func main() {
pdbFiles := util.RecursiveFiles(util.FlagPdbDir)
files := make([]string, 0, flagNum)
for i := 0; i < flagNum; i++ {
var index int = -1
for index == -1 || !util.IsPDB(pdbFiles[index]) {
// not guaranteed to terminate O_O
index = rand.Intn(len(pdbFiles))
}
files = append(files, pdbFiles[index])
pdbFiles = append(pdbFiles[:index], pdbFiles[index+1:]...)
}
for _, f := range files {
if flagPaths {
fmt.Println(f)
} else {
e := util.PDBRead(f)
fmt.Printf("%s%c\n", strings.ToLower(e.IdCode), e.Chains[0].Ident)
}
}
}
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
}