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sequence.go
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sequence.go
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package align
import (
"bytes"
"errors"
"fmt"
"math/rand"
"regexp"
"strings"
"unicode"
)
type Sequence interface {
Sequence() string
SequenceChar() []rune
CharAt(int) rune
Name() string
SetName(name string)
Comment() string
Length() int
LongestORF() (start, end int) // Detects the longest ORF in forward strand only
Reverse()
Complement() error // Returns an error if not nucleotide sequence
Translate(phase int) (Sequence, error) // Translates the sequence using the standard code
DetectAlphabet() int // Try to detect alphabet (nt or aa)
Clone() Sequence
}
type seq struct {
name string // Name of the sequence
sequence []rune // Sequence of nucleotides/aa
comment string // Comment if any
}
func NewSequence(name string, sequence []rune, comment string) *seq {
return &seq{
name,
sequence,
comment,
}
}
func (s *seq) Sequence() string {
return string(s.sequence)
}
func (s *seq) SequenceChar() []rune {
return s.sequence
}
func (s *seq) CharAt(i int) rune {
return s.sequence[i]
}
func (s *seq) Name() string {
return s.name
}
func (s *seq) SetName(name string) {
s.name = name
}
func (s *seq) Comment() string {
return s.comment
}
func (s *seq) Length() int {
return len(s.sequence)
}
// Detects the position of ATG giving the longest ORF
// Search is done in the forward strand only
//
// returns -1 is no ATG...STOP has been found
func (s *seq) LongestORF() (start, end int) {
start = -1
end = -1
re, _ := regexp.Compile("(ATG)(.{3})*?(TAA|TGA|TAG)")
//re.Longest()
idx := re.FindAllStringIndex(
strings.Replace(
strings.ToUpper(string(s.sequence)),
"U", "T", -1),
-1)
if idx != nil {
for _, pos := range idx {
if pos[1]-pos[0] > end-start {
end = pos[1]
start = pos[0]
}
}
}
return start, end
}
func RandomSequence(alphabet, length int) ([]rune, error) {
seq := make([]rune, length)
for i := 0; i < length; i++ {
switch alphabet {
case AMINOACIDS:
seq[i] = stdaminoacid[rand.Intn(len(stdaminoacid))]
case NUCLEOTIDS:
seq[i] = stdnucleotides[rand.Intn(len(stdnucleotides))]
default:
return nil, errors.New("Unexpected sequence alphabet type")
}
}
return seq, nil
}
// Reverses a sequence
func Reverse(seq []rune) {
for i, j := 0, len(seq)-1; i < j; i, j = i+1, j-1 {
seq[i], seq[j] = seq[j], seq[i]
}
}
// Reverse sequence order
func (s *seq) Reverse() {
Reverse(s.sequence)
}
// Complement sequence
func Complement(seq []rune) (err error) {
for i, n := range seq {
c, ok := complement_nuc_mapping[n]
if !ok {
err = fmt.Errorf("Character %c can not be complemented", n)
return
}
seq[i] = c
}
return
}
// Complement sequence
func (s *seq) Complement() error {
a := s.DetectAlphabet()
if a != NUCLEOTIDS && a != BOTH {
return fmt.Errorf("Wrong alphabet for Complementing sequence")
}
return Complement(s.sequence)
}
func (s *seq) DetectAlphabet() int {
isaa := true
isnt := true
for _, nt := range s.sequence {
nt = unicode.ToUpper(nt)
couldbent := false
couldbeaa := false
switch nt {
case 'A', 'C', 'B', 'R', 'G', '?', GAP, POINT, OTHER, 'D', 'K', 'S', 'H', 'M', 'N', 'V', 'X', 'T', 'W', 'Y':
couldbent = true
couldbeaa = true
case 'U', 'O':
couldbent = true
case 'Q', 'E', 'I', 'L', 'F', 'P', 'Z':
couldbeaa = true
}
isaa = isaa && couldbeaa
isnt = isnt && couldbent
}
if isnt && isaa {
return BOTH
} else if isnt {
return NUCLEOTIDS
} else if isaa {
return AMINOACIDS
} else {
return UNKNOWN
}
}
// Translates the given sequence start at nucleotide index "phase"
//
// If the sequence is not nucleotidic, then throws an error
// If sequence length is < 3+phase then thropws an error
func (s *seq) Translate(phase int) (tr Sequence, err error) {
var buffer bytes.Buffer
if s.DetectAlphabet() != NUCLEOTIDS && s.DetectAlphabet() != BOTH {
err = fmt.Errorf("Cannot translate this sequence, wrong alphabet")
return
}
if len(s.sequence) < 3+phase {
err = fmt.Errorf("Cannot translate a sequence with length < 3+phase (%s)", s.name)
return
}
for i := phase; i < len(s.sequence)-2; i += 3 {
codon := strings.Replace(strings.ToUpper(string(s.sequence[i:i+3])), "U", "T", -1)
aa, found := standardcode[codon]
if !found {
aa = 'X'
}
buffer.WriteRune(aa)
}
tr = NewSequence(s.name, []rune(buffer.String()), s.comment)
return
}
func (s *seq) Clone() Sequence {
seq2 := make([]rune, len(s.sequence))
copy(seq2, s.sequence)
return NewSequence(s.name, seq2, s.comment)
}