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 FindFragments(pdbDb PDBDatabase, blits bool,
queryHHM *hmm.HHM, qs seq.Sequence, start, end int) (*Fragments, error) {
pre := fmt.Sprintf("bcbgo-hhfrag-hhm-%d-%d_", start, end)
hhmFile, err := ioutil.TempFile("", pre)
if err != nil {
return nil, err
}
defer os.Remove(hhmFile.Name())
defer hhmFile.Close()
hhmName := hhmFile.Name()
if err := hmm.WriteHHM(hhmFile, queryHHM.Slice(start, end)); err != nil {
return nil, err
}
var results *hhr.HHR
if blits {
conf := hhsuite.HHBlitsDefault
conf.CPUs = 1
results, err = conf.Run(pdbDb.HHsuite(), hhmName)
} else {
conf := hhsuite.HHSearchDefault
conf.CPUs = 1
results, err = conf.Run(pdbDb.HHsuite(), hhmName)
}
if err != nil {
return nil, err
}
frags := make([]Fragment, 0, len(results.Hits))
for _, hit := range results.Hits {
hit.QueryStart += start
hit.QueryEnd += start
for _, splitted := range splitHit(hit) {
frag, err := NewFragment(pdbDb, qs, splitted)
if err != nil {
return nil, err
}
frags = append(frags, frag)
}
}
return &Fragments{
Frags: frags,
Start: start,
End: end,
}, nil
}
func main() {
inFasta := util.Arg(0)
outHHM := util.Arg(1)
hhblits := hhsuite.HHBlitsDefault
hhmake := hhsuite.HHMakePseudo
hhblits.Verbose = !flagQuiet
hhmake.Verbose = !flagQuiet
HHM, err := hhsuite.BuildHHM(
hhblits, hhmake, util.FlagSeqDB, inFasta)
util.Assert(err, "Error building HHM")
util.Assert(hmm.WriteHHM(util.CreateFile(outHHM), HHM),
"Error writing HHM '%s'", outHHM)
}