consensus.seqs summary file change

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index c30404ff965012565b39b8aec0cda823a3bfd139..3497579167210514496ac904f6c9f19d17140b16 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -10,6 +10,7 @@
 #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, 
@@ -46,7 +47,6 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
 int ChimeraSlayer::doPrep() {
        try {
                
-               
                //read in all query seqs
                vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
                
@@ -67,10 +67,11 @@ int ChimeraSlayer::doPrep() {
        
                //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++) {
@@ -102,8 +103,14 @@ int ChimeraSlayer::doPrep() {
                        //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++) {
                                        
@@ -127,8 +134,14 @@ int ChimeraSlayer::doPrep() {
                        //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; } 
@@ -148,6 +161,13 @@ int ChimeraSlayer::doPrep() {
                        
                        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;
@@ -159,7 +179,11 @@ int ChimeraSlayer::doPrep() {
        }
 }
 //***************************************************************************************************************
-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();
@@ -185,7 +209,7 @@ int ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                                }
                        }
                        
-                       printBlock(chimeraResults[0], out);
+                       printBlock(chimeraResults[0], chimeraFlag, out);
                        out << endl;
                }else {  out << querySeq->getName() << "\tno" << endl;  }
                
@@ -221,7 +245,7 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
                                        
                                        //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);
@@ -229,19 +253,30 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
                                }
                        }
                        
-                       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) {
@@ -255,7 +290,7 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
 int ChimeraSlayer::getChimeras(Sequence* query) {
        try {
                chimeraFlags = "no";
-               
+
                //filter query
                spotMap = runFilter(query);     
                
@@ -264,13 +299,13 @@ int ChimeraSlayer::getChimeras(Sequence* 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);
@@ -365,7 +400,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
        }
 }
 //***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
        try {
        //out << ":)\n";
                
@@ -377,7 +412,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
                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;
@@ -400,7 +435,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
        }
 }
 //***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
        try {
                
                string outputString = "";
@@ -411,7 +446,7 @@ string ChimeraSlayer::getBlock(data_struct data){
                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;
        }