func main() {
if flag.NArg() < 2 {
flag.Usage()
}
// If the quiet flag isn't set, enable verbose output.
if !flagQuiet {
mica.Verbose = true
}
// Open the fasta file specified for writing.
outFasta, err := os.Create(flag.Arg(1))
if err != nil {
fatalf("Could not write to '%s': %s\n", flag.Arg(1), err)
}
fastaWriter := fasta.NewWriter(outFasta)
fastaWriter.Asterisk = true
// 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.NewReadDB(flag.Arg(0))
if err != nil {
fatalf("Could not open '%s' database: %s\n", flag.Arg(0), err)
}
mica.Vprintln("")
// 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)
}
numSeqs := db.ComDB.NumSequences()
for orgSeqId := 0; orgSeqId < numSeqs; orgSeqId++ {
oseq, err := db.ComDB.ReadSeq(db.CoarseDB, orgSeqId)
if err != nil {
fatalf("Error reading seq id '%d': %s\n", orgSeqId, err)
}
if err := fastaWriter.Write(oseq.FastaSeq()); err != nil {
mica.Vprintf("Error writing seq '%s': %s\n", oseq.Name, err)
}
}
cleanup(db)
if err = fastaWriter.Flush(); err != nil {
fatalf("%s\n", err)
}
if err = outFasta.Close(); err != nil {
fatalf("%s\n", err)
}
}
func makeFineBlastDB(db *mica.DB, stdin *bytes.Buffer) (string, error) {
tmpDir, err := ioutil.TempDir("", "mica-fine-search-db")
if err != nil {
return "", fmt.Errorf("Could not create temporary directory: %s\n", err)
}
cmd := exec.Command(
flagMakeBlastDB, "-dbtype", "prot",
"-title", mica.FileBlastFine,
"-in", "-",
"-out", path.Join(tmpDir, mica.FileBlastFine))
cmd.Stdin = stdin
mica.Vprintf("Created temporary fine BLAST database in %s\n", tmpDir)
return tmpDir, mica.Exec(cmd)
}
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)
}