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Code refactoring

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This commit is contained in:
Eric Coissac
2022-01-14 15:36:39 +01:00
parent 402d54cb62
commit 2163db94d0
4 changed files with 32 additions and 24 deletions
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4
pkg/obialign/alignment.go
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@ -169,8 +169,8 @@ func BuildQualityConsensus(seqA, seqB obiseq.BioSequence, path []int,
qm = qA qm = qA
} }
if qB == qA { if qB == qA {
nuc := __four_bits_base_code__[sA[i]&31] | __four_bits_base_code__[sB[i]&31] nuc := _FourBitsBaseCode[sA[i]&31] | _FourBitsBaseCode[sB[i]&31]
consensus = append(consensus, __four_bits_base_decode__[nuc]) consensus = append(consensus, _FourBitsBaseDecode[nuc])
} }
q := qA + qB q := qA + qB

4
pkg/obialign/dnamatrix.go
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@ -74,8 +74,8 @@ func _MatchScoreRatio(a, b byte) (float64, float64) {
func _InitNucPartMatch() { func _InitNucPartMatch() {
for i, a := range __four_bits_base_code__ { for i, a := range _FourBitsBaseCode {
for j, b := range __four_bits_base_code__ { for j, b := range _FourBitsBaseCode {
_NucPartMatch[i][j] = _MatchRatio(a, b) _NucPartMatch[i][j] = _MatchRatio(a, b)
} }
} }

14
pkg/obialign/fourbitsencode.go
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@ -4,7 +4,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
) )
var __four_bits_base_code__ = []byte{0b0000, var _FourBitsBaseCode = []byte{0b0000,
// IUPAC nucleotide code Base // IUPAC nucleotide code Base
0b0001, // A Adenine 0b0001, // A Adenine
0b1110, // B C or G or T 0b1110, // B C or G or T
@ -38,7 +38,7 @@ var __four_bits_base_code__ = []byte{0b0000,
0b0000, 0b0000,
0b0000} 0b0000}
var __four_bits_base_decode__ = []byte{ var _FourBitsBaseDecode = []byte{
// 0b0000 0b0001 0b0010 0b0011 // 0b0000 0b0001 0b0010 0b0011
'.', 'a', 'c', 'm', '.', 'a', 'c', 'm',
// 0b0100 0b0101 0b0110 0b0111 // 0b0100 0b0101 0b0110 0b0111
@ -49,6 +49,14 @@ var __four_bits_base_decode__ = []byte{
'k', 'd', 'b', 'n', 'k', 'd', 'b', 'n',
} }
// Encode4bits encodes each nucleotide of a sequence into a binary
// code where the four low weigth bit of a byte correspond respectively
// to the four nucleotides A, C, G, T. Simple bases A, C, G, T are therefore
// represented by a code with only a single bit on, when anbiguous symboles
// like R, D or N have the bits corresponding to each nucleotide represented
// by the ambiguity set to 1.
// A byte slice can be provided (buffer) to preveent allocation of a new
// memory chunk by th function.
func Encode4bits(seq obiseq.BioSequence, buffer []byte) []byte { func Encode4bits(seq obiseq.BioSequence, buffer []byte) []byte {
length := seq.Length() length := seq.Length()
rawseq := seq.Sequence() rawseq := seq.Sequence()
@ -65,7 +73,7 @@ func Encode4bits(seq obiseq.BioSequence, buffer []byte) []byte {
if nuc == '.' || nuc == '-' { if nuc == '.' || nuc == '-' {
code = 0 code = 0
} else { } else {
code = __four_bits_base_code__[nuc&31] code = _FourBitsBaseCode[nuc&31]
} }
buffer = append(buffer, code) buffer = append(buffer, code)
} }

34
pkg/obialign/pairedendalign.go
View File

@ -51,17 +51,17 @@ func __get_matrix_from__(matrix *[]int, lenA, a, b int) (int, int, int) {
} }
func __pairing_score_pe_align__(baseA, qualA, baseB, qualB byte) int { func __pairing_score_pe_align__(baseA, qualA, baseB, qualB byte) int {
part_match := __nuc_part_match__[baseA&31][baseB&31] part_match := _NucPartMatch[baseA&31][baseB&31]
// log.Printf("id : %f A : %s %d B : %s %d\n", part_match, string(baseA), qualA, string(baseB), qualB) // log.Printf("id : %f A : %s %d B : %s %d\n", part_match, string(baseA), qualA, string(baseB), qualB)
switch { switch {
case part_match == 1: case part_match == 1:
// log.Printf("match\n") // log.Printf("match\n")
return __nuc_score_part_match_match__[qualA][qualB] return _NucScorePartMatchMatch[qualA][qualB]
case part_match == 0: case part_match == 0:
return __nuc_score_part_match_mismatch__[qualA][qualB] return _NucScorePartMatchMismatch[qualA][qualB]
default: default:
return int(part_match*float64(__nuc_score_part_match_match__[qualA][qualB]) + return int(part_match*float64(_NucScorePartMatchMatch[qualA][qualB]) +
(1-part_match)*float64(__nuc_score_part_match_mismatch__[qualA][qualB]) + 0.5) (1-part_match)*float64(_NucScorePartMatchMismatch[qualA][qualB]) + 0.5)
} }
} }
@ -73,7 +73,7 @@ func __fill_matrix_pe_left_align__(seqA, qualA, seqB, qualB []byte, gap int,
// The actual gap score is the gap score times the mismatch between // The actual gap score is the gap score times the mismatch between
// two bases with a score of 40 // two bases with a score of 40
gap = gap * __nuc_score_part_match_mismatch__[40][40] gap = gap * _NucScorePartMatchMismatch[40][40]
needed := (la + 1) * (lb + 1) needed := (la + 1) * (lb + 1)
@ -144,7 +144,7 @@ func __fill_matrix_pe_right_align__(seqA, qualA, seqB, qualB []byte, gap int,
// The actual gap score is the gap score times the mismatch between // The actual gap score is the gap score times the mismatch between
// two bases with a score of 40 // two bases with a score of 40
gap = gap * __nuc_score_part_match_mismatch__[40][40] gap = gap * _NucScorePartMatchMismatch[40][40]
needed := (la + 1) * (lb + 1) needed := (la + 1) * (lb + 1)
@ -215,9 +215,9 @@ func __fill_matrix_pe_right_align__(seqA, qualA, seqB, qualB []byte, gap int,
func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) { func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) {
if !__initialized_dna_score__ { if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix") log.Println("Initializing the DNA Scoring matrix")
InitDNAScoreMatrix() _InitDNAScoreMatrix()
} }
if arena.pointer == nil { if arena.pointer == nil {
@ -229,7 +229,7 @@ func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (in
&arena.pointer.score_matrix, &arena.pointer.score_matrix,
&arena.pointer.path_matrix) &arena.pointer.path_matrix)
arena.pointer.path = __backtracking__(arena.pointer.path_matrix, arena.pointer.path = _Backtracking(arena.pointer.path_matrix,
seqA.Length(), seqB.Length(), seqA.Length(), seqB.Length(),
&arena.pointer.path) &arena.pointer.path)
@ -238,9 +238,9 @@ func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (in
func PERightAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) { func PERightAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) {
if !__initialized_dna_score__ { if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix") log.Println("Initializing the DNA Scoring matrix")
InitDNAScoreMatrix() _InitDNAScoreMatrix()
} }
if arena.pointer == nil { if arena.pointer == nil {
@ -252,7 +252,7 @@ func PERightAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (i
&arena.pointer.score_matrix, &arena.pointer.score_matrix,
&arena.pointer.path_matrix) &arena.pointer.path_matrix)
arena.pointer.path = __backtracking__(arena.pointer.path_matrix, arena.pointer.path = _Backtracking(arena.pointer.path_matrix,
seqA.Length(), seqB.Length(), seqA.Length(), seqB.Length(),
&arena.pointer.path) &arena.pointer.path)
@ -269,9 +269,9 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
var raw_seqB, qual_seqB []byte var raw_seqB, qual_seqB []byte
var extra5, extra3 int var extra5, extra3 int
if !__initialized_dna_score__ { if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix") log.Println("Initializing the DNA Scoring matrix")
InitDNAScoreMatrix() _InitDNAScoreMatrix()
} }
index := obikmer.Index4mer(seqA, index := obikmer.Index4mer(seqA,
@ -323,7 +323,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
&arena.pointer.path_matrix) &arena.pointer.path_matrix)
} }
arena.pointer.path = __backtracking__(arena.pointer.path_matrix, arena.pointer.path = _Backtracking(arena.pointer.path_matrix,
len(raw_seqA), len(raw_seqB), len(raw_seqA), len(raw_seqB),
&arena.pointer.path) &arena.pointer.path)
@ -349,7 +349,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
score = 0 score = 0
for i, qualA := range qual_seqA { for i, qualA := range qual_seqA {
qualB := qual_seqB[i] qualB := qual_seqB[i]
score += __nuc_score_part_match_match__[qualA][qualB] score += _NucScorePartMatchMatch[qualA][qualB]
} }
arena.pointer.path = arena.pointer.path[:0] arena.pointer.path = arena.pointer.path[:0]
arena.pointer.path = append(arena.pointer.path, 0, part_len) arena.pointer.path = append(arena.pointer.path, 0, part_len)