#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() {
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; } }
+ChimeraSlayer::~ChimeraSlayer() {
+ delete decalc;
+ 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 = new char[length];\r
+ char* buf2 = new char[length];
memcpy(buf2, outAccString.c_str(), length);
MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
}
}
- outputString = getBlock(chimeraResults[0]);
+ outputString = getBlock(chimeraResults[0], chimeraFlag);
outputString += "\n";
-
- }else { outputString += querySeq->getName() + "\tno\n"; }
-
- //write to output file
- int length = outputString.length();
- char* buf = new char[length];\r
- memcpy(buf, outputString.c_str(), length);
+ //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;
+ 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;
+ }
+
+
return results;
}
catch(exception& e) {
int ChimeraSlayer::getChimeras(Sequence* query) {
try {
chimeraFlags = "no";
-
+
//filter query
spotMap = runFilter(query);
//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);
-
+
if (m->control_pressed) { return 0; }
string chimeraFlag = maligner->getResults(query, decalc);
if (m->control_pressed) { return 0; }
vector<results> Results = maligner->getOutput();
-
+
//found in testing realigning only made things worse
if (realign) {
ChimeraReAligner realigner(templateSeqs, match, misMatch);
}
}
//***************************************************************************************************************
-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;
}