func compressQueries(queryFileName string) (string, error) {
// dbDirLoc, err := ioutil.TempDir(flagTempFileDir, "temporary-compressed-query-db")
dbDirLoc := flagTempFileDir
dbDirLoc = dbDirLoc + "/temporary-compressed-query-db"
if flagQueryDBConf != "" {
qdbParams, err := os.Open(flagQueryDBConf)
if err != nil {
return "", fmt.Errorf("Failed to load query db conf: %s", err)
}
queryDBConf, err = mica.LoadDBConf(qdbParams)
if err != nil {
return "", fmt.Errorf("Failed to load query db conf: %s", err)
}
}
db, err := mica.NewWriteDB(false, queryDBConf, dbDirLoc)
handleFatalError("Failed to open new db", err)
mica.Vprintln("Starting query compress workers...")
pool := mica.StartCompressReducedWorkers(db)
seqId := db.ComDB.NumSequences()
mainQuit := make(chan struct{}, 0)
seqChan, err := mica.ReadOriginalSeqs(queryFileName, []byte{})
handleFatalError("Could not read query sequences", err)
mica.Vprintln("Reading sequences into query database...")
for readSeq := range seqChan {
// Do a non-blocking receive to see if main needs to quit.
select {
case <-mainQuit:
<-mainQuit // wait for cleanup to finish before exiting main.
return "", nil
default:
}
handleFatalError("Failed to read sequence", readSeq.Err)
queryDBConf.BlastDBSize += uint64(readSeq.Seq.Len())
redReadSeq := &mica.ReducedSeq{
&mica.Sequence{
Name: readSeq.Seq.Name,
Residues: readSeq.Seq.Residues,
Offset: readSeq.Seq.Offset,
Id: readSeq.Seq.Id,
},
}
seqId = pool.CompressReduced(seqId, redReadSeq)
}
mica.Vprintln("Cleaning up query database...")
mica.CleanupDB(db, &pool)
mica.Vprintln("")
return dbDirLoc, nil
}
func main() {
if flag.NArg() < 2 {
flag.Usage()
}
// If both 'append' and 'overwrite' flags are set, quit because the
// combination doesn't make sense.
if flagAppend && flagOverwrite {
fatalf("Both the 'append' and 'overwrite' flags are set. It does " +
"not make sense to set both of these flags.")
}
// If the quiet flag isn't set, enable verbose output.
if !flagQuiet {
mica.Verbose = true
}
// If the overwrite flag is set, remove whatever directory that may
// already be there.
if flagOverwrite {
if err := os.RemoveAll(flag.Arg(0)); err != nil {
fatalf("Could not remove existing database '%s': %s.",
flag.Arg(0), err)
}
}
// Create a new database for writing. If we're appending, we load
// the coarse database into memory, and setup the database for writing.
db, err := mica.NewWriteDB(flagAppend, dbConf, flag.Arg(0))
if err != nil {
fatalf("%s\n", err)
}
mica.Vprintln("")
pool := startCompressWorkers(db)
orgSeqId := db.ComDB.NumSequences()
mainQuit := make(chan struct{}, 0)
// If the process is killed, try to clean up elegantly.
// The idea is to preserve the integrity of the database.
attachSignalHandler(db, mainQuit, &pool)
// Start the CPU profile after all of the data has been read.
if len(flagCpuProfile) > 0 {
f, err := os.Create(flagCpuProfile)
if err != nil {
fatalf("%s\n", err)
}
pprof.StartCPUProfile(f)
}
for _, arg := range flag.Args()[1:] {
seqChan, err := mica.ReadOriginalSeqs(arg, ignoredResidues)
if err != nil {
log.Fatal(err)
}
if orgSeqId == 0 {
timer = time.Now()
}
for readSeq := range seqChan {
// Do a non-blocking receive to see if main needs to quit.
select {
case <-mainQuit:
<-mainQuit // wait for cleanup to finish before exiting main.
return
default:
}
if readSeq.Err != nil {
log.Fatal(err)
}
dbConf.BlastDBSize += uint64(readSeq.Seq.Len())
orgSeqId = pool.compress(orgSeqId, readSeq.Seq)
verboseOutput(db, orgSeqId)
if flagMaxSeedsGB > 0 && orgSeqId%10000 == 0 {
db.CoarseDB.Seeds.MaybeWipe(flagMaxSeedsGB)
runtime.GC()
}
}
}
mica.Vprintln("\n")
mica.Vprintf("Wrote %s.\n", mica.FileCompressed)
mica.Vprintf("Wrote %s.\n", mica.FileIndex)
cleanup(db, &pool)
}
