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Add the possibility to look for patterns allowing indels.

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Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
This commit is contained in:
Eric Coissac
2023-03-20 15:28:24 +07:00
parent 5fbe52368c
commit 27d6c60e25
14 changed files with 674 additions and 219 deletions
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63
pkg/obingslibrary/match.go
View File

@ -27,11 +27,11 @@ type DemultiplexMatch struct {
Error error
}
func (library *NGSLibrary) Compile(maxError int) error {
func (library *NGSLibrary) Compile(maxError int, allowsIndel bool) error {
for primers, marker := range *library {
err := marker.Compile(primers.Forward,
primers.Reverse,
maxError)
maxError, allowsIndel)
if err != nil {
return err
}
@ -57,15 +57,13 @@ func (library *NGSLibrary) ExtractBarcode(sequence *obiseq.BioSequence, inplace
return match.ExtractBarcode(sequence, inplace)
}
func (marker *Marker) Compile(forward, reverse string, maxError int) error {
func (marker *Marker) Compile(forward, reverse string, maxError int, allowsIndel bool) error {
var err error
marker.forward, err = obiapat.MakeApatPattern(forward,
maxError)
marker.forward, err = obiapat.MakeApatPattern(forward, maxError, allowsIndel)
if err != nil {
return err
}
marker.reverse, err = obiapat.MakeApatPattern(reverse,
maxError)
marker.reverse, err = obiapat.MakeApatPattern(reverse, maxError, allowsIndel)
if err != nil {
return err
}
@ -105,33 +103,34 @@ func (marker *Marker) Compile(forward, reverse string, maxError int) error {
return nil
}
func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
aseq, _ := obiapat.MakeApatSequence(sequence, false)
match := marker.forward.FindAllIndex(aseq, marker.taglength)
if len(match) > 0 {
start, end, nerr ,matched := marker.forward.BestMatch(aseq, marker.taglength,-1)
if matched {
sseq := sequence.String()
direct := sseq[match[0][0]:match[0][1]]
ftag := strings.ToLower(sseq[(match[0][0] - marker.taglength):match[0][0]])
direct := sseq[start:end]
ftag := strings.ToLower(sseq[(start - marker.taglength):start])
m := DemultiplexMatch{
ForwardMatch: direct,
ForwardTag: ftag,
BarcodeStart: match[0][1],
ForwardMismatches: match[0][2],
BarcodeStart: end,
ForwardMismatches: nerr,
IsDirect: true,
Error: nil,
}
rmatch := marker.creverse.FindAllIndex(aseq, match[0][1])
start, end, nerr ,matched = marker.creverse.BestMatch(aseq, start,-1)
if len(rmatch) > 0 {
if matched {
// extracting primer matches
reverse, _ := sequence.Subsequence(rmatch[0][0], rmatch[0][1], false)
reverse, _ := sequence.Subsequence(start,end, false)
defer reverse.Recycle()
reverse = reverse.ReverseComplement(true)
rtag, err := sequence.Subsequence(rmatch[0][1], rmatch[0][1]+marker.taglength, false)
rtag, err := sequence.Subsequence(end, end+marker.taglength, false)
defer rtag.Recycle()
srtag := ""
@ -143,8 +142,8 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
}
m.ReverseMatch = strings.ToLower(reverse.String())
m.ReverseMismatches = rmatch[0][2]
m.BarcodeEnd = rmatch[0][0]
m.ReverseMismatches = nerr
m.BarcodeEnd = start
m.ReverseTag = srtag
sample, ok := marker.samples[TagPair{ftag, srtag}]
@ -162,32 +161,32 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
return &m
}
match = marker.reverse.FindAllIndex(aseq, marker.taglength)
start, end, nerr ,matched = marker.reverse.BestMatch(aseq, marker.taglength,-1)
if len(match) > 0 {
if matched {
sseq := sequence.String()
reverse := strings.ToLower(sseq[match[0][0]:match[0][1]])
rtag := strings.ToLower(sseq[(match[0][0] - marker.taglength):match[0][0]])
reverse := strings.ToLower(sseq[start:end])
rtag := strings.ToLower(sseq[(start - marker.taglength):start])
m := DemultiplexMatch{
ReverseMatch: reverse,
ReverseTag: rtag,
BarcodeStart: match[0][1],
ReverseMismatches: match[0][2],
BarcodeStart: end,
ReverseMismatches: nerr,
IsDirect: false,
Error: nil,
}
rmatch := marker.cforward.FindAllIndex(aseq, match[0][1])
start, end, nerr ,matched = marker.cforward.BestMatch(aseq, end,-1)
if len(rmatch) > 0 {
if matched {
direct, _ := sequence.Subsequence(rmatch[0][0], rmatch[0][1], false)
direct, _ := sequence.Subsequence(start,end, false)
defer direct.Recycle()
direct = direct.ReverseComplement(true)
ftag, err := sequence.Subsequence(rmatch[0][1], rmatch[0][1]+marker.taglength, false)
ftag, err := sequence.Subsequence(end,end+marker.taglength, false)
defer ftag.Recycle()
sftag := ""
if err != nil {
@ -200,8 +199,8 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
m.ForwardMatch = direct.String()
m.ForwardTag = sftag
m.ReverseMismatches = rmatch[0][2]
m.BarcodeEnd = rmatch[0][0]
m.ReverseMismatches = nerr
m.BarcodeEnd = start
sample, ok := marker.samples[TagPair{sftag, rtag}]

18
pkg/obingslibrary/worker.go
View File

@ -8,6 +8,7 @@ type _Options struct {
discardErrors bool
unidentified string
allowedMismatch int
allowsIndel bool
withProgressBar bool
parallelWorkers int
batchSize int
@ -55,6 +56,14 @@ func OptionAllowedMismatches(count int) WithOption {
return f
}
func OptionAllowedIndel(allowed bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.allowsIndel = allowed
})
return f
}
// OptionParallelWorkers sets how many search
// jobs will be run in parallel.
func OptionParallelWorkers(nworkers int) WithOption {
@ -87,6 +96,10 @@ func (options Options) AllowedMismatch() int {
return options.pointer.allowedMismatch
}
func (options Options) AllowsIndel() bool {
return options.pointer.allowsIndel
}
func (options Options) WithProgressBar() bool {
return options.pointer.withProgressBar
}
@ -110,6 +123,7 @@ func MakeOptions(setters []WithOption) Options {
discardErrors: true,
unidentified: "",
allowedMismatch: 0,
allowsIndel: false,
withProgressBar: false,
parallelWorkers: 4,
batchSize: 1000,
@ -145,7 +159,7 @@ func ExtractBarcodeSlice(ngslibrary NGSLibrary,
opt := MakeOptions(options)
ngslibrary.Compile(opt.AllowedMismatch())
ngslibrary.Compile(opt.AllowedMismatch(),opt.AllowsIndel())
return _ExtractBarcodeSlice(ngslibrary, sequences, opt)
}
@ -155,7 +169,7 @@ func ExtractBarcodeSliceWorker(ngslibrary NGSLibrary,
opt := MakeOptions(options)
ngslibrary.Compile(opt.AllowedMismatch())
ngslibrary.Compile(opt.AllowedMismatch(),opt.AllowsIndel())
worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
return _ExtractBarcodeSlice(ngslibrary, sequences, opt)