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Small adjustment

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This commit is contained in:
Eric Coissac
2022-10-27 11:18:44 +02:00
parent 8aa323dad5
commit f3ddac0f50
10 changed files with 218 additions and 155 deletions
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29
pkg/obitools/obirefidx/obirefidx.go
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@@ -18,7 +18,6 @@ import (
func IndexSequence(seqidx int,
references obiseq.BioSequenceSlice,
refcounts []*obikmer.Table4mer,
taxo *obitax.Taxonomy) map[int]string {
sequence := references[seqidx]
@@ -28,23 +27,7 @@ func IndexSequence(seqidx int,
score := make([]int, len(references))
for i, ref := range references {
// maxe := goutils.MaxInt(sequence.Length(), ref.Length())
// mine := 0
// if refcounts != nil {
// mine, maxe = obikmer.Error4MerBounds(refcounts[seqidx], refcounts[i])
// }
lcs, alilength := obialign.FullLCSScore(sequence, ref, matrix)
// if lcs < 0 {
// log.Print("Max error wrongly estimated", mine, maxe)
// log.Println(string(sequence.Sequence()))
// log.Fatalln(string(ref.Sequence()))
// maxe := goutils.MaxInt(sequence.Length(), ref.Length())
// lcs, alilength = obialign.LCSScore(sequence, ref, matrix)
// }
score[i] = alilength - lcs
}
@@ -58,7 +41,7 @@ func IndexSequence(seqidx int,
log.Panicln(err)
}
ecotag_index := make(map[int]string)
obitag_index := make(map[int]string)
for _, idx := range o {
new_taxid, err := taxo.Taxon(references[idx].Taxid())
@@ -76,7 +59,7 @@ func IndexSequence(seqidx int,
if current_taxid.Taxid() != new_taxid.Taxid() {
if new_score > current_score {
ecotag_index[score[current_idx]] = fmt.Sprintf(
obitag_index[score[current_idx]] = fmt.Sprintf(
"%d@%s@%s",
current_taxid.Taxid(),
current_taxid.ScientificName(),
@@ -89,15 +72,15 @@ func IndexSequence(seqidx int,
}
}
ecotag_index[score[current_idx]] = fmt.Sprintf(
obitag_index[score[current_idx]] = fmt.Sprintf(
"%d@%s@%s",
current_taxid.Taxid(),
current_taxid.ScientificName(),
current_taxid.Rank())
sequence.SetAttribute("ecotag_ref_index", ecotag_index)
sequence.SetAttribute("obitag_ref_index", obitag_index)
return ecotag_index
return obitag_index
}
func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
@@ -142,7 +125,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBa
for l := range limits {
sl := obiseq.MakeBioSequenceSlice()
for i := l[0]; i < l[1]; i++ {
IndexSequence(i, references, refcounts, taxo)
IndexSequence(i, references, taxo)
sl = append(sl, references[i])
}
indexed.Push(obiiter.MakeBioSequenceBatch(l[0]/10, sl))