func main() {
if len(util.FlagCpuProf) > 0 {
f := util.CreateFile(util.FlagCpuProf)
pprof.StartCPUProfile(f)
defer f.Close()
defer pprof.StopCPUProfile()
}
if len(flagGobIt) > 0 {
astralDir := util.Arg(0)
dists := readAlignmentDists(astralDir)
enc := gob.NewEncoder(util.CreateFile(flagGobIt))
util.Assert(enc.Encode(dists), "Could not GOB encode distances")
return
}
var dists *intern.Table
if util.IsDir(util.Arg(0)) {
dists = readAlignmentDists(util.Arg(0))
} else {
dec := gob.NewDecoder(util.OpenFile(util.Arg(0)))
util.Assert(dec.Decode(&dists), "Could not GOB decode distances")
}
treeFile := util.Arg(1)
outPath := util.Arg(2)
treeReader := newick.NewReader(util.OpenFile(treeFile))
tree, err := treeReader.ReadTree()
util.Assert(err, "Could not read newick tree")
csvw := csv.NewWriter(util.CreateFile(outPath))
clusters := treeClusters(flagThreshold, dists, tree)
util.Assert(csvw.WriteAll(clusters))
}
func main() {
var f io.Reader
var err error
f = util.OpenFile(flag.Arg(0))
if strings.HasSuffix(flag.Arg(0), ".gz") {
f, err = gzip.NewReader(f)
util.Assert(err)
}
cifEntry, err := pdbx.Read(f)
util.Assert(err, "Could not read PDBx/mmCIF file")
fasEntries := make([]seq.Sequence, 0, 5)
for _, ent := range cifEntry.Entities {
for _, chain := range ent.Chains {
if !isChainUsable(chain) || len(ent.Seq) == 0 {
continue
}
fasEntry := seq.Sequence{
Name: chainHeader(chain),
Residues: ent.Seq,
}
fasEntries = append(fasEntries, fasEntry)
}
}
if len(fasEntries) == 0 {
util.Fatalf("Could not find any chains with amino acids.")
}
var fasOut io.Writer
if flag.NArg() == 1 {
fasOut = os.Stdout
} else {
if len(flagSplit) > 0 {
util.Fatalf("The '--split' option is incompatible with a single " +
"output file.")
}
fasOut = util.CreateFile(util.Arg(1))
}
if len(flagSplit) == 0 {
util.Assert(fasta.NewWriter(fasOut).WriteAll(fasEntries),
"Could not write FASTA file '%s'", fasOut)
} else {
for _, entry := range fasEntries {
fp := path.Join(flagSplit, fmt.Sprintf("%s.fasta", entry.Name))
out := util.CreateFile(fp)
w := fasta.NewWriter(out)
util.Assert(w.Write(entry), "Could not write to '%s'", fp)
util.Assert(w.Flush(), "Could not write to '%s'", fp)
}
}
}
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 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 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)
}
func main() {
outDir := util.Arg(0)
fasInps := util.Args()[1:]
util.Assert(os.MkdirAll(outDir, 0777))
fastaChan := make(chan string)
wg := new(sync.WaitGroup)
for i := 0; i < max(1, runtime.GOMAXPROCS(0)); i++ {
go func() {
wg.Add(1)
for fasta := range fastaChan {
util.Verbosef("Computing map for '%s'...", fasta)
fmap := util.GetFmap(fasta)
outF := path.Join(outDir, fmt.Sprintf("%s.fmap", fmap.Name))
util.FmapWrite(util.CreateFile(outF), fmap)
}
wg.Done()
}()
}
for _, fasta := range fasInps {
fastaChan <- fasta
}
close(fastaChan)
wg.Wait()
}
func search(c *command) {
c.assertLeastNArg(2)
// Some search options don't translate directly to command line parameters
// specified by the flag package.
if flagSearchDesc {
flagSearchOpts.Order = bowdb.OrderDesc
}
switch flagSearchSort {
case "cosine":
flagSearchOpts.SortBy = bowdb.SortByCosine
case "euclid":
flagSearchOpts.SortBy = bowdb.SortByEuclid
default:
util.Fatalf("Unknown sort field '%s'.", flagSearchSort)
}
db := util.OpenBowDB(c.flags.Arg(0))
bowPaths := c.flags.Args()[1:]
_, err := db.ReadAll()
util.Assert(err, "Could not read BOW database entries")
// always hide the progress bar here.
bows := util.ProcessBowers(bowPaths, db.Lib, false, flagCpu, true)
out, outDone := outputter()
// launch goroutines to search queries in parallel
wgSearch := new(sync.WaitGroup)
for i := 0; i < flagCpu; i++ {
wgSearch.Add(1)
go func() {
defer wgSearch.Done()
for b := range bows {
sr := db.Search(flagSearchOpts, b)
out <- searchResult{b, sr}
}
}()
}
wgSearch.Wait()
close(out)
<-outDone
util.Assert(db.Close())
}
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 main() {
a3mPath := util.Arg(0)
fa3m := util.OpenFile(a3mPath)
freader := fasta.NewReader(fa3m)
freader.TrustSequences = true
seqs, err := freader.ReadAll()
util.Assert(err, "Could not read fasta format '%s'", a3mPath)
util.Assert(fa3m.Close())
w := util.CreateFile(a3mPath)
fwriter := fasta.NewWriter(w)
fwriter.Columns = 0
for _, seq := range seqs {
if len(seq.Residues) > 0 {
util.Assert(fwriter.Write(seq))
}
}
util.Assert(fwriter.Flush())
util.Assert(w.Close())
}
func main() {
rfasta := util.OpenFasta(util.Arg(0))
dir := util.Arg(1)
util.Assert(os.MkdirAll(dir, 0777))
fr := fasta.NewReader(rfasta)
for {
s, err := fr.Read()
if err != nil {
if err == io.EOF {
break
}
util.Assert(err)
}
s.Name = strings.Fields(s.Name)[0]
fw := util.CreateFile(path.Join(dir, s.Name+".fasta"))
w := fasta.NewWriter(fw)
util.Assert(w.Write(s))
util.Assert(w.Flush())
util.Assert(fw.Close())
}
}
func main() {
pdbs := util.OpenFile(flag.Arg(0))
defer pdbs.Close()
entries, err := slct.NewReader(pdbs).ReadAll()
util.Assert(err)
for _, entry := range entries {
if flagPaths {
fmt.Println(util.PDBPath(entry.ChainID))
} else {
fmt.Println(entry.ChainID)
}
}
}
func main() {
pdbf1, chain1, s1, e1 := util.Arg(0), util.Arg(1), util.Arg(2), util.Arg(3)
pdbf2, chain2, s2, e2 := util.Arg(4), util.Arg(5), util.Arg(6), util.Arg(7)
entry1 := util.PDBRead(pdbf1)
entry2 := util.PDBRead(pdbf2)
s1n, e1n := util.ParseInt(s1), util.ParseInt(e1)
s2n, e2n := util.ParseInt(s2), util.ParseInt(e2)
r, err := pdb.RMSD(
entry1, chain1[0], s1n, e1n, entry2, chain2[0], s2n, e2n)
util.Assert(err)
fmt.Println(r)
}
func mkWeighted(c *command) {
c.assertLeastNArg(4)
train := util.Library(c.flags.Arg(0))
in := util.Library(c.flags.Arg(1))
outPath := c.flags.Arg(2)
bowPaths := c.flags.Args()[3:]
util.AssertOverwritable(outPath, flagOverwrite)
// The inverse-document-frequencies of each fragment in the "in" fragment
// library.
numFrags := in.Size()
idfs := make([]float32, numFrags)
for i := range idfs {
idfs[i] = 1 // pseudocount
}
// Compute the BOWs for each bower against the training fragment lib.
bows := util.ProcessBowers(bowPaths, train, false, flagCpu, util.FlagQuiet)
// Now tally the number of bowers that each fragment occurred in.
totalBows := float32(1) // for pseudocount correction
for bow := range bows {
totalBows += 1
for fragi := 0; fragi < numFrags; fragi++ {
if bow.Bow.Freqs[fragi] > 0 {
idfs[fragi]++
}
}
}
// Compute the IDF using the frequencies against all the BOWs.
for i := range idfs {
idfs[i] = float32(math.Log(float64(totalBows / idfs[i])))
}
// Finally, wrap the given library as a weighted library and save it.
wlib, err := fragbag.NewWeightedTfIdf(in, idfs)
util.Assert(err)
fragbag.Save(util.CreateFile(outPath), wlib)
}
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 main() {
rfasta := util.OpenFasta(util.Arg(0))
count, err := fasta.QuickSequenceCount(rfasta)
util.Assert(err)
fmt.Println(count)
}
func readFloat(s string) float64 {
num, err := strconv.ParseFloat(s, 64)
util.Assert(err, "Expected float, but got '%s'.", s)
return num
}
func main() {
pdbEntry := util.PDBRead(flag.Arg(0))
fasEntries := make([]seq.Sequence, 0, 5)
if !flagSeparateChains {
var fasEntry seq.Sequence
if len(pdbEntry.Chains) == 1 {
fasEntry.Name = chainHeader(pdbEntry.OneChain())
} else {
fasEntry.Name = fmt.Sprintf("%s", strings.ToLower(pdbEntry.IdCode))
}
seq := make([]seq.Residue, 0, 100)
for _, chain := range pdbEntry.Chains {
if isChainUsable(chain) {
seq = append(seq, chain.Sequence...)
}
}
fasEntry.Residues = seq
if len(fasEntry.Residues) == 0 {
util.Fatalf("Could not find any amino acids.")
}
fasEntries = append(fasEntries, fasEntry)
} else {
for _, chain := range pdbEntry.Chains {
if !isChainUsable(chain) {
continue
}
fasEntry := seq.Sequence{
Name: chainHeader(chain),
Residues: chain.Sequence,
}
fasEntries = append(fasEntries, fasEntry)
}
}
if len(fasEntries) == 0 {
util.Fatalf("Could not find any chains with amino acids.")
}
var fasOut io.Writer
if flag.NArg() == 1 {
fasOut = os.Stdout
} else {
if len(flagSplit) > 0 {
util.Fatalf("The '--split' option is incompatible with a single " +
"output file.")
}
fasOut = util.CreateFile(util.Arg(1))
}
if len(flagSplit) == 0 {
util.Assert(fasta.NewWriter(fasOut).WriteAll(fasEntries),
"Could not write FASTA file '%s'", fasOut)
} else {
for _, entry := range fasEntries {
fp := path.Join(flagSplit, fmt.Sprintf("%s.fasta", entry.Name))
out := util.CreateFile(fp)
w := fasta.NewWriter(out)
util.Assert(w.Write(entry), "Could not write to '%s'", fp)
util.Assert(w.Flush(), "Could not write to '%s'", fp)
}
}
}
func readAlignmentDists(dir string) *intern.Table {
dists := intern.NewTable(11000)
threads := util.FlagCpu
addDists := make(chan []pair)
alignFile := make(chan string)
done := make(chan struct{})
go func() {
for fileDists := range addDists {
for _, pair := range fileDists {
a1, a2 := dists.Atom(pair.key[0]), dists.Atom(pair.key[1])
dists.Set(a1, a2, pair.dist)
}
}
done <- struct{}{}
}()
wg := new(sync.WaitGroup)
for i := 0; i < threads; i++ {
wg.Add(1)
go func() {
for fpath := range alignFile {
log.Printf("Reading %s (%s)", fpath, time.Now())
f := util.OpenFile(fpath)
defer f.Close()
csvr := csv.NewReader(f)
csvr.Comma = '\t'
csvr.TrimLeadingSpace = true
csvr.FieldsPerRecord = -1 // data is poorly formatted
records, err := csvr.ReadAll()
util.Assert(err, "[%s]", fpath)
fileDists := make([]pair, 0, 100000)
for _, record := range records {
if len(record) != 9 {
continue
}
p := recordToDist(record)
fileDists = append(fileDists, p)
}
addDists <- fileDists
}
wg.Done()
}()
}
for _, fpath := range util.RecursiveFiles(dir) {
if strings.HasPrefix(path.Base(fpath), ".") {
continue
}
alignFile <- fpath
}
close(alignFile)
wg.Wait()
close(addDists)
<-done
return dists
}
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))
}