// Run will execute HHmake using the given configuration and query file path.
// The query should be a file path pointing to an MSA file (fasta, a2m or
// a3m) or an hhm file. It should NOT be just a single sequence.
//
// If you need to build an HHM from a single sequence, use the convenience
// function BuildHHM.
func (conf HHMakeConfig) Run(query string) (*hmm.HHM, error) {
hhmFile, err := ioutil.TempFile("", "bad-bcbgo-hhm")
if err != nil {
return nil, err
}
defer os.Remove(hhmFile.Name())
defer hhmFile.Close()
emission := strings.Fields(fmt.Sprintf(
"-pcm %d -pca %f -pcb %f -pcc %f",
conf.PCM, conf.PCA, conf.PCB, conf.PCC))
transition := strings.Fields(fmt.Sprintf(
"-gapb %f -gapd %f -gape %f -gapf %f -gapg %f -gapi %f",
conf.GapB, conf.GapD, conf.GapE, conf.GapF, conf.GapG, conf.GapI))
args := []string{
"-i", query,
"-o", hhmFile.Name(),
}
args = append(args, emission...)
args = append(args, transition...)
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 hmm.ReadHHM(hhmFile)
}
func main() {
hhmFile := util.Arg(0)
start := util.ParseInt(util.Arg(1))
end := util.ParseInt(util.Arg(2))
fhhm := util.OpenFile(hhmFile)
qhhm, err := hmm.ReadHHM(fhhm)
util.Assert(err)
util.Assert(hmm.WriteHHM(os.Stdout, qhhm.Slice(start, end)))
}
func (m MapConfig) MapFromHHM(pdbDb PDBDatabase, seqDb hhsuite.Database,
queryFasta string, queryHHM string) (*FragmentMap, error) {
qseq, err := getOneFastaSequence(queryFasta)
if err != nil {
return nil, err
}
fquery, err := os.Open(queryHHM)
if err != nil {
return nil, err
}
defer fquery.Close()
qhhm, err := hmm.ReadHHM(fquery)
if err != nil {
return nil, err
}
return m.computeMap(pdbDb, qseq, qhhm)
}
