X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=alignmentdb.cpp;h=9fec737778e01704e98f5c813e3c0554e7ab0981;hp=e2b1dc197eb8d3399156a3ca752bff5da267101f;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6 diff --git a/alignmentdb.cpp b/alignmentdb.cpp index e2b1dc1..9fec737 100644 --- a/alignmentdb.cpp +++ b/alignmentdb.cpp @@ -11,101 +11,143 @@ #include "kmerdb.hpp" #include "suffixdb.hpp" #include "blastdb.hpp" - +#include "referencedb.h" /**************************************************************************************************/ -AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){ // This assumes that the template database is in fasta format, may +AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){ // This assumes that the template database is in fasta format, may try { // need to alter this in the future? m = MothurOut::getInstance(); longest = 0; method = s; bool needToGenerate = true; + ReferenceDB* rdb = ReferenceDB::getInstance(); + bool silent = false; + threadID = tid; - m->mothurOutEndLine(); - m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush(); - - #ifdef USE_MPI - int pid, processors; - vector positions; + if (fastaFileName == "saved-silent") { + fastaFileName = "saved"; silent = true; + } - MPI_Status status; - MPI_File inMPI; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - MPI_Comm_size(MPI_COMM_WORLD, &processors); - int tag = 2001; - - char inFileName[1024]; - strcpy(inFileName, fastaFileName.c_str()); - - MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer + if (fastaFileName == "saved") { + int start = time(NULL); - if (pid == 0) { - positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs + if (!silent) { m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); } - //send file positions to all processes - for(int i = 1; i < processors; i++) { - MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); - MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); - } - }else{ - MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); - positions.resize(numSeqs+1); - MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + for (int i = 0; i < rdb->referenceSeqs.size(); i++) { + templateSequences.push_back(rdb->referenceSeqs[i]); + //save longest base + if (rdb->referenceSeqs[i].getUnaligned().length() >= longest) { longest = (rdb->referenceSeqs[i].getUnaligned().length()+1); } } + fastaFileName = rdb->getSavedReference(); + + numSeqs = templateSequences.size(); + if (!silent) { m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine(); } + + }else { + int start = time(NULL); + m->mothurOutEndLine(); + m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush(); + //bool aligned = false; + int tempLength = 0; + + #ifdef USE_MPI + int pid, processors; + vector positions; + + MPI_Status status; + MPI_File inMPI; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + MPI_Comm_size(MPI_COMM_WORLD, &processors); + int tag = 2001; + + char inFileName[1024]; + strcpy(inFileName, fastaFileName.c_str()); - //read file - for(int i=0;icontrol_pressed) { templateSequences.clear(); break; } + if (pid == 0) { + positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs + + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + }else{ + MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + positions.resize(numSeqs+1); + MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + } + + //read file + for(int i=0;icontrol_pressed) { templateSequences.clear(); break; } + + //read next sequence + int length = positions[i+1] - positions[i]; + char* buf4 = new char[length]; - //read next sequence - int length = positions[i+1] - positions[i]; - char* buf4 = new char[length]; + MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status); - MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status); - - string tempBuf = buf4; - if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } - delete buf4; + string tempBuf = buf4; + if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } + delete buf4; - istringstream iss (tempBuf,istringstream::in); - - Sequence temp(iss); + istringstream iss (tempBuf,istringstream::in); + + Sequence temp(iss); + if (temp.getName() != "") { + templateSequences.push_back(temp); + + if (rdb->save) { rdb->referenceSeqs.push_back(temp); } + + //save longest base + if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; } + if (tempLength != 0) { + if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; } + }else { tempLength = temp.getAligned().length(); } + } + } + + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + + MPI_File_close(&inMPI); + + #else + ifstream fastaFile; + m->openInputFile(fastaFileName, fastaFile); + + while (!fastaFile.eof()) { + Sequence temp(fastaFile); m->gobble(fastaFile); + + if (m->control_pressed) { templateSequences.clear(); break; } + if (temp.getName() != "") { templateSequences.push_back(temp); + + if (rdb->save) { rdb->referenceSeqs.push_back(temp); } + //save longest base - if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; } + if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); } + + if (tempLength != 0) { + if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; } + }else { tempLength = temp.getAligned().length(); } } } - - MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case - - MPI_File_close(&inMPI); + fastaFile.close(); + #endif - #else - ifstream fastaFile; - m->openInputFile(fastaFileName, fastaFile); - - while (!fastaFile.eof()) { - Sequence temp(fastaFile); m->gobble(fastaFile); - - if (m->control_pressed) { templateSequences.clear(); break; } + numSeqs = templateSequences.size(); + //all of this is elsewhere already! - if (temp.getName() != "") { - templateSequences.push_back(temp); - //save longest base - if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; } - } + m->mothurOut("DONE."); + m->mothurOutEndLine(); cout.flush(); + m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(templateSequences.size()) + " sequences."); m->mothurOutEndLine(); + } - fastaFile.close(); - #endif - - numSeqs = templateSequences.size(); - //all of this is elsewhere already! - - m->mothurOut("DONE."); - m->mothurOutEndLine(); cout.flush(); //in case you delete the seqs and then ask for them emptySequence = Sequence(); @@ -130,8 +172,9 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap #endif } else if(method == "suffix") { search = new SuffixDB(numSeqs); } - else if(method == "blast") { search = new BlastDB(gapOpen, gapExtend, match, misMatch); } + else if(method == "blast") { search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); } else { + method = "kmer"; m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine(); search = new KmerDB(fastaFileName, 8); @@ -157,6 +200,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap search->setNumSeqs(numSeqs); } + } catch(exception& e) { m->errorOut(e, "AlignmentDB", "AlignmentDB"); @@ -170,7 +214,7 @@ AlignmentDB::AlignmentDB(string s){ method = s; if(method == "suffix") { search = new SuffixDB(); } - else if(method == "blast") { search = new BlastDB(); } + else if(method == "blast") { search = new BlastDB("", 0); } else { search = new KmerDB(); } @@ -193,7 +237,7 @@ Sequence AlignmentDB::findClosestSequence(Sequence* seq) { try{ vector spot = search->findClosestSequences(seq, 1); - + if (spot.size() != 0) { return templateSequences[spot[0]]; } else { return emptySequence; }