func main() {
if len(util.FlagCpuProf) > 0 {
f := util.CreateFile(util.FlagCpuProf)
pprof.StartCPUProfile(f)
defer f.Close()
defer pprof.StopCPUProfile()
}
// Read all CATH domains, the best-of-all matrix, and the matrix for
// each aligner.
domains := readDomains(util.Arg(0))
boa := readMatrix(domains, util.Arg(1))
aligners := make([]aligner, 0)
flibs := make([]flib, 0)
for i := 2; i < util.NArg(); i += 2 {
fpath := util.Arg(i)
if path.Ext(fpath) == ".bowdb" {
db := util.OpenBowDB(fpath)
records, err := db.ReadAll()
util.Assert(err)
bowed := make([]bow.Bowed, domains.in.Len())
for _, b := range records {
if !domains.in.Exists(b.Id) {
util.Fatalf("Found ID in bowdb that isn't in the list "+
"of CATH domains provided: %s", b.Id)
}
bowed[domains.in.Atom(b.Id)] = b
}
flibs = append(flibs, flib{db, bowed, util.Arg(i + 1)})
} else {
aligners = append(aligners, aligner{
readMatrix(domains, fpath),
util.Arg(i + 1),
})
}
}
// Now remove CATH domains that don't have a corresponding structure file.
// We don't do this initially since the matrix files are indexed with
// respect to all CATH domains (includings ones without structure).
// This is an artifact of the fact that the matrices were generated with
// a very old version of CATH.
domains.removeOldDomains()
if a := matrixAuc(domains, boa, boa, flagThreshold); a != 1.0 {
util.Fatalf("Something is wrong. The AUC of the best-of-all matrix "+
"with respect to itself is %f, but it should be 1.0.", a)
}
if len(aligners) > 0 {
fmt.Println("Computing AUC for aligners...")
writeAuc := func(aligner aligner) struct{} {
w := util.CreateFile(aligner.outpath)
a := matrixAuc(domains, boa, aligner.matrix, flagThreshold)
fmt.Fprintf(w, "%f\n", a)
return struct{}{}
}
fun.ParMap(writeAuc, aligners)
}
if len(flibs) > 0 {
fmt.Println("Computing AUC for bowdbs...")
writeAuc := func(flib flib) struct{} {
w := util.CreateFile(flib.outpath)
a := flibAuc(domains, boa, flib, flagThreshold)
fmt.Fprintf(w, "%f\n", a)
return struct{}{}
}
fun.ParMap(writeAuc, flibs)
}
}
func mkSeqHMM(c *command) {
c.assertLeastNArg(3)
structLib := util.StructureLibrary(c.flags.Arg(0))
outPath := c.flags.Arg(1)
entries := c.flags.Args()[2:]
util.AssertOverwritable(outPath, flagOverwrite)
saveto := util.CreateFile(outPath)
// Stores intermediate files produced by hhmake.
tempDir, err := ioutil.TempDir("", "mk-seqlib-hmm")
util.Assert(err, "Could not create temporary directory.")
defer os.RemoveAll(tempDir)
// Initialize a MSA for each structural fragment.
var msas []seq.MSA
var msaChans []chan seq.Sequence
for i := 0; i < structLib.Size(); i++ {
msa := seq.NewMSA()
msa.SetLen(structLib.FragmentSize())
msas = append(msas, msa)
msaChans = append(msaChans, make(chan seq.Sequence))
}
// Now spin up a goroutine for each fragment that is responsible for
// adding a sequence slice to itself.
for i := 0; i < structLib.Size(); i++ {
addToMSA(msaChans[i], &msas[i])
}
// Create a channel that sends the PDB entries given.
entryChan := make(chan string)
go func() {
for _, fp := range entries {
entryChan <- fp
}
close(entryChan)
}()
progress := util.NewProgress(len(entries))
for i := 0; i < flagCpu; i++ {
wgPDBChains.Add(1)
go func() {
for entryPath := range entryChan {
_, chains, err := util.PDBOpen(entryPath)
progress.JobDone(err)
if err != nil {
continue
}
for _, chain := range chains {
structureToSequence(structLib, chain, nil, msaChans)
}
}
wgPDBChains.Done()
}()
}
wgPDBChains.Wait()
progress.Close()
// We've finishing reading all the PDB inputs. Now close the channels
// and let the sequence fragments finish.
for i := 0; i < structLib.Size(); i++ {
close(msaChans[i])
}
wgSeqFragments.Wait()
util.Verbosef("Building profile HMMs from MSAs...")
// Finally, add the sequence fragments to a new sequence fragment
// library and save.
hmms := make([]*seq.HMM, structLib.Size())
hhmake := func(i int) struct{} {
fname := path.Join(tempDir, fmt.Sprintf("%d.fasta", i))
f := util.CreateFile(fname)
util.Assert(msa.WriteFasta(f, msas[i]))
hhm, err := hhsuite.HHMakePseudo.Run(fname)
util.Assert(err)
hmms[i] = hhm.HMM
return struct{}{} // my unifier sucks, i guess
}
fun.ParMap(hhmake, fun.Range(0, structLib.Size()))
lib, err := fragbag.NewSequenceHMM(structLib.Name(), hmms)
util.Assert(err)
util.Assert(fragbag.Save(saveto, lib))
}