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|
/*
* distancecommand.cpp
* Mothur
*
* Created by Sarah Westcott on 5/7/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "distancecommand.h"
//**********************************************************************************************************************
vector<string> DistanceCommand::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 pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true, true); parameters.push_back(pfasta);
CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "","phylip-column",false,false, true); parameters.push_back(poutput);
CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap-jtt-pmb-pam-kimura", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
CommandParameter pfitcalc("fitcalc", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfitcalc);
CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false, true); parameters.push_back(pcutoff);
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, "DistanceCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string DistanceCommand::getHelpString(){
try {
string helpString = "";
helpString += "The dist.seqs command reads a file containing sequences and creates a distance file.\n";
helpString += "The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors. \n";
helpString += "The fasta parameter is required, unless you have a valid current fasta file.\n";
helpString += "The oldfasta and column parameters allow you to append the distances calculated to the column file.\n";
helpString += "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap for dna/rna sequences. If using protein sequences, your calc options are jtt, pmb, pam and kimura. 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 processors parameter allows you to specify number of processors to use. The default is 1.\n";
helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
helpString += "The dist.seqs command should be in the following format: \n";
helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string DistanceCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "phylip") { pattern = "[filename],[outputtag],dist"; }
else if (type == "column") { pattern = "[filename],dist-[filename],[outputtag],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, "DistanceCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(string option) : Command() {
try {
//allow user to run help
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;
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not found") {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required.\n"); abort = true; }
}else if (fastafile == "not open") { abort = true; }
else{ current->setFastaFile(fastafile); }
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); }
if (outputdir == ""){ outputdir += util.hasPath(fastafile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
calc = validParameter.valid(parameters, "calc");
if (calc == "not found") { calc = "onegap"; }
else {
if (calc == "default") { calc = "onegap"; }
}
string temp;
temp = validParameter.valid(parameters, "countends"); if(temp == "not found"){ temp = "T"; }
countends = util.isTrue(temp);
temp = validParameter.valid(parameters, "fitcalc"); if(temp == "not found"){ temp = "F"; }
fitCalc = util.isTrue(temp);
temp = validParameter.valid(parameters, "cutoff"); if(temp == "not found"){ temp = "1.0"; }
util.mothurConvert(temp, cutoff);
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
temp = validParameter.valid(parameters, "compress"); if(temp == "not found"){ temp = "F"; }
compress = util.isTrue(temp);
output = validParameter.valid(parameters, "output"); if(output == "not found"){ output = "column"; }
if (output == "phylip") { output = "lt"; }
if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both.\n"); abort=true; }
if ((column != "") && (oldfastafile != "") && (output != "column")) { m->mothurOut("You have provided column and oldfasta, indicating you want to append distances to your column file. Your output must be in column format to do so.\n"); abort=true; }
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"; }
if ((calc != "onegap") && (calc != "eachgap") && (calc != "nogaps") && (calc != "jtt") && (calc != "pmb") && (calc != "pam") && (calc != "kimura")) { m->mothurOut(calc + " is not a valid calc. Options are eachgap, onegap, nogaps, jtt, pmb, pam and kimura. I'll use onegap.\n"); calc = "onegap"; }
prot = false; //not using protein sequences
if ((calc == "jtt") || (calc == "pmb") || (calc == "pam") || (calc == "kimura")) { prot = true; }
}
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "DistanceCommand");
exit(1);
}
}
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(StorageDatabase*& storageDB, string outputFileRoot, double cut, string outputformat, int proc) : Command() {
try {
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
calc = "onegap";
countends = true;
fitCalc = false;
cutoff = cut;
processors = proc;
compress = false;
output = outputformat;
prot = false; //not using protein sequences
numDistsBelowCutoff = 0;
db = storageDB;
numNewFasta = db->getNumSeqs();
numSeqs = db->getNumSeqs();
if (!db->sameLength()) { m->mothurOut("[ERROR]: your sequences are not the same length, aborting.\n"); return; }
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);
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
util.mothurRemove(outputFile);
}
m->mothurOut("\nSequence\tTime\tNum_Dists_Below_Cutoff\n");
createProcesses(outputFile);
m->mothurOut("\nOutput File Names:\n"); m->mothurOut(outputFile+"\n\n");
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "DistanceCommand");
exit(1);
}
}
//**********************************************************************************************************************
int DistanceCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
numDistsBelowCutoff = 0;
ifstream inFASTA; util.openInputFile(fastafile, inFASTA);
if (prot) { db = new ProteinDB(inFASTA); }
else { db = new SequenceDB(inFASTA); }
inFASTA.close();
//save number of new sequence
numNewFasta = db->getNumSeqs();
//sanity check the oldfasta and column file as well as add oldfasta sequences to db
if ((oldfastafile != "") && (column != "")) { if (!(sanityCheck())) { return 0; } }
if (m->getControl_pressed()) { delete db; return 0; }
numSeqs = db->getNumSeqs();
if (!db->sameLength()) { m->mothurOut("[ERROR]: your sequences are not the same length, aborting.\n"); return 0; }
if (numSeqs < 2) { m->mothurOut("[ERROR]: you must have at least 2 sequences to calculate the distances, aborting.\n"); return 0; }
string outputFile;
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
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);
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
if (fitCalc) { variables["[outputtag]"] = "fit"; }
outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
//so we don't accidentally overwrite
if (outputFile == column) {
string tempcolumn = column + ".old";
rename(column.c_str(), tempcolumn.c_str());
}
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);
if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFile); return 0; }
ifstream fileHandle; fileHandle.open(outputFile.c_str());
if(fileHandle) {
gobble(fileHandle);
if (fileHandle.eof()) { 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{
if (!fitCalc) {
util.appendFiles(outputFile, column);
util.mothurRemove(outputFile);
outputFile = column;
}
}
outputTypes["column"].clear(); outputTypes["column"].push_back(outputFile);
}
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");
m->mothurOut(outputFile+"\n\n");
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); }
return 0;
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "execute");
exit(1);
}
}
/**************************************************************************************************/
void driverColumn(distanceData* params){
try {
ValidCalculators validCalculator;
DistCalc* distCalculator;
if (!params->prot) {
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->calc == "eachgap") { distCalculator = new eachGapDist(params->cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapDist(params->cutoff); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->calc == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(params->cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(params->cutoff); }
}
}
}else {
if (validCalculator.isValidCalculator("protdist", params->calc) ) {
if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); }
else if (params->calc == "pmb") { distCalculator = new PMB(params->cutoff); }
else if (params->calc == "pam") { distCalculator = new PAM(params->cutoff); }
else if (params->calc == "kimura") { distCalculator = new Kimura(params->cutoff); }
}
}
int startTime = time(nullptr);
params->count = 0;
string buffer = "";
for(int i=params->startLine;i<params->endLine;i++){
Sequence seqI; Protein seqIP; string nameI = "";
if (params->prot) { seqIP = params->db->getProt(i); nameI = seqIP.getName(); }
else { seqI = params->db->getSeq(i); nameI = seqI.getName(); }
for(int j=0;j<i;j++){
if (params->m->getControl_pressed()) { break; }
if ((i >= params->numNewFasta) && (j >= params->numNewFasta)) { break; }
double dist = 1.0; string nameJ = "";
if (params->prot) { Protein seqJP = params->db->getProt(j); nameJ = seqJP.getName(); dist = distCalculator->calcDist(seqIP, seqJP); }
else { Sequence seqJ = params->db->getSeq(j); nameJ = seqJ.getName(); dist = distCalculator->calcDist(seqI, seqJ); }
if(dist <= params->cutoff){
buffer += (nameI + " " + nameJ + " " + toString(dist) + "\n");
params->count++;
}
}
if(i % 100 == 0){ params->threadWriter->write(buffer); buffer = ""; params->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(nullptr) - startTime) + "\t" + toString(params->count) +"\n"); }
}
params->threadWriter->write(buffer);
if((params->endLine-1) % 100 != 0){ params->m->mothurOutJustToScreen(toString(params->endLine-1) + "\t" + toString(time(nullptr) - startTime) + "\t" + toString(params->count) +"\n"); }
delete distCalculator;
}
catch(exception& e) {
params->m->errorOut(e, "DistanceCommand", "driverColumn");
exit(1);
}
}
/**************************************************************************************************/
void driverLt(distanceData* params){
try {
ValidCalculators validCalculator;
DistCalc* distCalculator;
double cutoff = 1.0;
if (!params->prot) {
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->calc == "eachgap") { distCalculator = new eachGapDist(cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapDist(cutoff); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->calc == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(cutoff); }
}
}
}else {
if (validCalculator.isValidCalculator("protdist", params->calc) ) {
if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); }
else if (params->calc == "pmb") { distCalculator = new PMB(params->cutoff); }
else if (params->calc == "pam") { distCalculator = new PAM(params->cutoff); }
else if (params->calc == "kimura") { distCalculator = new Kimura(params->cutoff); }
}
}
int startTime = time(nullptr);
long long numSeqs = params->db->getNumSeqs();
//column file
ofstream outFile; params->util.openOutputFile(params->outputFileName, outFile);
outFile.setf(ios::fixed, ios::showpoint); outFile << setprecision(4);
if(params->startLine == 0){ outFile << numSeqs << endl; }
params->count = 0;
for(int i=params->startLine;i<params->endLine;i++){
Sequence seqI; Protein seqIP; string nameI = "";
if (params->prot) { seqIP = params->db->getProt(i); nameI = seqIP.getName(); }
else { seqI = params->db->getSeq(i); nameI = seqI.getName(); }
if (nameI.length() < 10) { while (nameI.length() < 10) { nameI += " "; } }
outFile << nameI;
for(int j=0;j<i;j++){
if (params->m->getControl_pressed()) { break; }
if ((i >= params->numNewFasta) && (j >= params->numNewFasta)) { break; }
double dist = 1.0;
if (params->prot) { Protein seqJP = params->db->getProt(j); dist = distCalculator->calcDist(seqIP, seqJP); }
else { Sequence seqJ = params->db->getSeq(j); dist = distCalculator->calcDist(seqI, seqJ); }
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"); }
}
if((params->endLine-1) % 100 != 0){ params->m->mothurOutJustToScreen(toString(params->endLine-1) + "\t" + toString(time(nullptr) - startTime) + "\t" + toString(params->count) +"\n"); }
outFile.close();
delete distCalculator;
}
catch(exception& e) {
params->m->errorOut(e, "DistanceCommand", "driverLt");
exit(1);
}
}
/**************************************************************************************************/
void driverSquare(distanceData* params){
try {
ValidCalculators validCalculator;
DistCalc* distCalculator;
double cutoff = 1.0;
if (!params->prot) {
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->calc == "eachgap") { distCalculator = new eachGapDist(cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapDist(cutoff); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(cutoff); }
else if (params->calc == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(cutoff); }
}
}
}else {
if (validCalculator.isValidCalculator("protdist", params->calc) ) {
if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); }
else if (params->calc == "pmb") { distCalculator = new PMB(params->cutoff); }
else if (params->calc == "pam") { distCalculator = new PAM(params->cutoff); }
else if (params->calc == "kimura") { distCalculator = new Kimura(params->cutoff); }
}
}
int startTime = time(nullptr);
//column file
ofstream outFile;
params->util.openOutputFile(params->outputFileName, outFile);
outFile.setf(ios::fixed, ios::showpoint); outFile << setprecision(4);
long long numSeqs = params->db->getNumSeqs();
if(params->startLine == 0){ outFile << numSeqs << endl; }
params->count = 0;
for(int i=params->startLine;i<params->endLine;i++){
Sequence seqI; Protein seqIP; string nameI = "";
if (params->prot) { seqIP = params->db->getProt(i); nameI = seqIP.getName(); }
else { seqI = params->db->getSeq(i); nameI = seqI.getName(); }
if (nameI.length() < 10) { while (nameI.length() < 10) { nameI += " "; } }
outFile << nameI << '\t';
for(int j=0;j<numSeqs;j++){
if (params->m->getControl_pressed()) { break; }
double dist = 1.0;
if (i == j) { dist = 0.0000; }
else {
if (params->prot) { Protein seqJP = params->db->getProt(j); dist = distCalculator->calcDist(seqIP, seqJP); }
else { Sequence seqJ = params->db->getSeq(j); dist = distCalculator->calcDist(seqI, seqJ); }
}
if(dist <= params->cutoff){ params->count++; }
outFile << dist << '\t';
}
outFile << endl;
if(i % 100 == 0){ params->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(nullptr) - startTime) + "\t" + toString(params->count) +"\n"); }
}
if((params->endLine-1) % 100 != 0){ params->m->mothurOutJustToScreen(toString(params->endLine-1) + "\t" + toString(time(nullptr) - startTime) + "\t" + toString(params->count) +"\n"); }
outFile.close();
delete distCalculator;
}
catch(exception& e) {
params->m->errorOut(e, "DistanceCommand", "driverSquare");
exit(1);
}
}
/**************************************************************************************************/
void driverFitCalc(distanceData* params){
try {
ValidCalculators validCalculator;
DistCalc* distCalculator;
if (!params->prot) {
if (params->countends) {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->calc == "eachgap") { distCalculator = new eachGapDist(params->cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapDist(params->cutoff); }
}
}else {
if (validCalculator.isValidCalculator("distance", params->calc) ) {
if (params->calc == "nogaps") { distCalculator = new ignoreGaps(params->cutoff); }
else if (params->calc == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(params->cutoff); }
else if (params->calc == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(params->cutoff); }
}
}
}else {
if (validCalculator.isValidCalculator("protdist", params->calc) ) {
if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); }
else if (params->calc == "pmb") { distCalculator = new PMB(params->cutoff); }
else if (params->calc == "pam") { distCalculator = new PAM(params->cutoff); }
else if (params->calc == "kimura") { distCalculator = new Kimura(params->cutoff); }
}
}
int startTime = time(nullptr);
params->count = 0;
string buffer = "";
for(int i=params->startLine;i<params->endLine;i++){
Sequence seqI; Protein seqIP; string nameI = "";
if (params->prot) { seqIP = params->oldFastaDB->getProt(i); nameI = seqIP.getName(); }
else { seqI = params->oldFastaDB->getSeq(i); nameI = seqI.getName(); }
for(int j = 0; j < params->db->getNumSeqs(); j++){
if (params->m->getControl_pressed()) { break; }
double dist = 1.0; string nameJ = "";
if (params->prot) { Protein seqJP = params->db->getProt(j); nameJ = seqJP.getName(); dist = distCalculator->calcDist(seqIP, seqJP); }
else { Sequence seqJ = params->db->getSeq(j); nameJ = seqJ.getName(); dist = distCalculator->calcDist(seqI, seqJ); }
if(dist <= params->cutoff){
buffer += nameI + " " + nameJ + " " + toString(dist) + "\n";
params->count++;
}
}
if(i % 100 == 0){ params->threadWriter->write(buffer); buffer = ""; params->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(nullptr) - startTime) + "\t" + toString(params->count) +"\n"); }
}
params->threadWriter->write(buffer);
if((params->endLine-1) % 100 != 0){ params->m->mothurOutJustToScreen(toString(params->endLine-1) + "\t" + toString(time(nullptr) - startTime) + "\t" + toString(params->count) +"\n"); }
delete distCalculator;
}
catch(exception& e) {
params->m->errorOut(e, "DistanceCommand", "driverFitCalc");
exit(1);
}
}
/**************************************************************************************************/
void DistanceCommand::createProcesses(string filename) {
try {
long long num = db->getNumSeqs();
long long distsBelowCutoff = 0;
time_t start, end;
time(&start);
//create array of worker threads
vector<std::thread*> workerThreads;
vector<distanceData*> data;
double numDists = 0;
if (output == "square") { numDists = 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; }
vector<linePair> lines;
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);
StorageDatabase* oldFastaDB;
if (fitCalc) {
ifstream inFASTA; util.openInputFile(oldfastafile, inFASTA);
if (!prot) { oldFastaDB = new SequenceDB(inFASTA); }
else { oldFastaDB = new ProteinDB(inFASTA); }
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;
distanceData* dataBundle = nullptr;
string extension = toString(i+1) + ".temp";
if (output == "column") {
threadWriter = new OutputWriter(synchronizedOutputFile);
dataBundle = new distanceData(threadWriter);
}else { dataBundle = new distanceData(filename+extension); }
dataBundle->setVariables(lines[i+1].start, lines[i+1].end, cutoff, db, oldFastaDB, calc, prot, numNewFasta, countends);
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;
distanceData* dataBundle = nullptr;
if (output == "column") {
threadWriter = new OutputWriter(synchronizedOutputFile);
dataBundle = new distanceData(threadWriter);
}else { dataBundle = new distanceData(filename); }
dataBundle->setVariables(lines[0].start, lines[0].end, cutoff, db, oldFastaDB, calc, prot, numNewFasta, countends);
if (output == "column") {
if (fitCalc) { driverFitCalc(dataBundle); }
else { driverColumn(dataBundle); }
}
else if (output == "lt") { driverLt(dataBundle); }
else { driverSquare(dataBundle); }
distsBelowCutoff = dataBundle->count;
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
distsBelowCutoff += 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];
}
if (output == "column") { synchronizedOutputFile->close(); delete threadWriter; }
delete dataBundle;
time(&end);
m->mothurOut("\nIt took " + toString(difftime(end, start)) + " secs to find distances for " + toString(num) + " sequences. " + toString(distsBelowCutoff+numDistsBelowCutoff) + " distances below cutoff " + toString(cutoff) + ".\n\n");
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "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.
//also check to make sure the 2 files have the same alignment length.
bool DistanceCommand::sanityCheck() {
try{
bool good = true;
//make sure the 2 fasta files have the same alignment length
ifstream in; util.openInputFile(fastafile, in);
int fastaAlignLength = 0;
if (in) {
if (!prot) {
Sequence tempIn(in);
fastaAlignLength = tempIn.getAligned().length();
}else {
Protein tempIn(in);
fastaAlignLength = tempIn.getAligned().size();
}
}
in.close();
ifstream in2; util.openInputFile(oldfastafile, in2);
int oldfastaAlignLength = 0;
if (in2) {
if (!prot) {
Sequence tempIn(in2);
oldfastaAlignLength = tempIn.getAligned().length();
}else {
Protein tempIn(in2);
oldfastaAlignLength = tempIn.getAligned().size();
}
}
in2.close();
if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length.\n"); return false; }
//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; }
if (!prot) {
Sequence temp(inFasta); gobble(inFasta);
if (temp.getName() != "") {
namesOldFasta.insert(temp.getName()); //save name
if (!fitCalc) { db->push_back(temp); }//add to DB
}
}else {
Protein temp(inFasta); gobble(inFasta);
if (temp.getName() != "") {
namesOldFasta.insert(temp.getName()); //save name
if (!fitCalc) { db->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, "DistanceCommand", "sanityCheck");
exit(1);
}
}
/**************************************************************************************************/
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