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few bug in the graph algorithm

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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
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34
pkg/obitools/obiconsensus/obiconsensus.go
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@@ -41,7 +41,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice, quorum float64) (*obiseq.BioSe
spectrum := graph.LinkSpectrum()
cum := make(map[int]int)
spectrum[1]=0
spectrum[1] = 0
for i := 2; i < len(spectrum); i++ {
spectrum[i] += spectrum[i-1]
cum[spectrum[i]]++
@@ -63,26 +63,36 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice, quorum float64) (*obiseq.BioSe
break
}
}
threshold /= 2
graph.FilterMin(threshold)
log.Printf("Graph size : %d\n", graph.Len())
seq,err := graph.LongestConsensus(seqs[0].Source())
// file, err := os.Create(
// fmt.Sprintf("%s.gml", seqs[0].Source()))
// if err != nil {
// fmt.Println(err)
// } else {
// file.WriteString(graph.GML())
// file.Close()
// }
seq, err := graph.LongestConsensus(seqs[0].Source())
seq.SetCount(len(seqs))
seq.SetAttribute("seq_length",seq.Len())
seq.SetAttribute("kmer_size",kmersize)
seq.SetAttribute("kmer_min_occur",threshold)
seq.SetAttribute("kmer_max_occur",graph.MaxLink())
seq.SetAttribute("filtered_graph_size",graph.Len())
seq.SetAttribute("full_graph_size",total_kmer)
seq.SetAttribute("seq_length", seq.Len())
seq.SetAttribute("kmer_size", kmersize)
seq.SetAttribute("kmer_min_occur", threshold)
seq.SetAttribute("kmer_max_occur", graph.MaxLink())
seq.SetAttribute("filtered_graph_size", graph.Len())
seq.SetAttribute("full_graph_size", total_kmer)
return seq,err
return seq, err
}
func Consensus(iterator obiiter.IBioSequence, quorum float64) obiiter.IBioSequence {
newIter := obiiter.MakeIBioSequence()
size:=10
size := 10
newIter.Add(1)
@@ -97,7 +107,7 @@ func Consensus(iterator obiiter.IBioSequence, quorum float64) obiiter.IBioSequen
for iterator.Next() {
seqs := iterator.Get()
consensus,err := BuildConsensus(seqs.Slice(),quorum)
consensus, err := BuildConsensus(seqs.Slice(), quorum)
if err == nil {
buffer = append(buffer, consensus)