*/
#include "chimeraslayercommand.h"
-#include "bellerophon.h"
-#include "pintail.h"
-#include "ccode.h"
-#include "chimeracheckrdp.h"
#include "chimeraslayer.h"
m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
- m->mothurOut("The chimera.slayer command parameters are fasta, template, filter, mask, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
+ m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
#ifdef USE_MPI
m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
#endif
- m->mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n");
m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
//m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. Found to make results worse. \n");
- m->mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
m->mothurOut("The chimera.slayer command should be in the following format: \n");
m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
-
- char outFilename[outputFileName.length()];
+
+ //char* outFilename = new char[outputFileName.length()];
+ //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+
+ char outFilename[1024];
strcpy(outFilename, outputFileName.c_str());
- char outAccnosFilename[accnosFileName.length()];
+ //char* outAccnosFilename = new char[accnosFileName.length()];
+ //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+
+ char outAccnosFilename[1024];
strcpy(outAccnosFilename, accnosFileName.c_str());
+
+ //char* inFileName = new char[fastafile.length()];
+ //memcpy(inFileName, fastafile.c_str(), fastafile.length());
- char inFileName[fastafile.length()];
+ char inFileName[1024];
strcpy(inFileName, fastafile.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
+ //delete inFileName;
+ //delete outFilename;
+ //delete outAccnosFilename;
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
if (pid == 0) { //you are the root process
m->mothurOutEndLine();
//print header
int length = outTemp.length();
- char buf2[length];
- strcpy(buf2, outTemp.c_str());
+ char* buf2 = new char[length];
+ memcpy(buf2, outTemp.c_str(), length);
+
MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
-
+ delete buf2;
+
MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
- MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
//figure out how many sequences you have to align
numSeqsPerProcessor = numSeqs / processors;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
if (tempResult != 0) { MPIWroteAccnos = true; }
}
}else{ //you are a child process
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numSeqs+1);
- MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+ MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = numSeqs / processors;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
MPI_File_close(&inMPI);
MPI_File_close(&outMPI);
MPI_File_close(&outMPIAccnos);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
//delete accnos file if blank
if (pid == 0) {
if(processors == 1){
ifstream inFASTA;
openInputFile(fastafile, inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ getNumSeqs(inFASTA, numSeqs);
inFASTA.close();
lines.push_back(new linePair(0, numSeqs));
lines.push_back(new linePair(startPos, numSeqsPerProcessor));
}
-
createProcesses(outputFileName, fastafile, accnosFileName);
rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
#else
ifstream inFASTA;
- openInputFile(candidateFileNames[s], inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ openInputFile(fastafile, inFASTA);
+ getNumSeqs(inFASTA, numSeqs);
inFASTA.close();
lines.push_back(new linePair(0, numSeqs));
if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
#endif
- appendFiles(tempHeader, outputFileName);
+ appendFiles(outputFileName, tempHeader);
remove(outputFileName.c_str());
rename(tempHeader.c_str(), outputFileName.c_str());
//**********************************************************************************************************************
#ifdef USE_MPI
int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
- try {
-
+ try {
MPI_Status status;
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
//read next sequence
int length = MPIPos[start+i+1] - MPIPos[start+i];
-
- char buf4[length];
+
+ char* buf4 = new char[length];
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
-
+
string tempBuf = buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
istringstream iss (tempBuf,istringstream::in);
+ delete buf4;
+
Sequence* candidateSeq = new Sequence(iss); gobble(iss);
-
+
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
if (candidateSeq->getAligned().length() != templateSeqsLength) {
m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
}else{
+
//find chimeras
chimera->getChimeras(candidateSeq);
-
+
if (m->control_pressed) { delete candidateSeq; return 1; }
-
+ //cout << "about to print" << endl;
//print results
bool isChimeric = chimera->print(outMPI, outAccMPI);
if (isChimeric) { MPIWroteAccnos = true; }
+
}
}
delete candidateSeq;
projects / mothur.git / blobdiff