Ejemplo n.º 1
0
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)
}
Ejemplo n.º 2
0
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)
}
Ejemplo n.º 3
0
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)
}
Ejemplo n.º 4
0
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)
}
Ejemplo n.º 5
0
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)
}
Ejemplo n.º 6
0
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)
}
Ejemplo n.º 7
0
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)
}