#include "chimeraslayer.h"
#include "chimerarealigner.h"
#include "kmerdb.hpp"
+#include "blastdb.hpp"
//***************************************************************************************************************
ChimeraSlayer::ChimeraSlayer(string file, string temp, string mode, int k, int ms, int mms, int win, float div,
}
}
//***************************************************************************************************************
-int ChimeraSlayer::doPrep() {
+ChimeraSlayer::ChimeraSlayer(string file, string temp, string name, string mode, int k, int ms, int mms, int win, float div,
+ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() {
try {
+ fastafile = file; templateSeqs = readSeqs(fastafile);
+ templateFileName = temp;
+ searchMethod = mode;
+ kmerSize = k;
+ match = ms;
+ misMatch = mms;
+ window = win;
+ divR = div;
+ minSim = minsim;
+ minCov = mincov;
+ minBS = minbs;
+ minSNP = minsnp;
+ parents = par;
+ iters = it;
+ increment = inc;
+ numWanted = numw;
+ realign = r;
+
+ //read name file and create nameMapRank
+ readNameFile(name);
+
+ decalc = new DeCalculator();
+ createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+
+ //run filter on template
+ for (int i = 0; i < templateSeqs.size(); i++) { runFilter(templateSeqs[i]); }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ChimeraSlayer::readNameFile(string name) {
+ try {
+ ifstream in;
+ m->openInputFile(name, in);
+
+ int maxRank = 0;
+ int minRank = 10000000;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ string thisname, repnames;
+
+ in >> thisname; m->gobble(in); //read from first column
+ in >> repnames; //read from second column
+
+ map<string, vector<string> >::iterator it = nameMapRank.find(thisname);
+ if (it == nameMapRank.end()) {
+
+ vector<string> splitRepNames;
+ m->splitAtComma(repnames, splitRepNames);
+
+ nameMapRank[thisname] = splitRepNames;
+
+ if (splitRepNames.size() > maxRank) { maxRank = splitRepNames.size(); }
+ if (splitRepNames.size() < minRank) { minRank = splitRepNames.size(); }
+
+ }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); }
+
+ m->gobble(in);
+ }
+ in.close();
+
+ //sanity check to make sure files match
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ map<string, vector<string> >::iterator it = nameMapRank.find(templateSeqs[i]->getName());
+
+ if (it == nameMapRank.end()) { m->mothurOut("[ERROR]: " + templateSeqs[i]->getName() + " is not in namesfile, but is in fastafile. Every name in fasta file must be in first column of names file."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+
+ if (maxRank == minRank) { m->mothurOut("[ERROR]: all sequences in namesfile have the same abundance, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "readNameFile");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+int ChimeraSlayer::doPrep() {
+ try {
//read in all query seqs
vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
//generate the kmerdb to pass to maligner
if (searchMethod == "kmer") {
- string rightTemplateFileName = "right." + templateFileName;
+ string templatePath = m->hasPath(templateFileName);
+ string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
- string leftTemplateFileName = "left." + templateFileName;
+ string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
#ifdef USE_MPI
for (int i = 0; i < templateSeqs.size(); i++) {
//leftside
kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
ifstream kmerFileTestLeft(kmerDBNameLeft.c_str());
+ bool needToGenerateLeft = true;
+
+ if(kmerFileTestLeft){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+ if (GoodFile) { needToGenerateLeft = false; }
+ }
- if(!kmerFileTestLeft){
+ if(needToGenerateLeft){
for (int i = 0; i < templateSeqs.size(); i++) {
//rightside
kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
ifstream kmerFileTestRight(kmerDBNameRight.c_str());
+ bool needToGenerateRight = true;
- if(!kmerFileTestRight){
+ if(kmerFileTestRight){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
+ if (GoodFile) { needToGenerateRight = false; }
+ }
+
+ if(needToGenerateRight){
for (int i = 0; i < templateSeqs.size(); i++) {
if (m->control_pressed) { return 0; }
databaseRight->setNumSeqs(templateSeqs.size());
#endif
+ }else if (searchMethod == "blast") {
+
+ //generate blastdb
+ databaseLeft = new BlastDB(-2.0, -1.0, match, misMatch);
+ for (int i = 0; i < templateSeqs.size(); i++) { databaseLeft->addSequence(*templateSeqs[i]); }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(templateSeqs.size());
}
return 0;
}
}
//***************************************************************************************************************
-ChimeraSlayer::~ChimeraSlayer() { delete decalc; if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; } }
+vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q) {
+ try {
+
+ vector<Sequence*> thisTemplate;
+
+ int thisRank;
+ string thisName = q->getName();
+ map<string, vector<string> >::iterator itRank = nameMapRank.find(thisName); // you will find it because we already sanity checked
+ thisRank = (itRank->second).size();
+
+ //create list of names we want to put into the template
+ set<string> namesToAdd;
+ for (itRank = nameMapRank.begin(); itRank != nameMapRank.end(); itRank++) {
+ if ((itRank->second).size() > thisRank) {
+ //you are more abundant than me
+ for (int i = 0; i < (itRank->second).size(); i++) {
+ namesToAdd.insert((itRank->second)[i]);
+ }
+ }
+ }
+
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (namesToAdd.count(templateSeqs[i]->getName()) != 0) {
+ thisTemplate.push_back(templateSeqs[i]);
+ }
+ }
+
+ string kmerDBNameLeft;
+ string kmerDBNameRight;
+
+ //generate the kmerdb to pass to maligner
+ if (searchMethod == "kmer") {
+ string templatePath = m->hasPath(templateFileName);
+ string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
+
+ string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
+#ifdef USE_MPI
+ for (int i = 0; i < thisTemplate.size(); i++) {
+
+ if (m->control_pressed) { return thisTemplate; }
+
+ string leftFrag = thisTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(thisTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+ if (m->control_pressed) { return thisTemplate; }
+
+ string rightFrag = thisTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(thisTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(thisTemplate.size());
+
+#else
+
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+
+ if (m->control_pressed) { return thisTemplate; }
+
+ string leftFrag = thisTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(thisTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+ if (m->control_pressed) { return thisTemplate; }
+
+ string rightFrag = thisTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(thisTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(thisTemplate.size());
+#endif
+ }else if (searchMethod == "blast") {
+
+ //generate blastdb
+ databaseLeft = new BlastDB(-2.0, -1.0, match, misMatch);
+ for (int i = 0; i < thisTemplate.size(); i++) { if (m->control_pressed) { return thisTemplate; } databaseLeft->addSequence(*thisTemplate[i]); }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+ }
+
+ return thisTemplate;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getTemplate");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+ChimeraSlayer::~ChimeraSlayer() {
+ delete decalc;
+ if (templateFileName != "self") {
+ if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
+ else if (searchMethod == "blast") { delete databaseLeft; }
+ }
+}
//***************************************************************************************************************
void ChimeraSlayer::printHeader(ostream& out) {
m->mothurOutEndLine();
}
}
- printBlock(chimeraResults[0], out);
+ printBlock(chimeraResults[0], chimeraFlag, out);
out << endl;
}else { out << querySeq->getName() << "\tno" << endl; }
//write to accnos file
int length = outAccString.length();
- char buf2[length];
- strcpy(buf2, outAccString.c_str());
+ char* buf2 = new char[length];
+ memcpy(buf2, outAccString.c_str(), length);
MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
+ delete buf2;
}
}
- outputString = getBlock(chimeraResults[0]);
+ outputString = getBlock(chimeraResults[0], chimeraFlag);
outputString += "\n";
-
- }else { outputString += querySeq->getName() + "\tno\n"; }
+ //cout << outputString << endl;
+ //write to output file
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+ delete buf;
+
+ }else {
+ outputString += querySeq->getName() + "\tno\n";
+ //cout << outputString << endl;
+ //write to output file
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+ delete buf;
+ }
- //write to output file
- int length = outputString.length();
- char buf[length];
- strcpy(buf, outputString.c_str());
- MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
-
return results;
}
catch(exception& e) {
int ChimeraSlayer::getChimeras(Sequence* query) {
try {
chimeraFlags = "no";
-
+
//filter query
spotMap = runFilter(query);
querySeq = query;
+ //you must create a template
+ vector<Sequence*> thisTemplate;
+ if (templateFileName != "self") { thisTemplate = templateSeqs; }
+ else { thisTemplate = getTemplate(query); } //fills thistemplate and creates the databases
+
+ if (m->control_pressed) { return 0; }
+
+ if (thisTemplate.size() == 0) { return 0; } //not chimeric
+
//referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
- maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
- slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
+ Maligner maligner(thisTemplate, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
+ Slayer slayer(window, increment, minSim, divR, iters, minSNP);
+ if (templateFileName == "self") {
+ if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
+ else if (searchMethod == "blast") { delete databaseLeft; }
+ }
+
if (m->control_pressed) { return 0; }
- string chimeraFlag = maligner->getResults(query, decalc);
+ string chimeraFlag = maligner.getResults(query, decalc);
if (m->control_pressed) { return 0; }
- vector<results> Results = maligner->getOutput();
-
+ vector<results> Results = maligner.getOutput();
+
//found in testing realigning only made things worse
if (realign) {
- ChimeraReAligner realigner(templateSeqs, match, misMatch);
+ ChimeraReAligner realigner(thisTemplate, match, misMatch);
realigner.reAlign(query, Results);
}
if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; }
//send to slayer
- chimeraFlags = slayer->getResults(query, seqsForSlayer);
+ chimeraFlags = slayer.getResults(query, seqsForSlayer);
if (m->control_pressed) { return 0; }
- chimeraResults = slayer->getOutput();
+ chimeraResults = slayer.getOutput();
//free memory
for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
}
- delete maligner;
- delete slayer;
+ //delete maligner;
+ //delete slayer;
return 0;
}
}
}
//***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
try {
//out << ":)\n";
out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
- out << "yes\t" << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
+ out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
//out << "Similarity of parents: " << data.ab << endl;
//out << "Similarity of query to parentA: " << data.qa << endl;
}
}
//***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
try {
string outputString = "";
outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t";
outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t";
- outputString += "yes\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
+ outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
return outputString;
}
projects / mothur.git / blobdiff