obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

few bug in the graph algorithm

Browse Source 
Former-commit-id: b61bdd9f671e2f5e90d32c1beac1ed84efa5e05c
This commit is contained in:
Eric Coissac
2023-03-27 22:43:45 +07:00
parent 245230ae12
commit e8a8f746d3
2 changed files with 91 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files

88
pkg/obikmer/debruijn.go
View File

@ -3,6 +3,7 @@ package obikmer
import (
"bytes"
"fmt"
"log"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@ -166,9 +167,10 @@ func (g *DeBruijnGraph) MaxNext(index uint64) (uint64, bool) {
max := uint(0)
rep := uint64(0)
for _, idx := range ns {
w, _ := g.graph[idx]
w := g.graph[idx]
if w > max {
rep = idx
max = w
}
}
@ -191,33 +193,34 @@ func (g *DeBruijnGraph) MaxPath() []uint64 {
}
func (g *DeBruijnGraph) LongestPath() []uint64 {
var path []uint64
var path []uint64
wmax := uint(0)
ok := true
starts:= g.Heads()
for _,idx := range starts {
starts := g.Heads()
log.Println(starts)
for _, idx := range starts {
lp := make([]uint64, 0, 1000)
ok = true
w := uint(0)
for ok {
nw:= g.graph[idx]
w+=nw
nw := g.graph[idx]
w += nw
lp = append(lp, idx)
idx, ok = g.MaxNext(idx)
}
log.Printf("max : %d current %d", wmax, w)
if w > wmax {
path=lp
wmax=w
path = lp
wmax = w
}
}
return path
}
func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence,error) {
func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence, error) {
path := g.LongestPath()
s := g.DecodePath(path)
@ -228,13 +231,12 @@ func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence,error)
"",
)
return &seq,nil
return &seq, nil
}
return nil,fmt.Errorf("cannot identify optimum path")
return nil, fmt.Errorf("cannot identify optimum path")
}
func (g *DeBruijnGraph) Heads() []uint64 {
rep := make([]uint64, 0, 10)
@ -281,13 +283,13 @@ func (g *DeBruijnGraph) DecodePath(path []uint64) string {
for _, idx := range path[1:] {
buf.WriteByte(decode[idx&3])
}
}
}
return buf.String()
}
func (g *DeBruijnGraph) BestConsensus(id string) (*obiseq.BioSequence,error) {
func (g *DeBruijnGraph) BestConsensus(id string) (*obiseq.BioSequence, error) {
path := g.MaxPath()
s := g.DecodePath(path)
@ -298,10 +300,10 @@ func (g *DeBruijnGraph) BestConsensus(id string) (*obiseq.BioSequence,error) {
"",
)
return &seq,nil
return &seq, nil
}
return nil,fmt.Errorf("cannot identify optimum path")
return nil, fmt.Errorf("cannot identify optimum path")
}
func (g *DeBruijnGraph) Weight(index uint64) int {
@ -374,3 +376,51 @@ func (graph *DeBruijnGraph) Push(sequence *obiseq.BioSequence) {
}
}
func (graph *DeBruijnGraph) GML() string {
buffer := bytes.NewBuffer(make([]byte, 0, 1000))
buffer.WriteString(
`graph [
comment "De Bruijn graph"
directed 1
`)
for idx := range graph.graph {
node := graph.DecodeNode(idx)
buffer.WriteString(
fmt.Sprintf("node [ id \"%s\" ]\n", node),
)
n := graph.Nexts(uint64(idx))
if len(n) == 0 {
idx <<= 2
idx &= graph.kmermask
node := graph.DecodeNode(idx)
buffer.WriteString(
fmt.Sprintf("node [ id \"%s\" \n label \"%s\" ]\n", node, node),
)
}
}
for idx, weight := range graph.graph {
src := graph.DecodeNode(idx)
label := decode[idx&3]
idx <<= 2
idx &= graph.kmermask
dst := graph.DecodeNode(idx)
buffer.WriteString(
fmt.Sprintf(`edge [ source "%s"
target "%s"
color "#00FF00"
label "%c[%d]"
]
`, src, dst, label, weight),
)
}
buffer.WriteString("]\n")
return buffer.String()
}