func mkStructure(c *command) {
c.assertNArg(2)
brkFile := c.flags.Arg(0)
saveto := c.flags.Arg(1)
util.AssertOverwritable(saveto, flagOverwrite)
brkContents, err := ioutil.ReadAll(util.OpenFile(c.flags.Arg(0)))
util.Assert(err)
pdbFragments := bytes.Split(brkContents, []byte("TER"))
fragments := make([][]structure.Coords, 0)
for i, pdbFrag := range pdbFragments {
pdbFrag = bytes.TrimSpace(pdbFrag)
if len(pdbFrag) == 0 {
continue
}
fragments = append(fragments, coords(i, pdbFrag))
}
libName := stripExt(path.Base(brkFile))
lib, err := fragbag.NewStructureAtoms(libName, fragments)
util.Assert(err)
fragbag.Save(util.CreateFile(saveto), lib)
}
func mkPaired(c *command) {
c.assertNArg(2)
in := util.Library(c.flags.Arg(0))
outPath := c.flags.Arg(1)
util.AssertOverwritable(outPath, flagOverwrite)
if _, ok := in.(fragbag.WeightedLibrary); ok {
util.Fatalf("%s is a weighted library (not allowed)", in.Name())
}
name := fmt.Sprintf("paired-%s", in.Name())
if fragbag.IsStructure(in) {
var pairs [][]structure.Coords
lib := in.(fragbag.StructureLibrary)
nfrags := lib.Size()
for i := 0; i < nfrags; i++ {
for j := 0; j < nfrags; j++ {
if i == j {
continue
}
f1, f2 := lib.Atoms(i), lib.Atoms(j)
pairs = append(pairs, append(f1, f2...))
}
}
pairLib, err := fragbag.NewStructureAtoms(name, pairs)
util.Assert(err)
fragbag.Save(util.CreateFile(outPath), pairLib)
} else if strings.Contains(in.Tag(), "hmm") {
var pairs []*seq.HMM
lib := in.(fragbag.SequenceLibrary)
nfrags := lib.Size()
for i := 0; i < nfrags; i++ {
for j := 0; j < nfrags; j++ {
if i == j {
continue
}
f1, f2 := lib.Fragment(i).(*seq.HMM), lib.Fragment(j).(*seq.HMM)
pairs = append(pairs, seq.HMMCat(f1, f2))
}
}
pairLib, err := fragbag.NewSequenceHMM(name, pairs)
util.Assert(err)
fragbag.Save(util.CreateFile(outPath), pairLib)
} else if strings.Contains(in.Tag(), "profile") {
util.Fatalf("Sequence profiles not implemented.")
} else {
util.Fatalf("Unrecognized fragment library: %s", in.Tag())
}
}
func mkBowDb(c *command) {
c.assertLeastNArg(3)
dbPath := c.flags.Arg(0)
flib := util.Library(c.flags.Arg(1))
bowPaths := c.flags.Args()[2:]
util.AssertOverwritable(dbPath, flagOverwrite)
db, err := bowdb.Create(flib, dbPath)
util.Assert(err)
bows := util.ProcessBowers(bowPaths, flib, false, flagCpu, util.FlagQuiet)
for b := range bows {
db.Add(b)
}
util.Assert(db.Close())
}
func mkSeqProfile(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)
// Initialize a frequency and null profile for each structural fragment.
var freqProfiles []*seq.FrequencyProfile
var fpChans []chan seq.Sequence
for i := 0; i < structLib.Size(); i++ {
fp := seq.NewFrequencyProfile(structLib.FragmentSize())
freqProfiles = append(freqProfiles, fp)
fpChans = append(fpChans, make(chan seq.Sequence))
}
// Now spin up a goroutine for each fragment that is responsible for
// adding a sequence slice to itself.
nullChan, nullProfile := addToNull()
for i := 0; i < structLib.Size(); i++ {
addToProfile(fpChans[i], freqProfiles[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, nullChan, fpChans)
}
}
wgPDBChains.Done()
}()
}
wgPDBChains.Wait()
progress.Close()
// We've finishing reading all the PDB inputs. Now close the channels
// and let the sequence fragments finish.
close(nullChan)
for i := 0; i < structLib.Size(); i++ {
close(fpChans[i])
}
wgSeqFragments.Wait()
// Finally, add the sequence fragments to a new sequence fragment
// library and save.
profs := make([]*seq.Profile, structLib.Size())
for i := 0; i < structLib.Size(); i++ {
profs[i] = freqProfiles[i].Profile(nullProfile)
}
lib, err := fragbag.NewSequenceProfile(structLib.Name(), profs)
util.Assert(err)
util.Assert(fragbag.Save(saveto, lib))
}
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))
}
