func blastCoarse(
db *cablastp.DB, stdin *bytes.Reader, stdout *bytes.Buffer) error {
flags := []string{"-db", path.Join(db.Path, cablastp.FileBlastCoarse),
"-outfmt", "5", "-num_iterations", s(flagIters),
"-dbsize", su(db.BlastDBSize)}
cmd := exec.Command(flagPsiBlast, flags...)
cmd.Stdin = stdin
cmd.Stdout = stdout
return cablastp.Exec(cmd)
}
func blastCoarse(
db *cablastp.DB, stdin *bytes.Reader, stdout *bytes.Buffer) error {
cmd := exec.Command(
flagDeltaBlast,
"-db", path.Join(db.Path, cablastp.FileBlastCoarse),
"-rpsdb", flagRPSPath,
"-outfmt", "5", "-dbsize", su(db.BlastDBSize))
cmd.Stdin = stdin
cmd.Stdout = stdout
return cablastp.Exec(cmd)
}
func blastCoarse(
db *cablastp.DB, stdin *bytes.Reader, stdout *bytes.Buffer) error {
cmd := exec.Command(
flagBlastp,
"-db", path.Join(db.Path, cablastp.FileBlastCoarse),
"-num_threads", s(flagGoMaxProcs),
"-outfmt", "5", "-dbsize", su(db.BlastDBSize))
cmd.Stdin = stdin
cmd.Stdout = stdout
return cablastp.Exec(cmd)
}
func blastFine(
db *cablastp.DB, blastFineDir string, stdin *bytes.Reader) error {
// We pass our own "-db" flag to blastp, but the rest come from user
// defined flags.
flags := []string{"-db", path.Join(blastFineDir, cablastp.FileBlastFine),
"-num_iterations", s(flagIters),
"-dbsize", su(db.BlastDBSize)}
flags = append(flags, blastArgs...)
cmd := exec.Command(flagPsiBlast, flags...)
cmd.Stdin = stdin
cmd.Stdout = os.Stdout
cmd.Stderr = os.Stderr
return cablastp.Exec(cmd)
}
func makeFineBlastDB(db *cablastp.DB, stdin *bytes.Buffer) (string, error) {
tmpDir, err := ioutil.TempDir("", "cablastp-fine-search-db")
if err != nil {
return "", fmt.Errorf("Could not create temporary directory: %s\n", err)
}
cmd := exec.Command(
flagMakeBlastDB, "-dbtype", "prot",
"-title", cablastp.FileBlastFine,
"-in", "-",
"-out", path.Join(tmpDir, cablastp.FileBlastFine))
cmd.Stdin = stdin
cablastp.Vprintf("Created temporary fine BLAST database in %s\n", tmpDir)
return tmpDir, cablastp.Exec(cmd)
}
func blastFine(
db *cablastp.DB, blastFineDir string, stdin *bytes.Reader) error {
// We pass our own "-db" flag to blastp, but the rest come from user
// defined flags.
// deltablast needs a rpsdb path
flags := []string{"-db", path.Join(blastFineDir, cablastp.FileBlastFine),
"-rpsdb", flagRPSPath,
"-dbsize", su(db.BlastDBSize)}
flags = append(flags, blastArgs...)
cmd := exec.Command(flagDeltaBlast, flags...)
cmd.Stdin = stdin
cmd.Stdout = os.Stdout
cmd.Stderr = os.Stderr
return cablastp.Exec(cmd)
}
func blastFine(
db *cablastp.DB, blastFineFile string, stdin *bytes.Reader) error {
// We pass our own "-db" flag to blastp, but the rest come from user
// defined flags.
flags := []string{
"-subject", blastFineFile,
"-dbsize", su(db.BlastDBSize),
"-num_threads", s(flagGoMaxProcs),
}
flags = append(flags, blastArgs...)
cmd := exec.Command(flagBlastp, flags...)
cmd.Stdin = stdin
cmd.Stdout = os.Stdout
cmd.Stderr = os.Stderr
return cablastp.Exec(cmd)
}
