Merge pull request #61 from metabarcoding/push-mvxssvnysyxn

Push mvxssvnysyxn

pkg/obioptions/version.go

@@ -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 = "27204d5"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.

pkg/obitools/obilowmask/entropy.qmd

@@ -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")
 ```

pkg/obitools/obilowmask/obilowmask.go

@@ -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

pkg/obitools/obimatrix/obimatrix.go

@@ -54,13 +54,13 @@ func NewMatrixData(naValue string, attributes ...string) *MatrixData {
 // It returns a pointer to the transposed MatrixData.
 func (matrix *MatrixData) TransposeMatrixData() *MatrixData {
 	m := MakeMatrixData(matrix.naValue, "id")
-	for k, v := range *&matrix.matrix {
+	for k, v := range matrix.matrix {
 		for kk, vv := range v {
 			if _, ok := m.matrix[kk]; !ok {
 				m.matrix[kk] = make(map[string]interface{})
 			}
 			m.matrix[kk][k] = vv
-			m.attributes[kk] = map[string]interface{}{"id": k}
+			m.attributes[kk] = map[string]interface{}{"id": kk}
 		}
 	}
 	return &m