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debug of obimultiplex

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Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
This commit is contained in:
Eric Coissac
2024-06-18 23:38:33 +02:00
parent 44533fb61e
commit a812fe8b72
9 changed files with 468 additions and 50 deletions
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15
pkg/obingslibrary/marker.go
View File

@ -27,6 +27,8 @@ type Marker struct {
Reverse_matching string
Forward_tag_delimiter byte
Reverse_tag_delimiter byte
Forward_tag_indels int
Reverse_tag_indels int
samples map[TagPair]*PCR
}
@ -335,6 +337,19 @@ func (marker *Marker) SetTagDelimiter(delim byte) {
marker.SetReverseTagDelimiter(delim)
}
func (marker *Marker) SetForwardTagIndels(indels int) {
marker.Forward_tag_indels = indels
}
func (marker *Marker) SetReverseTagIndels(indels int) {
marker.Reverse_tag_indels = indels
}
func (marker *Marker) SetTagIndels(indels int) {
marker.SetForwardTagIndels(indels)
marker.SetReverseTagIndels(indels)
}
func (marker *Marker) SetForwardAllowedMismatches(allowed_mismatches int) {
marker.Forward_error = allowed_mismatches
}

184
pkg/obingslibrary/multimatch.go
View File

@ -110,6 +110,63 @@ func lookForTag(seq string, delimiter byte) string {
return seq[begin:end]
}
func lookForRescueTag(seq string, delimiter byte, taglength, border, indel int) string {
// log.Info("lookForRescueTag")
i := len(seq) - 1
// Skip the border part not corresponding to the tag delimiter
for i >= 0 && seq[i] != delimiter {
i--
}
delimlen := 0
for i >= 0 && seq[i] == delimiter {
i--
delimlen++
}
if obiutils.Abs(delimlen-border) > indel {
return ""
}
// log.Infof("delimlen: %d", delimlen)
end := i + 1
i -= taglength - indel
for i >= 0 && seq[i] != delimiter {
i--
}
delimlen = 0
for i >= 0 && seq[i] == delimiter {
i--
delimlen++
}
if obiutils.Abs(delimlen-border) > indel {
return ""
}
delimlen = min(delimlen, border)
// log.Infof("delimlen: %d", delimlen)
begin := i + delimlen + 1
if i < 0 || obiutils.Abs(taglength-end+begin) > indel {
return ""
}
// log.Infof("begin: %d, end: %d", begin, end)
// log.Infof("seq: %s", seq)
// log.Infof("seq[begin:end]: %s", seq[begin:end])
return seq[begin:end]
}
func (marker *Marker) beginDelimitedTagExtractor(
sequence *obiseq.BioSequence,
begin int,
@ -131,6 +188,33 @@ func (marker *Marker) beginDelimitedTagExtractor(
return lookForTag(sequence.String()[fb:begin], delimiter)
}
func (marker *Marker) beginRescueTagExtractor(
sequence *obiseq.BioSequence,
begin int,
forward bool) string {
delimiter := marker.Forward_tag_delimiter
border := marker.Forward_spacer
taglength := marker.Forward_tag_length
delta := marker.Forward_tag_indels
if !forward {
taglength = marker.Reverse_tag_length
border = marker.Reverse_spacer
delimiter = marker.Reverse_tag_delimiter
delta = marker.Reverse_tag_indels
}
frglength := border + taglength
fb := begin - frglength*2
if fb < 0 {
fb = 0
}
return lookForRescueTag(sequence.String()[fb:begin], delimiter, taglength, border, delta)
}
func (marker *Marker) beginFixedTagExtractor(
sequence *obiseq.BioSequence,
begin int,
@ -183,6 +267,43 @@ func (marker *Marker) endDelimitedTagExtractor(
return lookForTag(tag_seq.ReverseComplement(true).String(), delimiter)
}
func (marker *Marker) endRescueTagExtractor(
sequence *obiseq.BioSequence,
end int,
forward bool) string {
delimiter := marker.Reverse_tag_delimiter
border := marker.Reverse_spacer
taglength := marker.Reverse_tag_length
delta := marker.Reverse_tag_indels
if !forward {
taglength = marker.Forward_tag_length
border = marker.Forward_spacer
delimiter = marker.Forward_tag_delimiter
delta = marker.Forward_tag_indels
}
frglength := border + taglength
fb := end + frglength*2
if fb > sequence.Len() {
fb = sequence.Len()
}
if end >= fb {
return ""
}
tag_seq, err := sequence.Subsequence(end, fb, false)
if err != nil {
log.Fatalf("Cannot extract sequence tag : %v", err)
}
return lookForRescueTag(tag_seq.ReverseComplement(true).String(), delimiter, taglength, border, delta)
}
func (marker *Marker) endFixedTagExtractor(
sequence *obiseq.BioSequence,
end int,
@ -218,13 +339,23 @@ func (marker *Marker) beginTagExtractor(
if marker.Forward_tag_delimiter == 0 {
return marker.beginFixedTagExtractor(sequence, begin, forward)
} else {
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
if marker.Forward_tag_indels == 0 {
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
} else {
// log.Warn("Rescue tag for forward primers")
return marker.beginRescueTagExtractor(sequence, begin, forward)
}
}
} else {
if marker.Reverse_tag_delimiter == 0 {
return marker.beginFixedTagExtractor(sequence, begin, forward)
} else {
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
if marker.Reverse_tag_indels == 0 {
return marker.beginDelimitedTagExtractor(sequence, begin, forward)
} else {
// log.Warn("Rescue tag for reverse/complement primers")
return marker.beginRescueTagExtractor(sequence, begin, forward)
}
}
}
}
@ -237,13 +368,23 @@ func (marker *Marker) endTagExtractor(
if marker.Reverse_tag_delimiter == 0 {
return marker.endFixedTagExtractor(sequence, end, forward)
} else {
return marker.endDelimitedTagExtractor(sequence, end, forward)
if marker.Reverse_tag_indels == 0 {
return marker.endDelimitedTagExtractor(sequence, end, forward)
} else {
// log.Warn("Rescue tag for reverse primers")
return marker.endRescueTagExtractor(sequence, end, forward)
}
}
} else {
if marker.Forward_tag_delimiter == 0 {
return marker.endFixedTagExtractor(sequence, end, forward)
} else {
return marker.endDelimitedTagExtractor(sequence, end, forward)
if marker.Forward_tag_indels == 0 {
return marker.endDelimitedTagExtractor(sequence, end, forward)
} else {
// log.Warn("Rescue tag for forward/complement primers")
return marker.endRescueTagExtractor(sequence, end, forward)
}
}
}
}
@ -264,6 +405,10 @@ func (library *NGSLibrary) TagExtractor(
forward_tag := marker.beginTagExtractor(sequence, begin, forward)
reverse_tag := marker.endTagExtractor(sequence, end, forward)
if !forward {
forward_tag, reverse_tag = reverse_tag, forward_tag
}
if forward_tag != "" {
annotations["obimultiplex_forward_tag"] = forward_tag
}
@ -347,14 +492,12 @@ func (library *NGSLibrary) SampleIdentifier(
case "hamming":
forward, fdistance = marker.ClosestForwardTag(tags.Forward, Hamming)
annotations["obimultiplex_forward_matching"] = "hamming"
annotations["obimultiplex_forward_tag_dist"] = fdistance
annotations["obimultiplex_forward_proposed_tag"] = forward
case "indel":
forward, fdistance = marker.ClosestForwardTag(tags.Forward, Levenshtein)
annotations["obimultiplex_forward_matching"] = "indel"
annotations["obimultiplex_forward_tag_dist"] = fdistance
annotations["obimultiplex_forward_proposed_tag"] = forward
}
annotations["obimultiplex_forward_tag_dist"] = fdistance
annotations["obimultiplex_forward_proposed_tag"] = forward
}
if tags.Reverse != "" {
@ -366,14 +509,12 @@ func (library *NGSLibrary) SampleIdentifier(
case "hamming":
reverse, rdistance = marker.ClosestReverseTag(tags.Reverse, Hamming)
annotations["obimultiplex_reverse_matching"] = "hamming"
annotations["obimultiplex_reverse_tag_dist"] = rdistance
annotations["obimultiplex_reverse_proposed_tag"] = reverse
case "indel":
reverse, rdistance = marker.ClosestReverseTag(tags.Reverse, Levenshtein)
annotations["obimultiplex_reverse_matching"] = "indel"
annotations["obimultiplex_reverse_tag_dist"] = rdistance
annotations["obimultiplex_reverse_proposed_tag"] = reverse
}
annotations["obimultiplex_reverse_tag_dist"] = rdistance
annotations["obimultiplex_reverse_proposed_tag"] = reverse
}
proposed := TagPair{forward, reverse}
@ -492,18 +633,22 @@ func (library *NGSLibrary) ExtractMultiBarcode(sequence *obiseq.BioSequence) (ob
annotations["obimultiplex_reverse_primer"] = primerseqs[from.Marker].Reverse
if from.Forward {
// With have a barcode in the orientation from the forward primer to the reverse
// Try to extract the forward primer match
if from.Begin < 0 || from.End > sequence.Len() {
barcode_error = true
annotations["obimultiplex_error"] = "Cannot extract forward match"
annotations["obimultiplex_error"] = "Cannot extract forward primer match"
} else {
annotations["obimultiplex_forward_match"] = sequence.String()[from.Begin:from.End]
}
// Try to extract the reverse primer match
sseq, err := sequence.Subsequence(match.Begin, match.End, false)
if err != nil {
barcode_error = true
annotations["obimultiplex_error"] = "Cannot extract reverse match"
annotations["obimultiplex_error"] = "Cannot extract reverse primer match"
} else {
annotations["obimultiplex_reverse_match"] = sseq.ReverseComplement(true).String()
}
@ -511,18 +656,22 @@ func (library *NGSLibrary) ExtractMultiBarcode(sequence *obiseq.BioSequence) (ob
annotations["obimultiplex_forward_error"] = from.Mismatches
annotations["obimultiplex_reverse_error"] = match.Mismatches
} else {
// With have a barcode in the orientation from the reverse primer to the forward
// Try to extract the reverse primer match
if from.Begin < 0 || from.End > sequence.Len() {
barcode_error = true
annotations["obimultiplex_error"] = "Cannot extract reverse match"
annotations["obimultiplex_error"] = "Cannot extract reverse primer match"
} else {
annotations["obimultiplex_reverse_match"] = sequence.String()[from.Begin:from.End]
}
// Try to extract the forward primer match
sseq, err := sequence.Subsequence(match.Begin, match.End, false)
if err != nil {
barcode_error = true
annotations["obimultiplex_error"] = "Cannot extract forward match"
annotations["obimultiplex_error"] = "Cannot extract forward primer match"
} else {
annotations["obimultiplex_forward_match"] = sseq.ReverseComplement(true).String()
}
@ -531,6 +680,7 @@ func (library *NGSLibrary) ExtractMultiBarcode(sequence *obiseq.BioSequence) (ob
annotations["obimultiplex_forward_error"] = match.Mismatches
}
// if we were able to extract the primer matches we can extract the barcode
if !barcode_error {
tags := library.TagExtractor(sequence, annotations, primerseqs[from.Marker], from.Begin, match.End, from.Forward)
@ -540,6 +690,8 @@ func (library *NGSLibrary) ExtractMultiBarcode(sequence *obiseq.BioSequence) (ob
return nil, fmt.Errorf("%s [%s] : Cannot extract barcode %d : %v", sequence.Id(), sequence.Source(), q, err)
}
annotations["obimultiplex_direction"] = map[bool]string{true: "forward", false: "reverse"}[from.Forward]
if !match.Forward {
barcode = barcode.ReverseComplement(true)
}

36
pkg/obingslibrary/ngslibrary.go
View File

@ -57,6 +57,8 @@ func (library *NGSLibrary) GetMarker(forward, reverse string) (*Marker, bool) {
Reverse_matching: "strict",
Forward_allows_indels: false,
Reverse_allows_indels: false,
Forward_tag_indels: 0,
Reverse_tag_indels: 0,
samples: make(map[TagPair]*PCR, 1000),
}
@ -122,6 +124,40 @@ func (library *NGSLibrary) SetTagSpacerFor(primer string, spacer int) {
}
}
func (library *NGSLibrary) SetForwardTagIndels(indels int) {
for _, marker := range library.Markers {
marker.SetForwardTagIndels(indels)
}
}
func (library *NGSLibrary) SetReverseTagIndels(indels int) {
for _, marker := range library.Markers {
marker.SetReverseTagIndels(indels)
}
}
func (library *NGSLibrary) SetTagIndels(indels int) {
library.SetForwardTagIndels(indels)
library.SetReverseTagIndels(indels)
}
func (library *NGSLibrary) SetTagIndelsFor(primer string, indels int) {
primer = strings.ToLower(primer)
primers, ok := library.Primers[primer]
if ok {
marker, ok := library.Markers[primers]
if ok {
if primer == primers.Forward {
marker.SetForwardTagIndels(indels)
} else {
marker.SetReverseTagIndels(indels)
}
}
}
}
func (library *NGSLibrary) SetForwardTagDelimiter(delim byte) {
for _, marker := range library.Markers {
marker.SetForwardTagDelimiter(delim)