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package seq
import "errors"
/*
base bases code
A A 1
C C 2
G G 4
T/U T 8
M A/C 3
R A/G 5
W A/T 9
S C/G 6
Y C/T 10
K G/T 12
V A/C/G 7
H A/C/T 11
D A/G/T 13
B C/G/T 14
N A/C/G/T 15
*/
var code2base = [16]byte{'-', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'}
// ErrInvalidDNABase means invalid DNA base
var ErrInvalidDNABase = errors.New("seq: invalid DNA base")
func base2code(b byte) (int, error) {
var c int
switch b {
case 'A', 'a':
c = 1
case 'C', 'c':
c = 2
case 'G', 'g':
c = 4
case 'T', 't', 'U', 'u':
c = 8
case 'N', 'n':
c = 15
case 'M', 'm':
c = 3
case 'R', 'r':
c = 5
case 'W', 'w':
c = 9
case 'S', 's':
c = 6
case 'Y', 'y':
c = 10
case 'K', 'k':
c = 12
case 'V', 'v':
c = 7
case 'H', 'h':
c = 11
case 'D', 'd':
c = 13
case 'B', 'b':
c = 14
case ' ', '*', '-':
c = 0
default:
return 0, ErrInvalidDNABase
}
return c, nil
}
// Bases2AmbBase converts list of bases to ambiguous base
func Bases2AmbBase(bs []byte) (byte, error) {
var code, c int
var err error
for _, b := range bs {
c, err = base2code(b)
if err != nil {
return 0, err
}
code |= c
}
return code2base[code], nil
}
// Codes2AmbCode converts list of codes of bases to code of ambiguous base
func Codes2AmbCode(codes []int) (int, error) {
var code int
for _, c := range codes {
code |= c
}
return code, nil
}
// AmbBase2Bases0 converts ambiguous base to bases it represents, slower than AmbBase2Bases
func AmbBase2Bases0(b byte) ([]byte, error) {
code, err := base2code(b)
if err != nil {
return nil, err
}
bases := []byte{}
var c int
for comb := 1; comb <= code; comb++ {
c = 0
for i := uint(0); i < 4; i++ {
if (comb>>i)&1 == 1 && // this combination needs this bit being 1
code&(1<<i) > 0 { // this bit is 1
c += 1 << i
}
}
if c == comb { // all bits are set
bases = append(bases, code2base[c])
}
}
return bases, nil
}
// AmbBase2Bases holds relationship of ambiguous base and bases it represents, faster than AmbBase2Bases0
var AmbBase2Bases = map[byte][]byte{
'A': {'A'},
'a': {'A'},
'C': {'C'},
'c': {'C'},
'G': {'G'},
'g': {'G'},
'T': {'T'},
't': {'T'},
'U': {'T'},
'u': {'T'},
'M': {'A', 'C', 'M'},
'm': {'A', 'C', 'M'},
'R': {'A', 'G', 'R'},
'r': {'A', 'G', 'R'},
'W': {'A', 'T', 'W'},
'w': {'A', 'T', 'W'},
'S': {'C', 'G', 'S'},
's': {'C', 'G', 'S'},
'Y': {'C', 'T', 'Y'},
'y': {'C', 'T', 'Y'},
'K': {'G', 'T', 'K'},
'k': {'G', 'T', 'K'},
'V': {'A', 'C', 'G', 'M', 'R', 'S', 'V'},
'v': {'A', 'C', 'G', 'M', 'R', 'S', 'V'},
'H': {'A', 'C', 'T', 'M', 'W', 'Y', 'H'},
'h': {'A', 'C', 'T', 'M', 'W', 'Y', 'H'},
'D': {'A', 'G', 'T', 'R', 'W', 'K', 'D'},
'd': {'A', 'G', 'T', 'R', 'W', 'K', 'D'},
'B': {'C', 'G', 'T', 'S', 'Y', 'K', 'B'},
'b': {'C', 'G', 'T', 'S', 'Y', 'K', 'B'},
'N': {'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'},
'n': {'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'},
}
// AmbCodes2Codes is code version of AmbBase2Bases
var AmbCodes2Codes = map[int][]int{
1: {1},
2: {2},
4: {4},
8: {8},
3: {1, 2, 3},
5: {1, 4, 5},
9: {1, 8, 9},
6: {2, 4, 6},
10: {2, 8, 10},
12: {4, 8, 12},
7: {1, 2, 4, 3, 5, 6, 7},
11: {1, 2, 8, 3, 9, 10, 11},
13: {1, 4, 8, 5, 9, 12, 13},
14: {2, 4, 8, 6, 10, 12, 14},
15: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15},
}
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