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 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() {
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 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
}
