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) }