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Linclust.cpp
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Linclust.cpp
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#include "Parameters.h"
#include "Util.h"
#include "DBWriter.h"
#include "CommandCaller.h"
#include "Debug.h"
#include "FileUtil.h"
#include "linclust.sh.h"
#include <cassert>
void setLinclustWorkflowDefaults(Parameters *p) {
p->spacedKmer = true;
p->covThr = 0.8;
p->maskMode = 0;
p->evalThr = 0.001;
p->seqIdThr = 0.9;
p->alignmentMode = Parameters::ALIGNMENT_MODE_SCORE_COV;
}
int linclust(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
setLinclustWorkflowDefaults(&par);
par.overrideParameterDescription((Command &)command, par.PARAM_RESCORE_MODE.uniqid, NULL, NULL, par.PARAM_RESCORE_MODE.category |MMseqsParameter::COMMAND_EXPERT );
par.overrideParameterDescription((Command &)command, par.PARAM_MAX_REJECTED.uniqid, NULL, NULL, par.PARAM_MAX_REJECTED.category |MMseqsParameter::COMMAND_EXPERT );
par.overrideParameterDescription((Command &)command, par.PARAM_MAX_ACCEPT.uniqid, NULL, NULL, par.PARAM_MAX_ACCEPT.category |MMseqsParameter::COMMAND_EXPERT );
par.parseParameters(argc, argv, command, 3);
const int dbType = DBReader<unsigned int>::parseDbType(par.db1.c_str());
if (FileUtil::directoryExists(par.db3.c_str()) == false) {
Debug(Debug::INFO) << "Tmp " << par.db3 << " folder does not exist or is not a directory.\n";
if (FileUtil::makeDir(par.db3.c_str()) == false) {
Debug(Debug::ERROR) << "Can not create tmp folder " << par.db3 << ".\n";
EXIT(EXIT_FAILURE);
} else {
Debug(Debug::INFO) << "Created dir " << par.db3 << "\n";
}
}
std::string hash = SSTR(par.hashParameter(par.filenames, par.linclustworkflow));
if(par.reuseLatest){
hash = FileUtil::getHashFromSymLink(par.db3+"/latest");
}
std::string tmpDir = par.db3+"/"+hash;
if (FileUtil::directoryExists(tmpDir.c_str())==false) {
if (FileUtil::makeDir(tmpDir.c_str()) == false) {
Debug(Debug::ERROR) << "Can not create sub tmp folder " << tmpDir << ".\n";
EXIT(EXIT_FAILURE);
}
}
par.filenames.pop_back();
par.filenames.push_back(tmpDir);
FileUtil::symlinkAlias(tmpDir, "latest");
CommandCaller cmd;
cmd.addVariable("REMOVE_TMP", par.removeTmpFiles ? "TRUE" : NULL);
cmd.addVariable("RUNNER", par.runner.c_str());
// save some values to restore them later
size_t alphabetSize = par.alphabetSize;
size_t kmerSize = par.kmerSize;
// # 1. Finding exact $k$-mer matches.
bool kmerSizeWasSet = false;
bool alphabetSizeWasSet = false;
bool clusterModeSet = false;
for (size_t i = 0; i < par.linclustworkflow.size(); i++) {
if (par.linclustworkflow[i]->uniqid == par.PARAM_K.uniqid && par.linclustworkflow[i]->wasSet) {
kmerSizeWasSet = true;
}
if (par.linclustworkflow[i]->uniqid == par.PARAM_ALPH_SIZE.uniqid && par.linclustworkflow[i]->wasSet) {
alphabetSizeWasSet = true;
}
if (par.linclustworkflow[i]->uniqid == par.PARAM_CLUSTER_MODE.uniqid && par.linclustworkflow[i]->wasSet) {
clusterModeSet = true;
}
}
const bool nonSymetric = (par.covMode == Parameters::COV_MODE_TARGET || par.covMode == Parameters::COV_MODE_QUERY);
if (clusterModeSet == false){
if (nonSymetric) {
par.clusteringMode = Parameters::GREEDY_MEM;
} else {
par.clusteringMode = Parameters::SET_COVER;
}
std::string cluMode = (par.clusteringMode==Parameters::GREEDY_MEM) ? "GREEDY MEM" : "SET COVER";
Debug(Debug::INFO) << "Set cluster mode " << cluMode << ".\n";
}
if (kmerSizeWasSet == false) {
par.kmerSize = Parameters::CLUST_LINEAR_DEFAULT_K;
}
if (alphabetSizeWasSet == false) {
par.alphabetSize = Parameters::CLUST_LINEAR_DEFAULT_ALPH_SIZE;
}
const bool isUngappedMode = par.alignmentMode == Parameters::ALIGNMENT_MODE_UNGAPPED;
if (isUngappedMode && Parameters::isEqualDbtype(dbType, Parameters::DBTYPE_HMM_PROFILE)) {
par.printUsageMessage(command, MMseqsParameter::COMMAND_ALIGN|MMseqsParameter::COMMAND_PREFILTER);
Debug(Debug::ERROR) << "Cannot use ungapped alignment mode with profile databases.\n";
EXIT(EXIT_FAILURE);
}
cmd.addVariable("ALIGN_MODULE", isUngappedMode ? "rescorediagonal" : "align");
// filter by diagonal in case of AA (do not filter for nucl, profiles, ...)
cmd.addVariable("FILTER", Parameters::isEqualDbtype(dbType, Parameters::DBTYPE_AMINO_ACIDS) ? "1" : NULL);
cmd.addVariable("KMERMATCHER_PAR", par.createParameterString(par.kmermatcher).c_str());
par.alphabetSize = alphabetSize;
par.kmerSize = kmerSize;
// # 2. Hamming distance pre-clustering
par.rescoreMode = Parameters::RESCORE_MODE_HAMMING;
par.filterHits = false;
float prevSeqId = par.seqIdThr;
// hamming distance does not work well with seq. id < 0.5 since it does not have an e-value criteria
par.seqIdThr = std::max(0.5f, par.seqIdThr);
// also coverage should not be under 0.5
float prevCov = par.covThr;
par.covThr = std::max(0.5f, par.covThr);
cmd.addVariable("HAMMING_PAR", par.createParameterString(par.rescorediagonal).c_str());
// set it back to old value
par.covThr = prevCov;
par.seqIdThr = prevSeqId;
par.rescoreMode = Parameters::RESCORE_MODE_SUBSTITUTION;
// # 3. Ungapped alignment filtering
par.filterHits = true;
cmd.addVariable("UNGAPPED_ALN_PAR", par.createParameterString(par.rescorediagonal).c_str());
// # 4. Local gapped sequence alignment.
par.maxResListLen = INT_MAX;
if (isUngappedMode) {
const int originalRescoreMode = par.rescoreMode;
par.rescoreMode = Parameters::RESCORE_MODE_ALIGNMENT;
cmd.addVariable("ALIGNMENT_PAR", par.createParameterString(par.rescorediagonal).c_str());
par.rescoreMode = originalRescoreMode;
} else {
cmd.addVariable("ALIGNMENT_PAR", par.createParameterString(par.align).c_str());
}
// # 5. Clustering using greedy set cover.
cmd.addVariable("CLUSTER_PAR", par.createParameterString(par.clust).c_str());
cmd.addVariable("MERGECLU_PAR", par.createParameterString(par.threadsandcompression).c_str());
FileUtil::writeFile(tmpDir + "/linclust.sh", linclust_sh, linclust_sh_len);
std::string program(tmpDir + "/linclust.sh");
cmd.execProgram(program.c_str(), par.filenames);
// Unreachable
assert(false);
return 0;
}