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finalise obilowmask

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This commit is contained in:
Eric Coissac
2025-11-11 21:41:09 +01:00
parent cef29005a5
commit ccc827afd3
3 changed files with 32 additions and 5 deletions
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2
pkg/obioptions/version.go
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@@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be
// commited
var _Commit = "07cdd6f"
var _Commit = "d35a32b"
var _Version = "Release 4.4.0"
// Version returns the version of the obitools package.

13
pkg/obitools/obilowmask/entropy.qmd
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@@ -313,7 +313,20 @@ cat(" ecn(k,4) =", ecn(okmer(k,4),4), "\n")
```
```{r}
sequence <- "ttcatcactcagcaatcctgaatgatGAGAGCTTTTTTTTTTTATATATATATATATGTATATGTATGAAATACACTtatgctccgtttgtttcgccgtaa"
re <- rev(c(0.8108602271901116,0.8108602271901116,0.8041354757148719,0.8041354757148719,0.8041354757148719,0.8041354757148719,0.8041354757148719,0.8041354757148719,0.7800272339058549,0.7800272339058549,0.7751610144606091,0.7751610144606091,0.7751610144606091,0.764858185548322,0.7325526601302021,0.7137620699527615,0.6789199521982864,0.6584536373623372,0.634002687184193,0.6075290415873623,0.5785545803330997,0.5785545803330997,0.5503220289212184,0.5315314387437778,0.4966893209893028,0.46077361820145696,0.42388221293245526,0.4009547969713408,0.3561142883497758,0.3561142883497758,0.3561142883497758,0.3561142883497758,0.3561142883497758,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.3418776106000334,0.35141814451677883,0.35141814451677883,0.35141814451677883,0.35141814451677883,0.35141814451677883,0.390029016052137,0.42781461756157363,0.45192285937059073,0.47238917420654,0.47238917420654,0.47238917420654,0.5092805794755417,0.5451962822633876,0.5800384000178626,0.602395141014297,0.6046146614886381,0.6046146614886381,0.6119084258128231,0.6119084258128231,0.6214217106113492,0.6424704346756562,0.6482381543085467,0.6635191587399633,0.6635191587399633,0.6635191587399633,0.6828444721058894,0.6950205907027562,0.696103322070051,0.696103322070051,0.696103322070051,0.696103322070051,0.696103322070051,0.696103322070051,0.696103322070051,0.696103322070051,0.696103322070051,0.7208976112999935))
di <- c(0.7208976112999935,0.6961033220700509,0.6961033220700509,0.6961033220700509,0.6961033220700509,0.6961033220700509,0.6961033220700509,0.6961033220700509,0.6961033220700509,0.6961033220700509,0.6950205907027562,0.6828444721058894,0.6635191587399633,0.6635191587399633,0.6635191587399633,0.6482381543085467,0.6424704346756562,0.6214217106113492,0.6119084258128231,0.6119084258128231,0.6046146614886382,0.6046146614886382,0.6023951410142971,0.5800384000178627,0.5451962822633876,0.5092805794755418,0.47238917420654003,0.47238917420654003,0.47238917420654003,0.4519228593705908,0.4278146175615737,0.39002901605213713,0.35141814451677894,0.35141814451677894,0.35141814451677894,0.35141814451677894,0.35141814451677883,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3418776106000333,0.3561142883497762,0.3561142883497762,0.3561142883497762,0.3561142883497762,0.3561142883497762,0.40095479697134073,0.42388221293245526,0.46077361820145696,0.4966893209893028,0.5315314387437778,0.5503220289212184,0.5785545803330997,0.5785545803330997,0.6075290415873625,0.6340026871841933,0.6584536373623374,0.6789199521982866,0.7137620699527616,0.7325526601302023,0.7648581855483221,0.7751610144606093,0.7751610144606093,0.7751610144606093,0.7800272339058549,0.7800272339058549,0.8041354757148721,0.8041354757148721,0.8041354757148721,0.8041354757148721,0.8041354757148721,0.8041354757148721,0.8108602271901116,0.8108602271901116)
ebidir <- tibble(direct=di,reverse=re) %>%
mutate(position = 1:length(re),
nucleotide = str_sub(sequence,position,position))
ebidir %>%
ggplot(aes(x=position,y=direct)) +
geom_line() +
scale_x_continuous(breaks = ebidir$position, labels = ebidir$nucleotide) +
ylim(0,1)+
geom_hline(yintercept=0.5, col = "red", linetype = "dashed")
```

22
pkg/obitools/obilowmask/obilowmask.go
View File

@@ -141,6 +141,8 @@ func LowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
minimier.Add(v)
}
// log.Warnf("taille du minimier %d @ %d", minimier.Len(), i)
// Retrieve and store current minimum
var ok bool
if data[i], ok = minimier.Min(); !ok {
@@ -302,9 +304,11 @@ func LowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
// Store entropy for position corresponding to start of k-mer
if s >= nwords && maskPositions[i-nwords+1] >= 0 {
if entropy == 0 {
log.Errorf("Zero entropy @ positon %d", i-nwords+1)
if entropy < 0 {
entropy = 0
}
entropy = math.Round(entropy*10000) / 10000
entropies[i-nwords+1] = entropy
}
}
@@ -327,10 +331,11 @@ func LowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
sequenceBytes := seqCopy.Sequence()
// Mask identified positions
for i := 0; i < len(sequenceBytes); i++ {
for i := range sequenceBytes {
if maskPositions[i] {
// Operation &^ 32 converts to UPPERCASE (clears bit 5)
sequenceBytes[i] = sequenceBytes[i] &^ 32
// sequenceBytes[i] = sequenceBytes[i] &^ 32
sequenceBytes[i] = mask
}
}
@@ -343,6 +348,15 @@ func LowMaskWorker(kmer_size int, level_max int, threshold float64, mode Masking
// Calculates entropies at all scales and masks positions
// whose minimum entropy is below the threshold.
masking := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
if sequence.Len() < kmer_size {
sequence.SetAttribute("obilowmask_error", "Sequence too short")
remove := make([]bool, sequence.Len())
for i := range remove {
remove[i] = true
}
return applyMaskMode(sequence, remove, maskChar)
}
bseq := sequence.Sequence()
// Identify ambiguities