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fasta.go
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fasta.go
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// Package fasta implements data structures and functions for reading, writing, and manipulating sequences in FASTA format.
package fasta
import (
"bufio"
"bytes"
"io"
"math"
"math/rand"
)
const (
DefaultLineLength = 70
)
var dic []byte
// Sequence holds a nucleotide or protein sequence.
type Sequence struct {
header string
data []byte
lineLength int
}
// A Sequence is read using a Scanner.
type Scanner struct {
r *bufio.Reader
line []byte
err error
isHeader bool
lastSequence bool
previousHeader, currentHeader string
firstSequence bool
data []byte
}
func (s *Sequence) Header() string { return s.header }
func (s *Sequence) Data() []byte { return s.data }
func (s *Sequence) LineLength() int { return s.lineLength }
// SetHeader replaces the existing header.
func (s *Sequence) SetHeader(h string) {
s.header = h
}
// SetLineLength replaces the current line length. If the line length passed is less than 1, it is assumed that effectively infinite lines are requested.
func (s *Sequence) SetLineLength(l int) {
s.lineLength = l
if s.lineLength < 1 {
s.lineLength = math.MaxInt64
}
}
// AppendToHeader appends the suffix suf to the header.
func (s *Sequence) AppendToHeader(suf string) {
s.header = s.header + suf
}
// Equals compares two sequences and returns true if their headers and data are identical.
func (a *Sequence) Equals(b *Sequence) bool {
if a.header != b.header {
return false
}
if len(a.data) != len(b.data) {
return false
}
return bytes.Equal(a.data, b.data)
return true
}
// String wraps the sequence into lines at most lineLength characters long.
func (s *Sequence) String() string {
var b []byte
b = append(b, '>')
b = append(b, s.header...)
b = append(b, '\n')
var c int
for _, r := range s.data {
b = append(b, r)
c++
if c == s.lineLength {
c = 0
b = append(b, '\n')
}
}
if c == 0 && len(b) > 0 {
b = b[:len(b)-1]
}
if len(b) > 0 {
return string(b)
} else {
return ""
}
}
// Method Shuffle randomizes the residues in a Sequence. The sequence composition remains unchanged.
func (s *Sequence) Shuffle(r *rand.Rand) {
d := s.data
r.Shuffle(len(d), func(i, j int) {
d[i], d[j] = d[j], d[i]
})
}
// Method Reverse reverses the residues of a Sequence.
func (s *Sequence) Reverse() {
d := s.data
for i, j := 0, len(d)-1; i < j; i, j = i+1, j-1 {
d[i], d[j] = d[j], d[i]
}
}
// Complement complements nucleotide sequences.
func (s *Sequence) Complement() {
if dic == nil {
dic = make([]byte, 256)
f := []byte("ACGTUWSMKRYBDHVNacgtuwsmkrybdhvn")
r := []byte("TGCAAWSKMYRVHDBNtgcaawskmyrvhdbn")
for i, _ := range dic {
dic[i] = byte(i)
}
for i, v := range f {
dic[v] = r[i]
}
}
for i, v := range s.data {
s.data[i] = dic[v]
}
}
// ReverseComplement reverse-complements a Sequence.
func (s *Sequence) ReverseComplement() {
s.Reverse()
s.Complement()
}
// ScanLine reads input line by line. It skips empty lines and marks headers. The last call to ScanLine should be followed by a call to Flush to retrieve any bytes not terminated by newline.
func (s *Scanner) ScanLine() bool {
var err error
s.line, err = s.r.ReadBytes('\n')
if err != nil {
s.err = err
return false
}
s.line = bytes.TrimRight(s.line, "\r\n")
if len(s.line) > 0 {
if s.line[0] == '>' {
s.isHeader = true
} else {
s.isHeader = false
}
return true
}
s.err = nil
return true
}
func (s *Scanner) IsHeader() bool {
return s.isHeader
}
// Line returns the last non-empty line scanned.
func (s *Scanner) Line() []byte {
return s.line
}
// Flush returns any bytes remaining in the buffer after the last call to ScanLine.
func (s *Scanner) Flush() []byte {
var dum []byte
if s.err == io.EOF {
return s.line
}
return dum
}
// Sequence returns the last Sequence scanned.
func (s *Scanner) Sequence() *Sequence {
seq := &Sequence{
header: s.previousHeader,
}
seq.data = make([]byte, len(s.data))
copy(seq.data, s.data)
seq.lineLength = DefaultLineLength
s.data = s.data[:0]
return seq
}
// Function NewSequence returns a new Sequence.
func NewSequence(h string, d []byte) *Sequence {
s := new(Sequence)
s.header = h
s.data = make([]byte, len(d))
copy(s.data, d)
s.lineLength = DefaultLineLength
return s
}
// ScanSequence reads input Sequence by Sequence.
func (s *Scanner) ScanSequence() bool {
if s.lastSequence {
return false
}
for s.ScanLine() {
if s.isHeader {
s.previousHeader = s.currentHeader
s.currentHeader = string(s.Line()[1:])
if s.firstSequence {
s.firstSequence = false
} else {
return true
}
} else {
s.data = append(s.data, s.Line()...)
}
}
s.lastSequence = true
if s.err == io.EOF {
s.data = append(s.data, s.Line()...)
}
s.previousHeader = s.currentHeader
if !s.firstSequence {
return true
} else {
return false
}
}
// NewScanner returns a new Scanner to read from r.
func NewScanner(r io.Reader) *Scanner {
rd := bufio.NewReader(r)
scanner := Scanner{
r: rd,
firstSequence: true,
}
return &scanner
}