func main() {
giMapper, err := giTaxid.Load(dictfile, true)
if err != nil {
log.Fatalf("Problem reading dict file: %s\n", err)
}
taxid, err := giMapper.GiTaxid(gi)
if err != nil {
log.Fatalf("Problem retrieving taxid from dict: %s\n", err)
}
fmt.Printf("%d\n", taxid)
}
// New creates a new NCBI taxonomy representation from the options given in opts
// returns the newly created taxonomy or any error it may encounter in the process
func New(nodesfn, namesfn, dictfn string, savemem bool) (*Taxonomy, error) {
// T : taxtree => tax
t := &Taxonomy{}
fmt.Fprintf(os.Stderr, "Creating new taxonomy tree ... ")
s1 := time.Now()
maxNodes, ewcl := wcl.FromFile(nodesfn)
if ewcl != nil {
return nil, ewcl
}
nodesf, eopen := os.OpenFile(nodesfn, os.O_RDONLY, 0644)
if eopen != nil {
return nil, eopen
}
nodesbuf := bufio.NewReader(io.Reader(nodesf))
tax, dict, ee := newTaxonomy(nodesbuf, maxNodes)
if ee != nil {
return nil, ee
}
s2 := time.Now()
dur := s2.Sub(s1)
fmt.Fprintf(os.Stderr, "Done (%.3f sec)\n", dur.Seconds())
// T.Name(s)
fmt.Fprintf(os.Stderr, "Filling names in taxonomy tree ... ")
s1 = time.Now()
err := tax.loadNames(namesfn, dict)
if err != nil {
return nil, err
}
s2 = time.Now()
dur = s2.Sub(s1)
fmt.Fprintf(os.Stderr, "Done (%.3f sec)\n", dur.Seconds())
// E, L, H
fmt.Fprintf(os.Stderr, "Creating indexes ... ")
s1 = time.Now()
E := make([]int, 0, maxNodes*2)
L := make([]int, 0, maxNodes*2)
H := make([]int, maxNodes)
tax.elh(1, 0, &E, &L, &H)
s2 = time.Now()
dur = s2.Sub(s1)
fmt.Fprintf(os.Stderr, "Done (%.3f sec)\n", dur.Seconds())
// M
fmt.Fprintf(os.Stderr, "Preprocessing RMQ ... ")
s1 = time.Now()
M := makeMatrix(maxNodes)
rmqPrep(&M, L[:len(L)-1], maxNodes)
s2 = time.Now()
dur = s2.Sub(s1)
fmt.Fprintf(os.Stderr, "Done (%.3f sec)\n", dur.Seconds())
fmt.Fprintf(os.Stderr, "Combining data ... ")
s1 = time.Now()
t.T = tax
t.D = dict
// t.E = make([]int, len(E))
// copy(t.E, E)
t.E = E
// t.L = make([]int, len(L))
// copy(t.L, L)
t.L = L
// t.H = make([]int, len(H))
// copy(t.H, H)
t.H = H
// t.M = make([][]int, len(M))
// for i := 0; i < len(M); i++ {
// t.M[i] = make([]int, len(M[0]))
// }
// copy(t.M, M)
t.M = M
s2 = time.Now()
dur = s2.Sub(s1)
fmt.Fprintf(os.Stderr, "Done (%.3f sec)\n", dur.Seconds())
t.G, err = giTaxid.Load(dictfn, savemem)
if err != nil {
return nil, err
}
return t, nil
}
