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Adds CSV as an input format

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Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
This commit is contained in:
Eric Coissac
2024-07-03 21:04:27 +02:00
parent 5d9ac261ff
commit bd855c4965
6 changed files with 249 additions and 56 deletions
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109
pkg/obitools/obicleandb/obicleandb.go
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@@ -35,68 +35,73 @@ func diagCoord(x, y, n int) int {
}
func SequenceTrustSlice(sequences obiseq.BioSequenceSlice) (obiseq.BioSequenceSlice, error) {
n := len(sequences)
score := make([]float64, n*(n-1)/2)
matrix := make([]uint64, sequences[0].Len()*sequences[0].Len())
for i, sa := range sequences {
for j, sb := range sequences[i+1:] {
lca, lali := obialign.FastLCSScore(sa, sb, -1, &matrix)
score[diagCoord(i, i+1+j, n)] = float64(lca) / float64(lali)
}
}
if n > 1 {
score := make([]float64, n*(n-1)/2)
matrix := make([]uint64, sequences[0].Len()*sequences[0].Len())
for i, sa := range sequences {
ss := make([]float64, 0, n-1)
for j, _ := range sequences {
if i == j {
continue
for i, sa := range sequences {
for j, sb := range sequences[i+1:] {
lca, lali := obialign.FastLCSScore(sa, sb, -1, &matrix)
score[diagCoord(i, i+1+j, n)] = float64(lca) / float64(lali)
}
}
for i, sa := range sequences {
ss := make([]float64, 0, n-1)
for j, _ := range sequences {
if i == j {
continue
}
s := score[diagCoord(i, j, n)]
if s == 0.0 {
log.Panicf("score[%d, %d] == 0.0", i, j)
}
ss = append(ss, score[diagCoord(i, j, n)])
s := score[diagCoord(i, j, n)]
if s == 0.0 {
log.Panicf("score[%d, %d] == 0.0", i, j)
}
ss = append(ss, score[diagCoord(i, j, n)])
sa.SetAttribute("obicleandb_dist", ss)
}
sa.SetAttribute("obicleandb_dist", ss)
}
scoremed := obistats.Median(score)
scorethr := 1 - 2*(1-scoremed)
mednorm := (scoremed - scorethr) / 2.0
scoremed := obistats.Median(score)
scorethr := 1 - 3*(1-scoremed)
mednorm := (scoremed - scorethr) / 2.0
for i, s := range score {
switch {
case s < scorethr:
score[i] = -1.0
case s < scoremed:
score[i] = (s-scorethr)/mednorm - 1.0
default:
score[i] = 1.0
}
}
// Tylos
for i, sa := range sequences {
ngroup := float64(sa.Count())
ss := make([]float64, 0, n-1)
sc := sa.Count()
for j, sb := range sequences {
if i == j {
continue
for i, s := range score {
switch {
case s < scorethr:
score[i] = -1.0
case s < scoremed:
score[i] = (s-scorethr)/mednorm - 1.0
default:
score[i] = 1.0
}
ss = append(ss, score[diagCoord(i, j, n)])
sc += sb.Count()
nt, _ := sb.GetFloatAttribute("obicleandb_trusted_on")
ngroup += score[diagCoord(i, j, n)] * nt
}
ngroup = max(0, ngroup)
sa.SetAttribute("obicleandb_trusted", 1.0-1.0/float64(ngroup+1))
sa.SetAttribute("obicleandb_trusted_on", ngroup)
sa.SetAttribute("obicleandb_median", scoremed)
sa.SetAttribute("obicleandb_ss", ss)
// Tylos
for i, sa := range sequences {
ngroup := float64(sa.Count())
ss := make(map[string]float64, n-1)
sc := sa.Count()
for j, sb := range sequences {
if i == j {
continue
}
ss[sb.Id()] = score[diagCoord(i, j, n)]
sc += sb.Count()
nt, _ := sb.GetFloatAttribute("obicleandb_trusted_on")
ngroup += score[diagCoord(i, j, n)] * nt
}
ngroup = max(0, ngroup)
sa.SetAttribute("obicleandb_trusted", 1.0-1.0/float64(ngroup+1))
sa.SetAttribute("obicleandb_trusted_on", ngroup)
sa.SetAttribute("obicleandb_median", scoremed)
sa.SetAttribute("obicleandb_scores", ss)
}
} else {
sequences[0].SetAttribute("obicleandb_median", 1.0)
}
return sequences, nil