// Run will execute HHsearch using the given configuration, database and query
// file path. The query can be a path to a fasta file, A3M file or HHM file.
// (As per the '-i' flag for hhsearch.)
func (conf HHSearchConfig) Run(db Database, query string) (*hhr.HHR, error) {
hhrFile, err := ioutil.TempFile("", "bcbgo-hhr")
if err != nil {
return nil, err
}
defer os.Remove(hhrFile.Name())
defer hhrFile.Close()
args := []string{
"-cpu", fmt.Sprintf("%d", conf.CPUs),
"-i", query,
"-d", db.ResolveHHSearch(),
"-o", hhrFile.Name(),
}
c := cmd.New(conf.Exec, args...)
if conf.Verbose {
fmt.Fprintf(os.Stderr, "\n%s\n", c)
c.Cmd.Stdout = os.Stdout
c.Cmd.Stderr = os.Stderr
}
if err := c.Run(); err != nil {
return nil, err
}
return hhr.Read(hhrFile)
}
// Run will execute HHblits using the given configuration, database and query
// file path. The query can be a path to a fasta file, A3M file or HHM file.
// (As per the '-i' flag for hhblits.)
func (conf HHBlitsConfig) Run(db Database, query string) (*hhr.HHR, error) {
// If the database is old style, it cannot be used with hhblits.
if db.isOldStyle() {
return nil, fmt.Errorf("An old-style database '%s' cannot be used "+
"with hhblits. It can only be used with hhsearch.", db)
}
hhrFile, err := ioutil.TempFile("", "bcbgo-hhr")
if err != nil {
return nil, err
}
defer os.Remove(hhrFile.Name())
defer hhrFile.Close()
args := []string{
"-cpu", fmt.Sprintf("%d", conf.CPUs),
"-i", query,
"-d", db.Resolve(),
"-n", fmt.Sprintf("%d", conf.Iterations),
"-mact", fmt.Sprintf("%f", conf.MAct),
"-o", hhrFile.Name(),
}
if len(conf.OutA3M) > 0 {
args = append(args, []string{"-oa3m", conf.OutA3M}...)
}
c := cmd.New(conf.Exec, args...)
if conf.Verbose {
fmt.Fprintf(os.Stderr, "\n%s\n", c)
c.Cmd.Stdout = os.Stdout
c.Cmd.Stderr = os.Stderr
}
if err := c.Run(); err != nil {
return nil, err
}
return hhr.Read(hhrFile)
}
