*
*/
-using namespace std;
-
#include "database.hpp"
#include "sequence.hpp"
/**************************************************************************************************/
-BlastDB::BlastDB(string fastaFileName, float gO, float gE, float m, float mM) : Database(fastaFileName),
-gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
-
- cout << "Generating the temporary BLAST database...\t"; cout.flush();
-
- int randNumber = rand();
- dbFileName = toString(randNumber) + ".template.unaligned.fasta";
- queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
- blastFileName = toString(randNumber) + ".blast";
+BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM, string b, int tid) : Database(),
+gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
+ try {
+ count = 0;
+ path = b;
+ threadID = tid;
-
- ofstream unalignedFastaFile;
- openOutputFile(dbFileName, unalignedFastaFile);
-
- for(int i=0;i<numSeqs;i++){ // generating a fasta file with unaligned template
- unalignedFastaFile << '>' << i << endl; // sequences, which will be input to formatdb
- unalignedFastaFile << templateSequences[i]->getUnaligned() << endl;
+ int randNumber = rand();
+ //int randNumber = 12345;
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ pid += getpid();
+#else
+ pid += toString(threadID);
+#endif
+
+
+ dbFileName = tag + pid + toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = tag + pid + toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = tag + pid + toString(randNumber) + ".blast";
+
+ //make sure blast exists in the write place
+ if (path == "") {
+ path = m->argv;
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ path += "blast/bin/";
+#else
+ path += "blast\\bin\\";
+#endif
+ }
+
+
+ string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
+#else
+ formatdbCommand = path + "formatdb.exe";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in;
+ formatdbCommand = m->getFullPathName(formatdbCommand);
+ int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
+#else
+ blastCommand = path + "blastall.exe";
+ //wrap entire string in ""
+ //blastCommand = "\"" + blastCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in2;
+ blastCommand = m->getFullPathName(blastCommand);
+ ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
+ string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+#else
+ megablastCommand = path + "megablast.exe";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in3;
+ megablastCommand = m->getFullPathName(megablastCommand);
+ ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
}
- unalignedFastaFile.close();
-
- string formatdbCommand = "~/Pipeline/src/cpp/production/blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
- system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
- // option tells formatdb that seqs are DNA, not prot
- cout << "DONE." << endl << endl; cout.flush();
- emptySequence = new Sequence();
- emptySequence->setName("no_match");
- emptySequence->setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- emptySequence->setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
-
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "BlastDB");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+BlastDB::BlastDB(string b, int tid) : Database() {
+ try {
+ count = 0;
+
+ path = b;
+ threadID = tid;
+
+ //make sure blast exists in the write place
+ if (path == "") {
+ path = m->argv;
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ path += "blast/bin/";
+#else
+ path += "blast\\bin\\";
+#endif
+ }
+
+ int randNumber = rand();
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ pid += getpid();
+#else
+ pid += toString(threadID);
+#endif
+
+ dbFileName = pid + toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = pid + toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = pid + toString(randNumber) + ".blast";
+
+ string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
+#else
+ formatdbCommand = path + "formatdb.exe";
+ //wrap entire string in ""
+ //formatdbCommand = "\"" + formatdbCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in;
+ formatdbCommand = m->getFullPathName(formatdbCommand);
+ int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
+#else
+ blastCommand = path + "blastall.exe";
+ //wrap entire string in ""
+ //blastCommand = "\"" + blastCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in2;
+ blastCommand = m->getFullPathName(blastCommand);
+ ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
+ string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+#else
+ megablastCommand = path + "megablast.exe";
+ //wrap entire string in ""
+ //megablastCommand = "\"" + megablastCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in3;
+ megablastCommand = m->getFullPathName(megablastCommand);
+ ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "BlastDB");
+ exit(1);
+ }
}
/**************************************************************************************************/
BlastDB::~BlastDB(){
- remove(queryFileName.c_str()); // let's clean stuff up and remove the temp files
- remove(dbFileName.c_str()); // let's clean stuff up and remove the temp files
- remove(blastFileName.c_str()); // let's clean stuff up and remove the temp files
+ try{
+ m->mothurRemove(queryFileName); // let's clean stuff up and remove the temp files
+ m->mothurRemove(dbFileName); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nsq")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nsi")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nsd")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nin")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nhr")); // let's clean stuff up and remove the temp files
+ m->mothurRemove(blastFileName.c_str()); // let's clean stuff up and remove the temp files
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "~BlastDB");
+ exit(1);
+ }
}
+/**************************************************************************************************/
+//assumes you have added all the template sequences using the addSequence function and run generateDB.
+vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
+ try{
+ vector<int> topMatches;
+
+ ofstream queryFile;
+ int randNumber = rand();
+ string pid = scrubName(seq->getName());
+
+ m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
+ queryFile << '>' << seq->getName() << endl;
+ queryFile << seq->getUnaligned() << endl;
+ queryFile.close();
+
+ // the goal here is to quickly survey the database to find the closest match. To do this we are using the default
+ // wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
+ // long. With this setting, it seems comparable in speed to the suffix tree approach.
+
+ string blastCommand;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ blastCommand = path + "blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
+ #else
+ blastCommand = "\"" + path + "blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
+ //wrap entire string in ""
+ blastCommand = "\"" + blastCommand + "\"";
+ #endif
+
+ system(blastCommand.c_str());
+
+ ifstream m8FileHandle;
+ m->openInputFile(blastFileName+pid+toString(randNumber), m8FileHandle, "no error");
+
+ string dummy;
+ int templateAccession;
+ m->gobble(m8FileHandle);
+
+ while(!m8FileHandle.eof()){
+ m8FileHandle >> dummy >> templateAccession >> searchScore;
+
+ //get rest of junk in line
+ while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; } }
+
+ m->gobble(m8FileHandle);
+ topMatches.push_back(templateAccession);
+ }
+ m8FileHandle.close();
+ m->mothurRemove((queryFileName+pid+toString(randNumber)));
+ m->mothurRemove((blastFileName+pid+toString(randNumber)));
+
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "findClosestSequences");
+ exit(1);
+ }
+
+}
/**************************************************************************************************/
+//assumes you have added all the template sequences using the addSequence function and run generateDB.
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
+ try{
+ vector<int> topMatches;
+ float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score;
+ Scores.clear();
+
+ ofstream queryFile;
+ int randNumber = rand();
+ string pid = scrubName(seq->getName());
+
+ m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
+ queryFile << '>' << seq->getName() << endl;
+ queryFile << seq->getUnaligned() << endl;
+ queryFile.close();
+// cout << seq->getUnaligned() << endl;
+ // the goal here is to quickly survey the database to find the closest match. To do this we are using the default
+ // wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
+ // long. With this setting, it seems comparable in speed to the suffix tree approach.
+//7000004128189528left 0 100 66 0 0 1 66 61 126 1e-31 131
+ string blastCommand;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
+ #else
+ //blastCommand = path + "blast\\bin\\megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ //blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
-Sequence* BlastDB::findClosestSequence(Sequence* candidate){
+ blastCommand = "\"" + path + "megablast\" -e 1e-10 -d " + "\"" + dbFileName + "\"" + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
+ //wrap entire string in ""
+ blastCommand = "\"" + blastCommand + "\"";
- ofstream queryFile;
- openOutputFile(queryFileName, queryFile);
- queryFile << '>' << candidate->getName() << endl;
- queryFile << candidate->getUnaligned() << endl;
- queryFile.close();
+ #endif
+ system(blastCommand.c_str());
+
+ ifstream m8FileHandle;
+ m->openInputFile(blastFileName+pid+toString(randNumber), m8FileHandle, "no error");
+ string dummy, eScore;
+ int templateAccession;
+ m->gobble(m8FileHandle);
+
+ while(!m8FileHandle.eof()){
+ m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
+// cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl;
+
+ //get rest of junk in line
+ //while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; }else{ cout << c; } } //
+ //cout << endl;
+ m->gobble(m8FileHandle);
+ if (searchScore >= minPerID) {
+ topMatches.push_back(templateAccession);
+ Scores.push_back(searchScore);
+ }
+//cout << templateAccession << endl;
+ }
+ m8FileHandle.close();
+ m->mothurRemove((queryFileName+pid+toString(randNumber)));
+ m->mothurRemove((blastFileName+pid+toString(randNumber)));
+//cout << "\n" ;
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "findClosestMegaBlast");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void BlastDB::addSequence(Sequence seq) {
+ try {
-// the goal here is to quickly survey the database to find the closest match. To do this we are using the default
-// wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
-// long. With this setting, it seems comparable in speed to the suffix tree approach.
-
- string blastCommand = "~/Pipeline/src/cpp/production/blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28";
- blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
- system(blastCommand.c_str());
+ ofstream unalignedFastaFile;
+ m->openOutputFileAppend(dbFileName, unalignedFastaFile);
- ifstream m8FileHandle;
- openInputFile(blastFileName, m8FileHandle);
+ // generating a fasta file with unaligned template
+ unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
+ unalignedFastaFile << seq.getUnaligned() << endl;
+ unalignedFastaFile.close();
- string dummy;
- int templateAccession;
- gobble(m8FileHandle);
- if(!m8FileHandle.eof()){
- m8FileHandle >> dummy >> templateAccession >> searchScore;
- m8FileHandle.close();
- return templateSequences[templateAccession];
+ count++;
}
- else{
- searchScore = 0.00;
- return emptySequence;
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "addSequence");
+ exit(1);
}
}
+/**************************************************************************************************/
+void BlastDB::generateDB() {
+ try {
+
+ //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+
+ string formatdbCommand;
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ #else
+ //formatdbCommand = path + "blast\\bin\\formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ formatdbCommand = "\"" + path + "formatdb\" -p F -o T -i " + "\"" + dbFileName + "\"";
+ //wrap entire string in ""
+ formatdbCommand = "\"" + formatdbCommand + "\"";
+ #endif
+ //cout << formatdbCommand << endl;
+ system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
+ // option tells formatdb that seqs are DNA, not prot
+ //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "generateDB");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+string BlastDB::scrubName(string seqName) {
+ try {
+
+ string cleanName = "";
+
+ for (int i = 0; i < seqName.length(); i++) {
+ if (isalnum(seqName[i])) { cleanName += seqName[i]; }
+ else { cleanName += "_"; }
+ }
+
+ return cleanName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "scrubName");
+ exit(1);
+ }
+}
/**************************************************************************************************/
+
+/**************************************************************************************************/
+
projects / mothur.git / blobdiff