mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-12-08 16:50:27 +00:00
First commit
This commit is contained in:
370
pkg/obiapat/pcr.go
Normal file
370
pkg/obiapat/pcr.go
Normal file
@@ -0,0 +1,370 @@
|
||||
package obiapat
|
||||
|
||||
import (
|
||||
"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
|
||||
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
|
||||
)
|
||||
|
||||
type __options__ struct {
|
||||
min_length int
|
||||
max_length int
|
||||
circular bool
|
||||
forward_error int
|
||||
reverse_error int
|
||||
buffer_size int
|
||||
batch_size int
|
||||
parallel_workers int
|
||||
}
|
||||
|
||||
type Options struct {
|
||||
pointer *__options__
|
||||
}
|
||||
|
||||
type WithOption func(Options)
|
||||
|
||||
func (options Options) MinLength() int {
|
||||
return options.pointer.min_length
|
||||
}
|
||||
|
||||
func (options Options) MaxLength() int {
|
||||
return options.pointer.max_length
|
||||
}
|
||||
|
||||
func (options Options) ForwardError() int {
|
||||
return options.pointer.forward_error
|
||||
}
|
||||
|
||||
func (options Options) ReverseError() int {
|
||||
return options.pointer.reverse_error
|
||||
}
|
||||
|
||||
func (options Options) Circular() bool {
|
||||
return options.pointer.circular
|
||||
}
|
||||
|
||||
func (opt Options) BufferSize() int {
|
||||
return opt.pointer.buffer_size
|
||||
}
|
||||
|
||||
func (opt Options) BatchSize() int {
|
||||
return opt.pointer.batch_size
|
||||
}
|
||||
|
||||
func (opt Options) ParallelWorkers() int {
|
||||
return opt.pointer.parallel_workers
|
||||
}
|
||||
|
||||
func MakeOptions(setters []WithOption) Options {
|
||||
o := __options__{
|
||||
min_length: 0,
|
||||
max_length: 0,
|
||||
forward_error: 0,
|
||||
reverse_error: 0,
|
||||
circular: false,
|
||||
parallel_workers: 4,
|
||||
batch_size: 100,
|
||||
buffer_size: 100,
|
||||
}
|
||||
|
||||
opt := Options{&o}
|
||||
|
||||
for _, set := range setters {
|
||||
set(opt)
|
||||
}
|
||||
|
||||
return opt
|
||||
}
|
||||
|
||||
func OptionMinLength(min_length int) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.min_length = min_length
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func OptionMaxLength(max_length int) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.max_length = max_length
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func OptionForwardError(max int) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.forward_error = max
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func OptionReverseError(max int) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.reverse_error = max
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func OptionCircular(circular bool) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.circular = circular
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func OptionBufferSize(size int) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.buffer_size = size
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func OptionParallelWorkers(nworkers int) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.parallel_workers = nworkers
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func OptionBatchSize(size int) WithOption {
|
||||
f := WithOption(func(opt Options) {
|
||||
opt.pointer.batch_size = size
|
||||
})
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func __pcr__(seq ApatSequence, sequence obiseq.BioSequence,
|
||||
forward, cfwd, reverse, crev ApatPattern,
|
||||
opt Options) obiseq.BioSequenceSlice {
|
||||
results := make(obiseq.BioSequenceSlice, 0, 10)
|
||||
|
||||
forward_matches := forward.FindAllIndex(seq)
|
||||
|
||||
if forward_matches != nil {
|
||||
|
||||
begin := forward_matches[0][0]
|
||||
length := seq.Length() - begin
|
||||
|
||||
if opt.pointer.max_length > 0 {
|
||||
length = forward_matches[len(forward_matches)-1][2] - begin + opt.MaxLength() + reverse.Length()
|
||||
}
|
||||
|
||||
if opt.Circular() {
|
||||
begin = 0
|
||||
length = seq.Length() + MAX_PAT_LEN
|
||||
}
|
||||
|
||||
reverse_matches := crev.FindAllIndex(seq, begin, length)
|
||||
|
||||
if reverse_matches != nil {
|
||||
for _, fm := range forward_matches {
|
||||
|
||||
posi := fm[0]
|
||||
|
||||
if posi < seq.Length() {
|
||||
|
||||
erri := fm[2]
|
||||
|
||||
for _, rm := range reverse_matches {
|
||||
posj := rm[0]
|
||||
if posj < seq.Length() {
|
||||
posj := rm[1]
|
||||
errj := rm[2]
|
||||
length = 0
|
||||
|
||||
if posj > posi {
|
||||
length = rm[0] - fm[1]
|
||||
} else {
|
||||
if opt.Circular() {
|
||||
length = rm[0] + seq.Length() - posi - forward.Length()
|
||||
}
|
||||
}
|
||||
if length > 0 && // For when primers touch or overlap
|
||||
(opt.MinLength() == 0 || length >= opt.MinLength()) &&
|
||||
(opt.MaxLength() == 0 || length <= opt.MaxLength()) {
|
||||
amplicon, _ := sequence.Subsequence(fm[1], rm[0], opt.pointer.circular)
|
||||
annot := amplicon.Annotations()
|
||||
goutils.CopyMap(annot, sequence.Annotations())
|
||||
annot["forward_primer"] = forward.String()
|
||||
|
||||
match, _ := sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
|
||||
annot["forward_match"] = match.String()
|
||||
match.Revoke()
|
||||
|
||||
annot["forward_error"] = erri
|
||||
|
||||
annot["reverse_primer"] = reverse.String()
|
||||
match, _ = sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)
|
||||
match = match.ReverseComplement(true)
|
||||
annot["reverse_match"] = match.String()
|
||||
match.Revoke()
|
||||
|
||||
annot["reverse_error"] = errj
|
||||
results = append(results, amplicon)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
forward_matches = reverse.FindAllIndex(seq)
|
||||
|
||||
if forward_matches != nil {
|
||||
|
||||
begin := forward_matches[0][0]
|
||||
length := seq.Length() - begin
|
||||
|
||||
if opt.pointer.max_length > 0 {
|
||||
length = forward_matches[len(forward_matches)-1][2] - begin + opt.MaxLength() + reverse.Length()
|
||||
}
|
||||
|
||||
if opt.Circular() {
|
||||
begin = 0
|
||||
length = seq.Length() + MAX_PAT_LEN
|
||||
}
|
||||
|
||||
reverse_matches := cfwd.FindAllIndex(seq, begin, length)
|
||||
|
||||
if reverse_matches != nil {
|
||||
for _, fm := range forward_matches {
|
||||
|
||||
posi := fm[0]
|
||||
|
||||
if posi < seq.Length() {
|
||||
|
||||
erri := fm[2]
|
||||
|
||||
for _, rm := range reverse_matches {
|
||||
posj := rm[0]
|
||||
if posj < seq.Length() {
|
||||
posj := rm[1]
|
||||
errj := rm[2]
|
||||
length = 0
|
||||
|
||||
if posj > posi {
|
||||
length = rm[0] - fm[1]
|
||||
} else {
|
||||
if opt.Circular() {
|
||||
length = rm[0] + seq.Length() - posi - forward.Length()
|
||||
}
|
||||
}
|
||||
if length > 0 && // For when primers touch or overlap
|
||||
(opt.MinLength() == 0 || length >= opt.MinLength()) &&
|
||||
(opt.MaxLength() == 0 || length <= opt.MaxLength()) {
|
||||
amplicon, _ := sequence.Subsequence(fm[1], rm[0], opt.pointer.circular)
|
||||
amplicon = amplicon.ReverseComplement(true)
|
||||
|
||||
annot := amplicon.Annotations()
|
||||
goutils.CopyMap(annot, sequence.Annotations())
|
||||
annot["forward_primer"] = forward.String()
|
||||
|
||||
match, _ := sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)
|
||||
match.ReverseComplement(true)
|
||||
annot["forward_match"] = match.String()
|
||||
match.Revoke()
|
||||
|
||||
annot["forward_error"] = errj
|
||||
|
||||
annot["reverse_primer"] = reverse.String()
|
||||
match, _ = sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
|
||||
annot["reverse_match"] = match.String()
|
||||
match.Revoke()
|
||||
|
||||
annot["reverse_error"] = erri
|
||||
results = append(results, amplicon)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return results
|
||||
}
|
||||
|
||||
func PCR(sequence obiseq.BioSequence,
|
||||
forward, reverse string, options ...WithOption) obiseq.BioSequenceSlice {
|
||||
|
||||
opt := MakeOptions(options)
|
||||
|
||||
seq, _ := MakeApatSequence(sequence, opt.Circular())
|
||||
|
||||
fwd, _ := MakeApatPattern(forward, opt.ForwardError())
|
||||
rev, _ := MakeApatPattern(reverse, opt.ReverseError())
|
||||
cfwd, _ := fwd.ReverseComplement()
|
||||
crev, _ := rev.ReverseComplement()
|
||||
|
||||
results := __pcr__(seq, sequence,
|
||||
fwd, cfwd, rev, crev,
|
||||
opt)
|
||||
|
||||
seq.Free()
|
||||
|
||||
fwd.Free()
|
||||
rev.Free()
|
||||
cfwd.Free()
|
||||
crev.Free()
|
||||
|
||||
return results
|
||||
}
|
||||
|
||||
func PCRSlice(sequences obiseq.BioSequenceSlice,
|
||||
forward, reverse string, options ...WithOption) obiseq.BioSequenceSlice {
|
||||
|
||||
results := make(obiseq.BioSequenceSlice, 0, len(sequences))
|
||||
|
||||
opt := MakeOptions(options)
|
||||
|
||||
fwd, _ := MakeApatPattern(forward, opt.ForwardError())
|
||||
rev, _ := MakeApatPattern(reverse, opt.ReverseError())
|
||||
cfwd, _ := fwd.ReverseComplement()
|
||||
crev, _ := rev.ReverseComplement()
|
||||
|
||||
if len(sequences) > 0 {
|
||||
seq, _ := MakeApatSequence(sequences[0], opt.Circular())
|
||||
amplicons := __pcr__(seq, sequences[0],
|
||||
fwd, cfwd, rev, crev,
|
||||
opt)
|
||||
|
||||
if len(amplicons) > 0 {
|
||||
results = append(results, amplicons...)
|
||||
}
|
||||
|
||||
for _, sequence := range sequences[1:] {
|
||||
seq, _ := MakeApatSequence(sequence, opt.Circular(), seq)
|
||||
amplicons = __pcr__(seq, sequence,
|
||||
fwd, cfwd, rev, crev,
|
||||
opt)
|
||||
if len(amplicons) > 0 {
|
||||
results = append(results, amplicons...)
|
||||
}
|
||||
}
|
||||
|
||||
seq.Free()
|
||||
}
|
||||
|
||||
fwd.Free()
|
||||
rev.Free()
|
||||
cfwd.Free()
|
||||
crev.Free()
|
||||
|
||||
return results
|
||||
}
|
||||
|
||||
func PCRSliceWorker(forward, reverse string,
|
||||
options ...WithOption) obiseq.SeqSliceWorker {
|
||||
|
||||
worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
|
||||
return PCRSlice(sequences, forward, reverse, options...)
|
||||
}
|
||||
|
||||
return worker
|
||||
}
|
||||
Reference in New Issue
Block a user