc) {
try {
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
//defaults
calc = "onegap";
countends = true;
fitCalc = false;
cutoff = cut;
processors = proc;
compress = false;
output = outputformat;
match = 1.0;
misMatch = -1.0;
gapOpen = -2.0;
gapExtend = -1.0;
align = "needleman";
kmerSize = 7;
kmerDB = kDB;
lengths = lths;
if (cutoff <= 0.05) { kmerCutoff = -1.0; }
else if ((cutoff > 0.05) && (cutoff <= 0.15)) { kmerCutoff = -0.50; }
else if ((cutoff > 0.15) && (cutoff <= 0.25)) { kmerCutoff = -0.25; }
else { kmerCutoff = -0.1; }
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.
numDistsBelowCutoff = 0;
alignDB = storageDB;
long long numSeqs = alignDB->getNumSeqs();
if (numSeqs < 2) { m->mothurOut("[ERROR]: you must have at least 2 sequences to calculate the distances, aborting.\n"); return; }
string outputFile;
map<string, string> variables;
variables["[filename]"] = outputFileRoot;
if (output == "lt") { //does the user want lower triangle phylip formatted file
variables["[outputtag]"] = "phylip";
outputFile = getOutputFileName("phylip", variables);
util.mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
}else if (output == "column") { //user wants column format
if (fitCalc) { variables["[outputtag]"] = "fit"; }
outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
util.mothurRemove(outputFile);
}
time_t start, end; time(&start);
m->mothurOut("\nSequence\tTime\tNum_Dists_Below_Cutoff\n");
createProcesses(outputFile);
time(&end);
m->mothurOut("\nIt took " + toString(difftime(end, start)) + " secs to find distances for " + toString(numSeqs) + " sequences. " + toString(numDistsBelowCutoff) + " distances below cutoff " + toString(cutoff) + ".\n\n");
m->mothurOut("\nOutput File Names:\n"); m->mothurOut(outputFile+"\n\n");
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int PairwiseSeqsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
time_t start, end; time(&start);
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.
numDistsBelowCutoff = 0;
ifstream inFASTA; util.openInputFile(fastaFileName, inFASTA);
alignDB = new SequenceDB(inFASTA, kmerSize, kmerDB, lengths);
inFASTA.close();
//sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
if ((oldfastafile != "") && (column != "")) { if (!(sanityCheck())) { return 0; } }
if (m->getControl_pressed()) { delete alignDB; return 0; }
long long numSeqs = alignDB->getNumSeqs();
string outputFile = "";
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastaFileName));
if ((oldfastafile != "") && (column != "")) { variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(oldfastafile)); }
if (output == "lt") { //does the user want lower triangle phylip formatted file
variables["[outputtag]"] = "phylip";
outputFile = getOutputFileName("phylip", variables);
util.mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
}else if (output == "column") { //user wants column format
if (fitCalc) { variables["[outputtag]"] = "fit"; }
outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
util.mothurRemove(outputFile);
}else { //assume square
variables["[outputtag]"] = "square";
outputFile = getOutputFileName("phylip", variables);
util.mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
m->mothurOut("\nSequence\tTime\tNum_Dists_Below_Cutoff\n");
createProcesses(outputFile);
delete alignDB;
if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFile); return 0; }
if(util.isBlank(outputFile)) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.\n"); }
//append the old column file to the new one
if ((oldfastafile != "") && (column != "")) {
//we had to rename the column file so we didnt overwrite above, but we want to keep old name
if (outputFile == column) {
string tempcolumn = column + ".old";
util.appendFiles(tempcolumn, outputFile);
util.mothurRemove(tempcolumn);
}else{
util.appendFiles(outputFile, column);
util.mothurRemove(outputFile);
outputFile = column;
}
outputTypes["column"].clear(); outputTypes["column"].push_back(outputFile);
}
if (compress) {
m->mothurOut("Compressing...\n");
m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)\n");
system(("gzip -v " + outputFile).c_str());
outputNames.push_back(outputFile + ".gz");
}else { outputNames.push_back(outputFile); }
time(&end);
m->mothurOut("\nIt took " + toString(difftime(end, start)) + " secs to find distances for " + toString(numSeqs) + " sequences. " + toString(numDistsBelowCutoff) + " distances below cutoff " + toString(cutoff) + ".\n\n");
if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFile); return 0; }
//set phylip file as new current phylipfile
string currentName = "";
itTypes = outputTypes.find("phylip");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setPhylipFile(currentName); }
}
//set column file as new current columnfile
itTypes = outputTypes.find("column");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setColumnFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************************/
struct pairwiseData {
string align, distcalcType, outputFileName;
unsigned long long start, end;
long long count;
float match, misMatch, gapOpen, gapExtend, cutoff, kmerCutoff;
int longestBase, kmerSize;
bool countends;
vector< vector< int > > kmerDB; //kmerDB[0] = vector<int> maxKmers long, contains kmer counts
vector< vector< int > > oldkmerDB; //kmerDB[0] = vector<int> maxKmers long, contains kmer counts
vector< int > lengths;
vector< int > oldlengths;
StorageDatabase* alignDB;
SequenceDB oldFastaDB;
OutputWriter* threadWriter;
MothurOut* m;
Utils util;
pairwiseData(){}
pairwiseData(OutputWriter* ofn) {
threadWriter = ofn;
m = MothurOut::getInstance();
}
pairwiseData(string ofn) {
outputFileName = ofn;
m = MothurOut::getInstance();
}
void setVariables(string al, string di, bool co, string op, StorageDatabase* DB, SequenceDB oldDB, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, float cu, float kcut, int ksz, vector< vector< int > > kdb, vector< int > le, vector< vector< int > > okdb, vector< int > ole) {
align = al;
distcalcType = di;
countends = co;
alignDB = DB;
oldFastaDB = oldDB;
cutoff = cu;
start = st;
end = en;
match = ma;
misMatch = misMa;
gapOpen = gapO;
gapExtend = gapE;
longestBase = thr;
kmerDB = kdb;
oldkmerDB = okdb;
lengths = le;
oldlengths = ole;
kmerSize = ksz;
kmerCutoff = kcut;
count = 0;
}
};
/***********************************************************************/
vector<kmerCount> getUniqueKmers(vector<int> seqsKmers, int i){
vector<kmerCount> uniques;
for (int k = 0; k < seqsKmers.size(); k++) {
if (seqsKmers[k] != 0) {
kmerCount thisKmer(k, seqsKmers[k]);
uniques.push_back(thisKmer);
}
}
return uniques;
}
/**************************************************************************************************/
//the higher the kmercutoff the higher the aligned dist. As kmercutoff approaches 0, aligned dist aproaches 1.
int driverColumn(pairwiseData* params){
try {
int startTime = time(nullptr);
Alignment* alignment;
if(params->align == "gotoh") { alignment = new GotohOverlap(params->gapOpen, params->gapExtend, params->match, params->misMatch, params->longestBase); }
else if(params->align == "needleman") { alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase); }
else if(params->align == "noalign") { alignment = new NoAlign(); }
else {
params->m->mothurOut(params->align + " is not a valid alignment option. I will run the command using needleman.\n");
alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase);
}
ValidCalculators validCalculator;
DistCalc* distCalculator;
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->distcalcType == "eachgap") { distCalculator = new eachGapDist(params->cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapDist(params->cutoff); }
//else if (params->distcalcType == "onegap") { distCalculator = new oneGapDist(1.0); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(params->cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(params->cutoff); }
}
}
KmerDist kmerDistCalculator(params->kmerSize);
double kmerCutoff = params->kmerCutoff;
for(int i=params->start;i<params->end;i++){
Sequence seq = params->alignDB->getSeq(i);
vector<kmerCount> seqA = getUniqueKmers(params->kmerDB[i], i);
for(int j=0;j<i;j++){
if (params->m->getControl_pressed()) { break; }
vector<int> seqB = params->kmerDB[j];
int length = min(params->lengths[i], params->lengths[j]);
vector<double> kmerDist = kmerDistCalculator.calcDist(seqA, seqB, length);
if (kmerDist[0] <= kmerCutoff) {
Sequence seqI = seq;
Sequence seqJ = params->alignDB->getSeq(j);
if (seq.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seq.getUnaligned().length()+1); }
if (seqJ.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seqJ.getUnaligned().length()+1); }
alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
seqI.setAligned(alignment->getSeqAAln());
seqJ.setAligned(alignment->getSeqBAln());
double dist = distCalculator->calcDist(seqI, seqJ);
if(dist <= params->cutoff){ params->count++; params->threadWriter->write(seqI.getName() + ' ' + seqJ.getName() + ' ' + toString(dist) + "\n"); }
}
}
if((i+1) % 100 == 0){ params->m->mothurOutJustToScreen(toString(i+1) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n"); }
}
params->m->mothurOutJustToScreen(toString(params->end-1) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n");
delete alignment; delete distCalculator;
return 0;
}
catch(exception& e) {
params->m->errorOut(e, "PairwiseSeqsCommand", "driver");
exit(1);
}
}
/**************************************************************************************************/
int driverFitCalc(pairwiseData* params){
try {
int startTime = time(nullptr);
Alignment* alignment;
if(params->align == "gotoh") { alignment = new GotohOverlap(params->gapOpen, params->gapExtend, params->match, params->misMatch, params->longestBase); }
else if(params->align == "needleman") { alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase); }
else if(params->align == "noalign") { alignment = new NoAlign(); }
else {
params->m->mothurOut(params->align + " is not a valid alignment option. I will run the command using needleman.\n");
alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase);
}
ValidCalculators validCalculator;
DistCalc* distCalculator;
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->distcalcType == "eachgap") { distCalculator = new eachGapDist(params->cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapDist(params->cutoff); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(params->cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(params->cutoff); }
}
}
KmerDist kmerDistCalculator(params->kmerSize);
double kmerCutoff = params->kmerCutoff;
for(int i=params->start;i<params->end;i++){ //for each oldDB fasta seq calc the distance to every new seq in alignDB
Sequence seq = params->oldFastaDB.getSeq(i);
vector<kmerCount> seqA = getUniqueKmers(params->oldkmerDB[i], i);
for(int j = 0; j < params->alignDB->getNumSeqs(); j++){
if (params->m->getControl_pressed()) { break; }
vector<int> seqB = params->kmerDB[j];
int length = min(params->oldlengths[i], params->lengths[j]);
vector<double> kmerDist = kmerDistCalculator.calcDist(seqA, seqB, length);
if (kmerDist[0] <= kmerCutoff) {
Sequence seqI = seq;
Sequence seqJ = params->alignDB->getSeq(j);
if (seq.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seq.getUnaligned().length()+1); }
if (seqJ.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seqJ.getUnaligned().length()+1); }
alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
seqI.setAligned(alignment->getSeqAAln());
seqJ.setAligned(alignment->getSeqBAln());
double dist = distCalculator->calcDist(seqI, seqJ);
if(dist <= params->cutoff){ params->count++; params->threadWriter->write(seqI.getName() + ' ' + seqJ.getName() + ' ' + toString(dist) + "\n"); }
}
}
if((i+1) % 100 == 0){ params->m->mothurOutJustToScreen(toString(i+1) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n"); }
}
params->m->mothurOutJustToScreen(toString(params->end-1) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n");
delete alignment; delete distCalculator;
return 0;
}
catch(exception& e) {
params->m->errorOut(e, "PairwiseSeqsCommand", "driverFitCalc");
exit(1);
}
}
/**************************************************************************************************/
int driverLt(pairwiseData* params){
try {
int startTime = time(nullptr);
Alignment* alignment;
if(params->align == "gotoh") { alignment = new GotohOverlap(params->gapOpen, params->gapExtend, params->match, params->misMatch, params->longestBase); }
else if(params->align == "needleman") { alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase); }
else if(params->align == "noalign") { alignment = new NoAlign(); }
else {
params->m->mothurOut(params->align + " is not a valid alignment option. I will run the command using needleman.\n");
alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase);
}
ValidCalculators validCalculator;
DistCalc* distCalculator;
double cutoff = 1.0;
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->distcalcType == "eachgap") { distCalculator = new eachGapDist(cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapDist(cutoff); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(cutoff); }
}
}
//column file
ofstream outFile;
params->util.openOutputFile(params->outputFileName, outFile);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
if(params->start == 0){ outFile << params->alignDB->getNumSeqs() << endl; }
for(int i=params->start;i<params->end;i++){
Sequence seq = params->alignDB->getSeq(i);
if (seq.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seq.getUnaligned().length()+1); }
string name = seq.getName();
if (name.length() < 10) { while (name.length() < 10) { name += " "; } seq.setName(name); } //pad with spaces to make compatible
outFile << name;
for(int j=0;j<i;j++){
if (params->m->getControl_pressed()) { break; }
Sequence seqI = seq;
Sequence seqJ = params->alignDB->getSeq(j);
if (seqJ.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seqJ.getUnaligned().length()+1); }
alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
seqI.setAligned(alignment->getSeqAAln());
seqJ.setAligned(alignment->getSeqBAln());
double dist = distCalculator->calcDist(seqI, seqJ);
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
if(dist <= params->cutoff){ params->count++; }
outFile << '\t' << dist;
}
outFile << endl;
if(i % 100 == 0){ params->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n"); }
}
params->m->mothurOutJustToScreen(toString(params->end-1) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n");
outFile.close();
delete alignment;
delete distCalculator;
return 1;
}
catch(exception& e) {
params->m->errorOut(e, "PairwiseSeqsCommand", "driver");
exit(1);
}
}
/**************************************************************************************************/
int driverSquare(pairwiseData* params){
try {
int startTime = time(nullptr);
Alignment* alignment;
if(params->align == "gotoh") { alignment = new GotohOverlap(params->gapOpen, params->gapExtend, params->match, params->misMatch, params->longestBase); }
else if(params->align == "needleman") { alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase); }
else if(params->align == "noalign") { alignment = new NoAlign(); }
else {
params->m->mothurOut(params->align + " is not a valid alignment option. I will run the command using needleman.\n");
alignment = new NeedlemanOverlap(params->gapOpen, params->match, params->misMatch, params->longestBase);
}
ValidCalculators validCalculator;
DistCalc* distCalculator;
double cutoff = 1.0;
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->distcalcType == "eachgap") { distCalculator = new eachGapDist(cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapDist(cutoff); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->distcalcType) ) {
if (params->distcalcType == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->distcalcType == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(cutoff); }
else if (params->distcalcType == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(cutoff); }
}
}
//column file
ofstream outFile;
params->util.openOutputFile(params->outputFileName, outFile);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
long long numSeqs = params->alignDB->getNumSeqs();
if(params->start == 0){ outFile << numSeqs << endl; }
for(int i=params->start;i<params->end;i++){
Sequence seq = params->alignDB->getSeq(i);
if (seq.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seq.getUnaligned().length()+1); }
string name = seq.getName();
if (name.length() < 10) { while (name.length() < 10) { name += " "; } seq.setName(name); } //pad with spaces to make compatible
outFile << name;
for(int j=0;j<numSeqs;j++){
if (params->m->getControl_pressed()) { break; }
Sequence seqI = seq;
Sequence seqJ = params->alignDB->getSeq(j);
if (seqJ.getUnaligned().length() > alignment->getnRows()) { alignment->resize(seqJ.getUnaligned().length()+1); }
alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
seqI.setAligned(alignment->getSeqAAln());
seqJ.setAligned(alignment->getSeqBAln());
double dist = distCalculator->calcDist(seqI, seqJ);
if(dist <= params->cutoff){ params->count++; }
outFile << '\t' << dist;
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
}
outFile << endl;
if(i % 100 == 0){ params->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n"); }
}
params->m->mothurOutJustToScreen(toString(params->end-1) + "\t" + toString(time(nullptr) - startTime)+ "\t" + toString(params->count) +"\n");
outFile.close();
delete alignment;
delete distCalculator;
return 1;
}
catch(exception& e) {
params->m->errorOut(e, "PairwiseSeqsCommand", "driver");
exit(1);
}
}
/**************************************************************************************************/
void PairwiseSeqsCommand::createProcesses(string filename) {
try {
vector<linePair> lines;
vector<std::thread*> workerThreads;
vector<pairwiseData*> data;
long long numSeqs = alignDB->getNumSeqs();
long long numDists = 0;
if (output == "square") { numDists = numSeqs * numSeqs; }
else { for(int i=0;i<numSeqs;i++){ for(int j=0;j<i;j++){ numDists++; if (numDists > processors) { break; } } } }
if (numDists < processors) { processors = numDists; }
for (int i = 0; i < processors; i++) {
linePair 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);
}
}
auto synchronizedOutputFile = std::make_shared<SynchronizedOutputFile>(filename);
synchronizedOutputFile->setFixedShowPoint(); synchronizedOutputFile->setPrecision(4);
SequenceDB oldFastaDB; vector< int > oldlengths; vector< vector< int > > oldkmerDB;
if (fitCalc) {
ifstream inFASTA; util.openInputFile(oldfastafile, inFASTA);
oldFastaDB = SequenceDB(inFASTA, kmerSize, oldkmerDB, oldlengths);
inFASTA.close();
lines.clear();
if (processors > oldFastaDB.getNumSeqs()) { processors = oldFastaDB.getNumSeqs(); }
int remainingSeqs = oldFastaDB.getNumSeqs();
int startIndex = 0;
for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
int numSeqsToFit = remainingSeqs; //case for last processor
if (remainingProcessors != 1) { numSeqsToFit = ceil(remainingSeqs / remainingProcessors); }
lines.push_back(linePair(startIndex, (startIndex+numSeqsToFit))); //startIndex, endIndex
startIndex = startIndex + numSeqsToFit;
remainingSeqs -= numSeqsToFit;
}
}
//Lauch worker threads
for (int i = 0; i < processors-1; i++) {
OutputWriter* threadWriter = nullptr;
pairwiseData* dataBundle = nullptr;
string extension = toString(i+1) + ".temp";
if (output == "column") {
threadWriter = new OutputWriter(synchronizedOutputFile);
dataBundle = new pairwiseData(threadWriter);
}else { dataBundle = new pairwiseData(filename+extension); }
dataBundle->setVariables(align, calc, countends, output, alignDB, oldFastaDB, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, kmerCutoff, kmerSize, kmerDB, lengths, oldkmerDB, oldlengths);
data.push_back(dataBundle);
std::thread* thisThread = nullptr;
if (output == "column") {
if (fitCalc) { thisThread = new std::thread(driverFitCalc, dataBundle); }
else { thisThread = new std::thread(driverColumn, dataBundle); }
}
else if (output == "lt") { thisThread = new std::thread(driverLt, dataBundle); }
else { thisThread = new std::thread(driverSquare, dataBundle); }
workerThreads.push_back(thisThread);
}
OutputWriter* threadWriter = nullptr;
pairwiseData* dataBundle = nullptr;
if (output == "column") {
threadWriter = new OutputWriter(synchronizedOutputFile);
dataBundle = new pairwiseData(threadWriter);
}else { dataBundle = new pairwiseData(filename); }
dataBundle->setVariables(align, calc, countends, output, alignDB, oldFastaDB, lines[0].start, lines[0].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, kmerCutoff, kmerSize, kmerDB, lengths, oldkmerDB, oldlengths);
if (output == "column") {
if (fitCalc) { driverFitCalc(dataBundle); }
else { driverColumn(dataBundle); }
delete threadWriter;
}
else if (output == "lt") { driverLt(dataBundle); }
else { driverSquare(dataBundle); }
numDistsBelowCutoff = dataBundle->count;
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
numDistsBelowCutoff += data[i]->count;
if (output == "column") { delete data[i]->threadWriter; }
else {
string extension = toString(i+1) + ".temp";
util.appendFiles((filename+extension), filename);
util.mothurRemove(filename+extension);
}
delete data[i];
delete workerThreads[i];
}
delete dataBundle;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
exit(1);
}
}
/**************************************************************************************************/
//its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
//but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
bool PairwiseSeqsCommand::sanityCheck() {
try{
bool good = true;
//read fasta file and save names as well as adding them to the alignDB
set<string> namesOldFasta;
ifstream inFasta; util.openInputFile(oldfastafile, inFasta);
while (!inFasta.eof()) {
if (m->getControl_pressed()) { inFasta.close(); return good; }
Sequence temp(inFasta); gobble(inFasta);
if (temp.getName() != "") {
namesOldFasta.insert(temp.getName()); //save name
if (!fitCalc) { alignDB->push_back(temp); }//add to DB
}
}
inFasta.close();
//read through the column file checking names and removing distances above the cutoff
ifstream inDist; util.openInputFile(column, inDist);
ofstream outDist;
string outputFile = column + ".temp";
util.openOutputFile(outputFile, outDist);
string name1, name2;
float dist;
while (!inDist.eof()) {
if (m->getControl_pressed()) { inDist.close(); outDist.close(); util.mothurRemove(outputFile); return good; }
inDist >> name1; gobble(inDist); inDist >> name2; gobble(inDist); inDist >> dist; gobble(inDist);
//both names are in fasta file and distance is below cutoff
if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) { good = false; break; }
else{ if (dist <= cutoff) { numDistsBelowCutoff++; outDist << name1 << '\t' << name2 << '\t' << dist << endl; } }
}
inDist.close(); outDist.close();
if (good) {
util.mothurRemove(column);
rename(outputFile.c_str(), column.c_str());
}else{
util.mothurRemove(outputFile); //temp file is bad because file mismatch above
}
return good;
}
catch(exception& e) {
m->errorOut(e, "PairwiseSeqsCommand", "sanityCheck");
exit(1);
}
}
/**************************************************************************************************/
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