translate nucleic sequence in it's corresponding amino acid sequence
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0
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Goal of the program
The goal of the program is to translate a nucleic acid sequence into it's corresponding amino acid sequence. The nucleic sequences
have to be formatted in a specific format called fasta. There is an existing implementation of this program in C here: emboss transeq
Fasta format
A fasta file looks like this:
>sequenceId comment
nucleic sequence
for example:
>Seq1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
>Seq2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GGTAGGTACCGCCCTAAGNCTCCTAATCCGAGCAGAACTANGCCAACCCGGAGCCCTTCTGGGAGACGAC
AATCAACATAAAA
A nucleic sequence is a string composed of the letters A, C, T, G, U, N
Expected output
A combinaison of 3 nucleic acid, named codon, gives a specif amino acid, for exemple GCT is the code for Alanine, symbolised by the letter A
With the Seq1 define above:
codon CCT TTA TCT AAT CTT TGG AGC ATG ...
amino acid P L S N L W S M ...
The expected output is:
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
Specific rules
The program takes 4 parameters:
clean: if true, write STOP codon asXinstead of*
trim: if true, remove allXand*chars from the right end of the amino - acid sequence
alternative: different way to compute reverse frame
frame: a string value in["1", "2", "3", "F", "-1", "-2", "-3", "R", "6" ]
The frame define the position in the nucleic sequence to start from:
-frame 1
|-frame 2
||-frame 3
|||
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
|||
||-frame -1
|-frame -2
-frame -3
frame "F" = "1", "2", "3"
frame "R" = "-1", "-2", "-3"
frame "6" = "1", "2", "3", "-1", "-2", "-3"
In the output file, we add the frame used to the sequenceId: sequenceId = sequenceId_frame
For example if the program is used with frame=6, the expected output is
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq1_2 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
LYLIFGA*AGIVGTALSLLIRAEPSPVPTPLLILRPSRSLYPHFT
>Seq1_3 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
FI*SLEHELA*LEPPSASSSVQNPVLYQHLF*FFGHPEVYILILX
>Seq1_4 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
VK*GYRLLDGRRIRRGVGTGLGSARMRRLRAVPTMPAHAPKIR*R
>Seq1_5 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
KMRI*TSGWPKNQKRCWYRTGFCTDEEAEGGSNYASSCSKD*IKX
>Seq1_6 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
*NEDIDFWMAEESEEVLVQDWVLHG*GG*GRFQLCQLMLQRLDKG
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
>Seq2_2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
VGTALXLLIRAELXQPGALLGDDNQHKX
>Seq2_3 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
*VPP*XS*SEQNXANPEPFWETTINIK
>Seq2_4 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
LC*LSSPRRAPGWXSSARIRXLRAVPT
>Seq2_5 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FMLIVVSQKGSGLA*FCSD*EX*GGTYX
>Seq2_6 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FYVDCRLPEGLRVGXVLLGLGXLGRYLP
Improvements
- Is the code easy to read / understand ?
- Is the code idiomatic ?
- Any other improvements (performance, doc...)
( full project with tests + flags handling is avaible on github: gotranseq)
code :
package transeq
import (
"bufio"
"bytes"
"context"
"encoding/binary"
"fmt"
"io"
"runtime"
"sync"
)
var (
letterCode = map[byte]uint8{
'A': aCode,
'C': cCode,
'T': tCode,
'G': gCode,
'N': nCode,
'U': uCode,
}
standard = map[string]byte{
"TTT": 'F',
"TCT": 'S',
"TAT": 'Y',
"TGT": 'C',
"TTC": 'F',
"TCC": 'S',
"TAC": 'Y',
"TGC": 'C',
"TTA": 'L',
"TCA": 'S',
"TAA": '*',
"TGA": '*',
"TTG": 'L',
"TCG": 'S',
"TAG": '*',
"TGG": 'W',
"CTT": 'L',
"CCT": 'P',
"CAT": 'H',
"CGT": 'R',
"CTC": 'L',
"CCC": 'P',
"CAC": 'H',
"CGC": 'R',
"CTA": 'L',
"CCA": 'P',
"CAA": 'Q',
"CGA": 'R',
"CTG": 'L',
"CCG": 'P',
"CAG": 'Q',
"CGG": 'R',
"ATT": 'I',
"ACT": 'T',
"AAT": 'N',
"AGT": 'S',
"ATC": 'I',
"ACC": 'T',
"AAC": 'N',
"AGC": 'S',
"ATA": 'I',
"ACA": 'T',
"AAA": 'K',
"AGA": 'R',
"ATG": 'M',
"ACG": 'T',
"AAG": 'K',
"AGG": 'R',
"GTT": 'V',
"GCT": 'A',
"GAT": 'D',
"GGT": 'G',
"GTC": 'V',
"GCC": 'A',
"GAC": 'D',
"GGC": 'G',
"GTA": 'V',
"GCA": 'A',
"GAA": 'E',
"GGA": 'G',
"GTG": 'V',
"GCG": 'A',
"GAG": 'E',
"GGG": 'G',
}
)
const (
nCode = uint8(0)
aCode = uint8(1)
cCode = uint8(2)
tCode = uint8(3)
uCode = uint8(3)
gCode = uint8(4)
stopByte = '*'
unknown = 'X'
// Length of the array to store code/bytes
// uses gCode because it's the biggest uint8 of all codes
arrayCodeSize = (uint32(gCode) | uint32(gCode)<<8 | uint32(gCode)<<16) + 1
)
func createCodeArray(clean bool) byte {
resultMap := map[uint32]byte{}
twoLetterMap := map[string]byte{}
tmpCode := make(uint8, 4)
for codon, aaCode := range standard {
// generate 3 letter code
for i := 0; i < 3; i++ {
tmpCode[i] = letterCode[codon[i]]
}
// each codon is represented by an unique uint32:
// each possible nucleotide is represented by an uint8 (255 possibility)
// the three first bytes are the the code for each nucleotide
// last byte is unused ( eq to uint8(0) )
// example:
// codon 'ACG' ==> uint32(aCode) | uint32(cCode)<<8 | uint32(gCode)<<16
uint32Code := uint32(tmpCode[0]) | uint32(tmpCode[1])<<8 | uint32(tmpCode[2])<<16
resultMap[uint32Code] = aaCode
// generate 2 letter code
codes, ok := twoLetterMap[codon[0:2]]
if !ok {
twoLetterMap[codon[0:2]] = byte{aaCode}
} else {
twoLetterMap[codon[0:2]] = append(codes, aaCode)
}
}
for twoLetterCodon, codes := range twoLetterMap {
uniqueAA := true
for i := 0; i < len(codes); i++ {
if codes[i] != codes[0] {
uniqueAA = false
}
}
if uniqueAA {
first := letterCode[twoLetterCodon[0]]
second := letterCode[twoLetterCodon[1]]
uint32Code := uint32(first) | uint32(second)<<8
resultMap[uint32Code] = codes[0]
}
}
// if clean is specified, we want to replace all '*' by 'X' in the output
// sequence, so replace all occurrences of '*' directly in the ref map
if clean {
for k, v := range resultMap {
if v == stopByte {
resultMap[k] = unknown
}
}
}
r := make(byte, arrayCodeSize)
for k, v := range resultMap {
r[k] = v
}
return r
}
func computeFrames(frameName string) (frames int, reverse bool, err error) {
frames = make(int, 6)
reverse = false
switch frameName {
case "1":
frames[0] = 1
case "2":
frames[1] = 1
case "3":
frames[2] = 1
case "F":
for i := 0; i < 3; i++ {
frames[i] = 1
}
case "-1":
frames[3] = 1
reverse = true
case "-2":
frames[4] = 1
reverse = true
case "-3":
frames[5] = 1
reverse = true
case "R":
for i := 3; i < 6; i++ {
frames[i] = 1
}
reverse = true
case "6":
for i := range frames {
frames[i] = 1
}
reverse = true
default:
err = fmt.Errorf("wrong value for -f | --frame parameter: %s", frameName)
}
return frames, reverse, err
}
type writer struct {
buf *bytes.Buffer
currentLineLen int
bytesToTrim int
}
func (w *writer) addByte(b byte) {
w.buf.WriteByte(b)
w.currentLineLen++
if b == stopByte || b == unknown {
w.bytesToTrim++
} else {
w.bytesToTrim = 0
}
}
func (w *writer) addUnknown() {
w.buf.WriteByte(unknown)
w.currentLineLen++
w.bytesToTrim++
}
func (w *writer) newLine() {
w.buf.WriteByte('n')
w.currentLineLen = 0
w.bytesToTrim++
}
const (
// size of the buffer for writing to file
maxBufferSize = 1024 * 1024 * 30
// max line size for sequence
maxLineSize = 60
// suffixes ta add to sequence id for each frame
suffixes = "123456"
)
// Translate read a fata file, translate each sequence to the corresponding prot sequence in the specified frame
func Translate(inputSequence io.Reader, out io.Writer, frame string, clean, trim, alternative bool) error {
arrayCode := createCodeArray(clean)
framesToGenerate, reverse, err := computeFrames(frame)
if err != nil {
return err
}
fnaSequences := make(chan encodedSequence, 10)
errs := make(chan error, 1)
var wg sync.WaitGroup
ctx, cancel := context.WithCancel(context.Background())
defer cancel()
for nWorker := 0; nWorker < runtime.NumCPU(); nWorker++ {
wg.Add(1)
go func() {
defer wg.Done()
startPosition := make(int, 3)
w := &writer{
buf: bytes.NewBuffer(nil),
bytesToTrim: 0,
currentLineLen: 0,
}
for sequence := range fnaSequences {
select {
case <-ctx.Done():
return
default:
}
frameIndex := 0
startPosition[0], startPosition[1], startPosition[2] = 0, 1, 2
idSize := int(binary.LittleEndian.Uint32(sequence[0:4]))
nuclSeqLength := len(sequence) - idSize
Translate:
for _, startPos := range startPosition {
if framesToGenerate[frameIndex] == 0 {
frameIndex++
continue
}
// sequence id should look like
// >sequenceID_<frame> comment
idEnd := bytes.IndexByte(sequence[4:idSize], ' ')
if idEnd != -1 {
w.buf.Write(sequence[4 : 4+idEnd])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
w.buf.Write(sequence[4+idEnd : idSize])
} else {
w.buf.Write(sequence[4:idSize])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
}
w.newLine()
// if in trim mode, nb of bytes to trim (nb of successive 'X', '*' and 'n'
// from right end of the sequence)
w.bytesToTrim = 0
w.currentLineLen = 0
// read the sequence 3 letters at a time, starting at a specific position
// corresponding to the frame
for pos := startPos + 2 + idSize; pos < len(sequence); pos += 3 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
// create an uint32 from the codon, to retrieve the corresponding
// AA from the map
codonCode := uint32(sequence[pos-2]) | uint32(sequence[pos-1])<<8 | uint32(sequence[pos])<<16
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 2 nucleotid long, try to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 2 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
codonCode := uint32(sequence[len(sequence)-2]) | uint32(sequence[len(sequence)-1])<<8
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 1 nucleotid long, no way to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 1 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
w.addUnknown()
}
if trim && w.bytesToTrim > 0 {
// remove the last bytesToTrim bytes of the buffer
// as they are 'X', '*' or 'n'
w.buf.Truncate(w.buf.Len() - w.bytesToTrim)
w.currentLineLen -= w.bytesToTrim
}
if w.currentLineLen != 0 {
w.newLine()
}
frameIndex++
}
if reverse && frameIndex < 6 {
// get the complementary sequence.
// Basically, switch
// A <-> T
// C <-> G
// N is not modified
for i, n := range sequence[idSize:] {
switch n {
case aCode:
sequence[i+idSize] = tCode
case tCode:
// handle both tCode and uCode
sequence[i+idSize] = aCode
case cCode:
sequence[i+idSize] = gCode
case gCode:
sequence[i+idSize] = cCode
default:
//case N -> leave it
}
}
// reverse the sequence
for i, j := idSize, len(sequence)-1; i < j; i, j = i+1, j-1 {
sequence[i], sequence[j] = sequence[j], sequence[i]
}
if !alternative {
// Staden convention: Frame -1 is the reverse-complement of the sequence
// having the same codon phase as frame 1. Frame -2 is the same phase as
// frame 2. Frame -3 is the same phase as frame 3
//
// use the matrix to keep track of the forward frame as it depends on the
// length of the sequence
switch nuclSeqLength % 3 {
case 0:
startPosition[0], startPosition[1], startPosition[2] = 0, 2, 1
case 1:
startPosition[0], startPosition[1], startPosition[2] = 1, 0, 2
case 2:
startPosition[0], startPosition[1], startPosition[2] = 2, 1, 0
}
}
// run the same loop, but with the reverse-complemented sequence
goto Translate
}
if w.buf.Len() > maxBufferSize {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
w.buf.Reset()
}
pool.Put(sequence)
}
if w.buf.Len() > 0 {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
}
}()
}
readSequenceFromFasta(ctx, inputSequence, fnaSequences)
wg.Wait()
select {
case err, ok := <-errs:
if ok {
return err
}
default:
}
return nil
}
func readSequenceFromFasta(ctx context.Context, inputSequence io.Reader, fnaSequences chan encodedSequence) {
feeder := &fastaChannelFeeder{
idBuffer: bytes.NewBuffer(nil),
commentBuffer: bytes.NewBuffer(nil),
sequenceBuffer: bytes.NewBuffer(nil),
fastaChan: fnaSequences,
}
// fasta format is:
//
// >sequenceID some comments on sequence
// ACAGGCAGAGACACGACAGACGACGACACAGGAGCAGACAGCAGCAGACGACCACATATT
// TTTGCGGTCACATGACGACTTCGGCAGCGA
//
// see https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp
// section 1 for details
scanner := bufio.NewScanner(inputSequence)
Loop:
for scanner.Scan() {
line := scanner.Bytes()
if len(line) == 0 {
continue
}
if line[0] == '>' {
if feeder.idBuffer.Len() > 0 {
select {
case <-ctx.Done():
break Loop
default:
}
feeder.sendFasta()
}
feeder.reset()
// parse the ID of the sequence. ID is formatted like this:
// >sequenceID comments
seqID := bytes.SplitN(line, byte{' '}, 2)
feeder.idBuffer.Write(seqID[0])
if len(seqID) > 1 {
feeder.commentBuffer.WriteByte(' ')
feeder.commentBuffer.Write(seqID[1])
}
} else {
// if the line doesn't start with '>', then it's a part of the
// nucleotide sequence, so write it to the buffer
feeder.sequenceBuffer.Write(line)
}
}
// don't forget to push last sequence
select {
case <-ctx.Done():
default:
feeder.sendFasta()
}
close(fnaSequences)
}
// a type to hold an encoded fasta sequence
//
// s[0:4] stores the size of the sequence id + the size of the comment as an uint32 (little endian)
// s[4:idSize] stores the sequence id, and the comment id there is one
// s[idSize:] stores the nucl sequence
type encodedSequence byte
var pool = sync.Pool{
New: func() interface{} {
return make(encodedSequence, 512)
},
}
func getSizedSlice(idSize, requiredSize int) encodedSequence {
s := pool.Get().(encodedSequence)
binary.LittleEndian.PutUint32(s[0:4], uint32(idSize))
for len(s) < requiredSize {
s = append(s, byte(0))
}
return s[0:requiredSize]
}
func (f *fastaChannelFeeder) sendFasta() {
idSize := 4 + f.idBuffer.Len() + f.commentBuffer.Len()
requiredSize := idSize + f.sequenceBuffer.Len()
s := getSizedSlice(idSize, requiredSize)
if f.commentBuffer.Len() > 0 {
copy(s[idSize-f.commentBuffer.Len():idSize], f.commentBuffer.Bytes())
}
copy(s[4:4+f.idBuffer.Len()], f.idBuffer.Bytes())
// convert the sequence of bytes to an array of uint8 codes,
// so a codon (3 nucleotides | 3 bytes ) can be represented
// as an uint32
for i, b := range f.sequenceBuffer.Bytes() {
switch b {
case 'A':
s[i+idSize] = aCode
case 'C':
s[i+idSize] = cCode
case 'G':
s[i+idSize] = gCode
case 'T', 'U':
s[i+idSize] = tCode
case 'N':
s[i+idSize] = nCode
default:
fmt.Printf("WARNING: invalid char in sequence %s: %s, ignoring", s[4:4+idSize], string(b))
}
}
f.fastaChan <- s
}
type fastaChannelFeeder struct {
idBuffer, commentBuffer, sequenceBuffer *bytes.Buffer
fastaChan chan encodedSequence
}
func (f *fastaChannelFeeder) reset() {
f.idBuffer.Reset()
f.sequenceBuffer.Reset()
f.commentBuffer.Reset()
}
performance go bioinformatics multiprocessing
asked 11 mins ago
felix
69839
add a comment |
up vote
0
down vote
favorite
Goal of the program
The goal of the program is to translate a nucleic acid sequence into it's corresponding amino acid sequence. The nucleic sequences
have to be formatted in a specific format called fasta. There is an existing implementation of this program in C here: emboss transeq
Fasta format
A fasta file looks like this:
>sequenceId comment
nucleic sequence
for example:
>Seq1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
>Seq2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GGTAGGTACCGCCCTAAGNCTCCTAATCCGAGCAGAACTANGCCAACCCGGAGCCCTTCTGGGAGACGAC
AATCAACATAAAA
A nucleic sequence is a string composed of the letters A, C, T, G, U, N
Expected output
A combinaison of 3 nucleic acid, named codon, gives a specif amino acid, for exemple GCT is the code for Alanine, symbolised by the letter A
With the Seq1 define above:
codon CCT TTA TCT AAT CTT TGG AGC ATG ...
amino acid P L S N L W S M ...
The expected output is:
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
Specific rules
The program takes 4 parameters:
clean: if true, write STOP codon asXinstead of*
trim: if true, remove allXand*chars from the right end of the amino - acid sequence
alternative: different way to compute reverse frame
frame: a string value in["1", "2", "3", "F", "-1", "-2", "-3", "R", "6" ]
The frame define the position in the nucleic sequence to start from:
-frame 1
|-frame 2
||-frame 3
|||
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
|||
||-frame -1
|-frame -2
-frame -3
frame "F" = "1", "2", "3"
frame "R" = "-1", "-2", "-3"
frame "6" = "1", "2", "3", "-1", "-2", "-3"
In the output file, we add the frame used to the sequenceId: sequenceId = sequenceId_frame
For example if the program is used with frame=6, the expected output is
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq1_2 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
LYLIFGA*AGIVGTALSLLIRAEPSPVPTPLLILRPSRSLYPHFT
>Seq1_3 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
FI*SLEHELA*LEPPSASSSVQNPVLYQHLF*FFGHPEVYILILX
>Seq1_4 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
VK*GYRLLDGRRIRRGVGTGLGSARMRRLRAVPTMPAHAPKIR*R
>Seq1_5 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
KMRI*TSGWPKNQKRCWYRTGFCTDEEAEGGSNYASSCSKD*IKX
>Seq1_6 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
*NEDIDFWMAEESEEVLVQDWVLHG*GG*GRFQLCQLMLQRLDKG
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
>Seq2_2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
VGTALXLLIRAELXQPGALLGDDNQHKX
>Seq2_3 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
*VPP*XS*SEQNXANPEPFWETTINIK
>Seq2_4 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
LC*LSSPRRAPGWXSSARIRXLRAVPT
>Seq2_5 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FMLIVVSQKGSGLA*FCSD*EX*GGTYX
>Seq2_6 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FYVDCRLPEGLRVGXVLLGLGXLGRYLP
Improvements
- Is the code easy to read / understand ?
- Is the code idiomatic ?
- Any other improvements (performance, doc...)
( full project with tests + flags handling is avaible on github: gotranseq)
code :
package transeq
import (
"bufio"
"bytes"
"context"
"encoding/binary"
"fmt"
"io"
"runtime"
"sync"
)
var (
letterCode = map[byte]uint8{
'A': aCode,
'C': cCode,
'T': tCode,
'G': gCode,
'N': nCode,
'U': uCode,
}
standard = map[string]byte{
"TTT": 'F',
"TCT": 'S',
"TAT": 'Y',
"TGT": 'C',
"TTC": 'F',
"TCC": 'S',
"TAC": 'Y',
"TGC": 'C',
"TTA": 'L',
"TCA": 'S',
"TAA": '*',
"TGA": '*',
"TTG": 'L',
"TCG": 'S',
"TAG": '*',
"TGG": 'W',
"CTT": 'L',
"CCT": 'P',
"CAT": 'H',
"CGT": 'R',
"CTC": 'L',
"CCC": 'P',
"CAC": 'H',
"CGC": 'R',
"CTA": 'L',
"CCA": 'P',
"CAA": 'Q',
"CGA": 'R',
"CTG": 'L',
"CCG": 'P',
"CAG": 'Q',
"CGG": 'R',
"ATT": 'I',
"ACT": 'T',
"AAT": 'N',
"AGT": 'S',
"ATC": 'I',
"ACC": 'T',
"AAC": 'N',
"AGC": 'S',
"ATA": 'I',
"ACA": 'T',
"AAA": 'K',
"AGA": 'R',
"ATG": 'M',
"ACG": 'T',
"AAG": 'K',
"AGG": 'R',
"GTT": 'V',
"GCT": 'A',
"GAT": 'D',
"GGT": 'G',
"GTC": 'V',
"GCC": 'A',
"GAC": 'D',
"GGC": 'G',
"GTA": 'V',
"GCA": 'A',
"GAA": 'E',
"GGA": 'G',
"GTG": 'V',
"GCG": 'A',
"GAG": 'E',
"GGG": 'G',
}
)
const (
nCode = uint8(0)
aCode = uint8(1)
cCode = uint8(2)
tCode = uint8(3)
uCode = uint8(3)
gCode = uint8(4)
stopByte = '*'
unknown = 'X'
// Length of the array to store code/bytes
// uses gCode because it's the biggest uint8 of all codes
arrayCodeSize = (uint32(gCode) | uint32(gCode)<<8 | uint32(gCode)<<16) + 1
)
func createCodeArray(clean bool) byte {
resultMap := map[uint32]byte{}
twoLetterMap := map[string]byte{}
tmpCode := make(uint8, 4)
for codon, aaCode := range standard {
// generate 3 letter code
for i := 0; i < 3; i++ {
tmpCode[i] = letterCode[codon[i]]
}
// each codon is represented by an unique uint32:
// each possible nucleotide is represented by an uint8 (255 possibility)
// the three first bytes are the the code for each nucleotide
// last byte is unused ( eq to uint8(0) )
// example:
// codon 'ACG' ==> uint32(aCode) | uint32(cCode)<<8 | uint32(gCode)<<16
uint32Code := uint32(tmpCode[0]) | uint32(tmpCode[1])<<8 | uint32(tmpCode[2])<<16
resultMap[uint32Code] = aaCode
// generate 2 letter code
codes, ok := twoLetterMap[codon[0:2]]
if !ok {
twoLetterMap[codon[0:2]] = byte{aaCode}
} else {
twoLetterMap[codon[0:2]] = append(codes, aaCode)
}
}
for twoLetterCodon, codes := range twoLetterMap {
uniqueAA := true
for i := 0; i < len(codes); i++ {
if codes[i] != codes[0] {
uniqueAA = false
}
}
if uniqueAA {
first := letterCode[twoLetterCodon[0]]
second := letterCode[twoLetterCodon[1]]
uint32Code := uint32(first) | uint32(second)<<8
resultMap[uint32Code] = codes[0]
}
}
// if clean is specified, we want to replace all '*' by 'X' in the output
// sequence, so replace all occurrences of '*' directly in the ref map
if clean {
for k, v := range resultMap {
if v == stopByte {
resultMap[k] = unknown
}
}
}
r := make(byte, arrayCodeSize)
for k, v := range resultMap {
r[k] = v
}
return r
}
func computeFrames(frameName string) (frames int, reverse bool, err error) {
frames = make(int, 6)
reverse = false
switch frameName {
case "1":
frames[0] = 1
case "2":
frames[1] = 1
case "3":
frames[2] = 1
case "F":
for i := 0; i < 3; i++ {
frames[i] = 1
}
case "-1":
frames[3] = 1
reverse = true
case "-2":
frames[4] = 1
reverse = true
case "-3":
frames[5] = 1
reverse = true
case "R":
for i := 3; i < 6; i++ {
frames[i] = 1
}
reverse = true
case "6":
for i := range frames {
frames[i] = 1
}
reverse = true
default:
err = fmt.Errorf("wrong value for -f | --frame parameter: %s", frameName)
}
return frames, reverse, err
}
type writer struct {
buf *bytes.Buffer
currentLineLen int
bytesToTrim int
}
func (w *writer) addByte(b byte) {
w.buf.WriteByte(b)
w.currentLineLen++
if b == stopByte || b == unknown {
w.bytesToTrim++
} else {
w.bytesToTrim = 0
}
}
func (w *writer) addUnknown() {
w.buf.WriteByte(unknown)
w.currentLineLen++
w.bytesToTrim++
}
func (w *writer) newLine() {
w.buf.WriteByte('n')
w.currentLineLen = 0
w.bytesToTrim++
}
const (
// size of the buffer for writing to file
maxBufferSize = 1024 * 1024 * 30
// max line size for sequence
maxLineSize = 60
// suffixes ta add to sequence id for each frame
suffixes = "123456"
)
// Translate read a fata file, translate each sequence to the corresponding prot sequence in the specified frame
func Translate(inputSequence io.Reader, out io.Writer, frame string, clean, trim, alternative bool) error {
arrayCode := createCodeArray(clean)
framesToGenerate, reverse, err := computeFrames(frame)
if err != nil {
return err
}
fnaSequences := make(chan encodedSequence, 10)
errs := make(chan error, 1)
var wg sync.WaitGroup
ctx, cancel := context.WithCancel(context.Background())
defer cancel()
for nWorker := 0; nWorker < runtime.NumCPU(); nWorker++ {
wg.Add(1)
go func() {
defer wg.Done()
startPosition := make(int, 3)
w := &writer{
buf: bytes.NewBuffer(nil),
bytesToTrim: 0,
currentLineLen: 0,
}
for sequence := range fnaSequences {
select {
case <-ctx.Done():
return
default:
}
frameIndex := 0
startPosition[0], startPosition[1], startPosition[2] = 0, 1, 2
idSize := int(binary.LittleEndian.Uint32(sequence[0:4]))
nuclSeqLength := len(sequence) - idSize
Translate:
for _, startPos := range startPosition {
if framesToGenerate[frameIndex] == 0 {
frameIndex++
continue
}
// sequence id should look like
// >sequenceID_<frame> comment
idEnd := bytes.IndexByte(sequence[4:idSize], ' ')
if idEnd != -1 {
w.buf.Write(sequence[4 : 4+idEnd])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
w.buf.Write(sequence[4+idEnd : idSize])
} else {
w.buf.Write(sequence[4:idSize])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
}
w.newLine()
// if in trim mode, nb of bytes to trim (nb of successive 'X', '*' and 'n'
// from right end of the sequence)
w.bytesToTrim = 0
w.currentLineLen = 0
// read the sequence 3 letters at a time, starting at a specific position
// corresponding to the frame
for pos := startPos + 2 + idSize; pos < len(sequence); pos += 3 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
// create an uint32 from the codon, to retrieve the corresponding
// AA from the map
codonCode := uint32(sequence[pos-2]) | uint32(sequence[pos-1])<<8 | uint32(sequence[pos])<<16
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 2 nucleotid long, try to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 2 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
codonCode := uint32(sequence[len(sequence)-2]) | uint32(sequence[len(sequence)-1])<<8
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 1 nucleotid long, no way to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 1 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
w.addUnknown()
}
if trim && w.bytesToTrim > 0 {
// remove the last bytesToTrim bytes of the buffer
// as they are 'X', '*' or 'n'
w.buf.Truncate(w.buf.Len() - w.bytesToTrim)
w.currentLineLen -= w.bytesToTrim
}
if w.currentLineLen != 0 {
w.newLine()
}
frameIndex++
}
if reverse && frameIndex < 6 {
// get the complementary sequence.
// Basically, switch
// A <-> T
// C <-> G
// N is not modified
for i, n := range sequence[idSize:] {
switch n {
case aCode:
sequence[i+idSize] = tCode
case tCode:
// handle both tCode and uCode
sequence[i+idSize] = aCode
case cCode:
sequence[i+idSize] = gCode
case gCode:
sequence[i+idSize] = cCode
default:
//case N -> leave it
}
}
// reverse the sequence
for i, j := idSize, len(sequence)-1; i < j; i, j = i+1, j-1 {
sequence[i], sequence[j] = sequence[j], sequence[i]
}
if !alternative {
// Staden convention: Frame -1 is the reverse-complement of the sequence
// having the same codon phase as frame 1. Frame -2 is the same phase as
// frame 2. Frame -3 is the same phase as frame 3
//
// use the matrix to keep track of the forward frame as it depends on the
// length of the sequence
switch nuclSeqLength % 3 {
case 0:
startPosition[0], startPosition[1], startPosition[2] = 0, 2, 1
case 1:
startPosition[0], startPosition[1], startPosition[2] = 1, 0, 2
case 2:
startPosition[0], startPosition[1], startPosition[2] = 2, 1, 0
}
}
// run the same loop, but with the reverse-complemented sequence
goto Translate
}
if w.buf.Len() > maxBufferSize {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
w.buf.Reset()
}
pool.Put(sequence)
}
if w.buf.Len() > 0 {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
}
}()
}
readSequenceFromFasta(ctx, inputSequence, fnaSequences)
wg.Wait()
select {
case err, ok := <-errs:
if ok {
return err
}
default:
}
return nil
}
func readSequenceFromFasta(ctx context.Context, inputSequence io.Reader, fnaSequences chan encodedSequence) {
feeder := &fastaChannelFeeder{
idBuffer: bytes.NewBuffer(nil),
commentBuffer: bytes.NewBuffer(nil),
sequenceBuffer: bytes.NewBuffer(nil),
fastaChan: fnaSequences,
}
// fasta format is:
//
// >sequenceID some comments on sequence
// ACAGGCAGAGACACGACAGACGACGACACAGGAGCAGACAGCAGCAGACGACCACATATT
// TTTGCGGTCACATGACGACTTCGGCAGCGA
//
// see https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp
// section 1 for details
scanner := bufio.NewScanner(inputSequence)
Loop:
for scanner.Scan() {
line := scanner.Bytes()
if len(line) == 0 {
continue
}
if line[0] == '>' {
if feeder.idBuffer.Len() > 0 {
select {
case <-ctx.Done():
break Loop
default:
}
feeder.sendFasta()
}
feeder.reset()
// parse the ID of the sequence. ID is formatted like this:
// >sequenceID comments
seqID := bytes.SplitN(line, byte{' '}, 2)
feeder.idBuffer.Write(seqID[0])
if len(seqID) > 1 {
feeder.commentBuffer.WriteByte(' ')
feeder.commentBuffer.Write(seqID[1])
}
} else {
// if the line doesn't start with '>', then it's a part of the
// nucleotide sequence, so write it to the buffer
feeder.sequenceBuffer.Write(line)
}
}
// don't forget to push last sequence
select {
case <-ctx.Done():
default:
feeder.sendFasta()
}
close(fnaSequences)
}
// a type to hold an encoded fasta sequence
//
// s[0:4] stores the size of the sequence id + the size of the comment as an uint32 (little endian)
// s[4:idSize] stores the sequence id, and the comment id there is one
// s[idSize:] stores the nucl sequence
type encodedSequence byte
var pool = sync.Pool{
New: func() interface{} {
return make(encodedSequence, 512)
},
}
func getSizedSlice(idSize, requiredSize int) encodedSequence {
s := pool.Get().(encodedSequence)
binary.LittleEndian.PutUint32(s[0:4], uint32(idSize))
for len(s) < requiredSize {
s = append(s, byte(0))
}
return s[0:requiredSize]
}
func (f *fastaChannelFeeder) sendFasta() {
idSize := 4 + f.idBuffer.Len() + f.commentBuffer.Len()
requiredSize := idSize + f.sequenceBuffer.Len()
s := getSizedSlice(idSize, requiredSize)
if f.commentBuffer.Len() > 0 {
copy(s[idSize-f.commentBuffer.Len():idSize], f.commentBuffer.Bytes())
}
copy(s[4:4+f.idBuffer.Len()], f.idBuffer.Bytes())
// convert the sequence of bytes to an array of uint8 codes,
// so a codon (3 nucleotides | 3 bytes ) can be represented
// as an uint32
for i, b := range f.sequenceBuffer.Bytes() {
switch b {
case 'A':
s[i+idSize] = aCode
case 'C':
s[i+idSize] = cCode
case 'G':
s[i+idSize] = gCode
case 'T', 'U':
s[i+idSize] = tCode
case 'N':
s[i+idSize] = nCode
default:
fmt.Printf("WARNING: invalid char in sequence %s: %s, ignoring", s[4:4+idSize], string(b))
}
}
f.fastaChan <- s
}
type fastaChannelFeeder struct {
idBuffer, commentBuffer, sequenceBuffer *bytes.Buffer
fastaChan chan encodedSequence
}
func (f *fastaChannelFeeder) reset() {
f.idBuffer.Reset()
f.sequenceBuffer.Reset()
f.commentBuffer.Reset()
}
performance go bioinformatics multiprocessing
asked 11 mins ago
felix
69839
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Goal of the program
The goal of the program is to translate a nucleic acid sequence into it's corresponding amino acid sequence. The nucleic sequences
have to be formatted in a specific format called fasta. There is an existing implementation of this program in C here: emboss transeq
Fasta format
A fasta file looks like this:
>sequenceId comment
nucleic sequence
for example:
>Seq1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
>Seq2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GGTAGGTACCGCCCTAAGNCTCCTAATCCGAGCAGAACTANGCCAACCCGGAGCCCTTCTGGGAGACGAC
AATCAACATAAAA
A nucleic sequence is a string composed of the letters A, C, T, G, U, N
Expected output
A combinaison of 3 nucleic acid, named codon, gives a specif amino acid, for exemple GCT is the code for Alanine, symbolised by the letter A
With the Seq1 define above:
codon CCT TTA TCT AAT CTT TGG AGC ATG ...
amino acid P L S N L W S M ...
The expected output is:
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
Specific rules
The program takes 4 parameters:
clean: if true, write STOP codon asXinstead of*
trim: if true, remove allXand*chars from the right end of the amino - acid sequence
alternative: different way to compute reverse frame
frame: a string value in["1", "2", "3", "F", "-1", "-2", "-3", "R", "6" ]
The frame define the position in the nucleic sequence to start from:
-frame 1
|-frame 2
||-frame 3
|||
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
|||
||-frame -1
|-frame -2
-frame -3
frame "F" = "1", "2", "3"
frame "R" = "-1", "-2", "-3"
frame "6" = "1", "2", "3", "-1", "-2", "-3"
In the output file, we add the frame used to the sequenceId: sequenceId = sequenceId_frame
For example if the program is used with frame=6, the expected output is
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq1_2 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
LYLIFGA*AGIVGTALSLLIRAEPSPVPTPLLILRPSRSLYPHFT
>Seq1_3 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
FI*SLEHELA*LEPPSASSSVQNPVLYQHLF*FFGHPEVYILILX
>Seq1_4 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
VK*GYRLLDGRRIRRGVGTGLGSARMRRLRAVPTMPAHAPKIR*R
>Seq1_5 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
KMRI*TSGWPKNQKRCWYRTGFCTDEEAEGGSNYASSCSKD*IKX
>Seq1_6 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
*NEDIDFWMAEESEEVLVQDWVLHG*GG*GRFQLCQLMLQRLDKG
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
>Seq2_2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
VGTALXLLIRAELXQPGALLGDDNQHKX
>Seq2_3 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
*VPP*XS*SEQNXANPEPFWETTINIK
>Seq2_4 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
LC*LSSPRRAPGWXSSARIRXLRAVPT
>Seq2_5 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FMLIVVSQKGSGLA*FCSD*EX*GGTYX
>Seq2_6 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FYVDCRLPEGLRVGXVLLGLGXLGRYLP
Improvements
- Is the code easy to read / understand ?
- Is the code idiomatic ?
- Any other improvements (performance, doc...)
( full project with tests + flags handling is avaible on github: gotranseq)
code :
package transeq
import (
"bufio"
"bytes"
"context"
"encoding/binary"
"fmt"
"io"
"runtime"
"sync"
)
var (
letterCode = map[byte]uint8{
'A': aCode,
'C': cCode,
'T': tCode,
'G': gCode,
'N': nCode,
'U': uCode,
}
standard = map[string]byte{
"TTT": 'F',
"TCT": 'S',
"TAT": 'Y',
"TGT": 'C',
"TTC": 'F',
"TCC": 'S',
"TAC": 'Y',
"TGC": 'C',
"TTA": 'L',
"TCA": 'S',
"TAA": '*',
"TGA": '*',
"TTG": 'L',
"TCG": 'S',
"TAG": '*',
"TGG": 'W',
"CTT": 'L',
"CCT": 'P',
"CAT": 'H',
"CGT": 'R',
"CTC": 'L',
"CCC": 'P',
"CAC": 'H',
"CGC": 'R',
"CTA": 'L',
"CCA": 'P',
"CAA": 'Q',
"CGA": 'R',
"CTG": 'L',
"CCG": 'P',
"CAG": 'Q',
"CGG": 'R',
"ATT": 'I',
"ACT": 'T',
"AAT": 'N',
"AGT": 'S',
"ATC": 'I',
"ACC": 'T',
"AAC": 'N',
"AGC": 'S',
"ATA": 'I',
"ACA": 'T',
"AAA": 'K',
"AGA": 'R',
"ATG": 'M',
"ACG": 'T',
"AAG": 'K',
"AGG": 'R',
"GTT": 'V',
"GCT": 'A',
"GAT": 'D',
"GGT": 'G',
"GTC": 'V',
"GCC": 'A',
"GAC": 'D',
"GGC": 'G',
"GTA": 'V',
"GCA": 'A',
"GAA": 'E',
"GGA": 'G',
"GTG": 'V',
"GCG": 'A',
"GAG": 'E',
"GGG": 'G',
}
)
const (
nCode = uint8(0)
aCode = uint8(1)
cCode = uint8(2)
tCode = uint8(3)
uCode = uint8(3)
gCode = uint8(4)
stopByte = '*'
unknown = 'X'
// Length of the array to store code/bytes
// uses gCode because it's the biggest uint8 of all codes
arrayCodeSize = (uint32(gCode) | uint32(gCode)<<8 | uint32(gCode)<<16) + 1
)
func createCodeArray(clean bool) byte {
resultMap := map[uint32]byte{}
twoLetterMap := map[string]byte{}
tmpCode := make(uint8, 4)
for codon, aaCode := range standard {
// generate 3 letter code
for i := 0; i < 3; i++ {
tmpCode[i] = letterCode[codon[i]]
}
// each codon is represented by an unique uint32:
// each possible nucleotide is represented by an uint8 (255 possibility)
// the three first bytes are the the code for each nucleotide
// last byte is unused ( eq to uint8(0) )
// example:
// codon 'ACG' ==> uint32(aCode) | uint32(cCode)<<8 | uint32(gCode)<<16
uint32Code := uint32(tmpCode[0]) | uint32(tmpCode[1])<<8 | uint32(tmpCode[2])<<16
resultMap[uint32Code] = aaCode
// generate 2 letter code
codes, ok := twoLetterMap[codon[0:2]]
if !ok {
twoLetterMap[codon[0:2]] = byte{aaCode}
} else {
twoLetterMap[codon[0:2]] = append(codes, aaCode)
}
}
for twoLetterCodon, codes := range twoLetterMap {
uniqueAA := true
for i := 0; i < len(codes); i++ {
if codes[i] != codes[0] {
uniqueAA = false
}
}
if uniqueAA {
first := letterCode[twoLetterCodon[0]]
second := letterCode[twoLetterCodon[1]]
uint32Code := uint32(first) | uint32(second)<<8
resultMap[uint32Code] = codes[0]
}
}
// if clean is specified, we want to replace all '*' by 'X' in the output
// sequence, so replace all occurrences of '*' directly in the ref map
if clean {
for k, v := range resultMap {
if v == stopByte {
resultMap[k] = unknown
}
}
}
r := make(byte, arrayCodeSize)
for k, v := range resultMap {
r[k] = v
}
return r
}
func computeFrames(frameName string) (frames int, reverse bool, err error) {
frames = make(int, 6)
reverse = false
switch frameName {
case "1":
frames[0] = 1
case "2":
frames[1] = 1
case "3":
frames[2] = 1
case "F":
for i := 0; i < 3; i++ {
frames[i] = 1
}
case "-1":
frames[3] = 1
reverse = true
case "-2":
frames[4] = 1
reverse = true
case "-3":
frames[5] = 1
reverse = true
case "R":
for i := 3; i < 6; i++ {
frames[i] = 1
}
reverse = true
case "6":
for i := range frames {
frames[i] = 1
}
reverse = true
default:
err = fmt.Errorf("wrong value for -f | --frame parameter: %s", frameName)
}
return frames, reverse, err
}
type writer struct {
buf *bytes.Buffer
currentLineLen int
bytesToTrim int
}
func (w *writer) addByte(b byte) {
w.buf.WriteByte(b)
w.currentLineLen++
if b == stopByte || b == unknown {
w.bytesToTrim++
} else {
w.bytesToTrim = 0
}
}
func (w *writer) addUnknown() {
w.buf.WriteByte(unknown)
w.currentLineLen++
w.bytesToTrim++
}
func (w *writer) newLine() {
w.buf.WriteByte('n')
w.currentLineLen = 0
w.bytesToTrim++
}
const (
// size of the buffer for writing to file
maxBufferSize = 1024 * 1024 * 30
// max line size for sequence
maxLineSize = 60
// suffixes ta add to sequence id for each frame
suffixes = "123456"
)
// Translate read a fata file, translate each sequence to the corresponding prot sequence in the specified frame
func Translate(inputSequence io.Reader, out io.Writer, frame string, clean, trim, alternative bool) error {
arrayCode := createCodeArray(clean)
framesToGenerate, reverse, err := computeFrames(frame)
if err != nil {
return err
}
fnaSequences := make(chan encodedSequence, 10)
errs := make(chan error, 1)
var wg sync.WaitGroup
ctx, cancel := context.WithCancel(context.Background())
defer cancel()
for nWorker := 0; nWorker < runtime.NumCPU(); nWorker++ {
wg.Add(1)
go func() {
defer wg.Done()
startPosition := make(int, 3)
w := &writer{
buf: bytes.NewBuffer(nil),
bytesToTrim: 0,
currentLineLen: 0,
}
for sequence := range fnaSequences {
select {
case <-ctx.Done():
return
default:
}
frameIndex := 0
startPosition[0], startPosition[1], startPosition[2] = 0, 1, 2
idSize := int(binary.LittleEndian.Uint32(sequence[0:4]))
nuclSeqLength := len(sequence) - idSize
Translate:
for _, startPos := range startPosition {
if framesToGenerate[frameIndex] == 0 {
frameIndex++
continue
}
// sequence id should look like
// >sequenceID_<frame> comment
idEnd := bytes.IndexByte(sequence[4:idSize], ' ')
if idEnd != -1 {
w.buf.Write(sequence[4 : 4+idEnd])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
w.buf.Write(sequence[4+idEnd : idSize])
} else {
w.buf.Write(sequence[4:idSize])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
}
w.newLine()
// if in trim mode, nb of bytes to trim (nb of successive 'X', '*' and 'n'
// from right end of the sequence)
w.bytesToTrim = 0
w.currentLineLen = 0
// read the sequence 3 letters at a time, starting at a specific position
// corresponding to the frame
for pos := startPos + 2 + idSize; pos < len(sequence); pos += 3 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
// create an uint32 from the codon, to retrieve the corresponding
// AA from the map
codonCode := uint32(sequence[pos-2]) | uint32(sequence[pos-1])<<8 | uint32(sequence[pos])<<16
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 2 nucleotid long, try to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 2 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
codonCode := uint32(sequence[len(sequence)-2]) | uint32(sequence[len(sequence)-1])<<8
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 1 nucleotid long, no way to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 1 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
w.addUnknown()
}
if trim && w.bytesToTrim > 0 {
// remove the last bytesToTrim bytes of the buffer
// as they are 'X', '*' or 'n'
w.buf.Truncate(w.buf.Len() - w.bytesToTrim)
w.currentLineLen -= w.bytesToTrim
}
if w.currentLineLen != 0 {
w.newLine()
}
frameIndex++
}
if reverse && frameIndex < 6 {
// get the complementary sequence.
// Basically, switch
// A <-> T
// C <-> G
// N is not modified
for i, n := range sequence[idSize:] {
switch n {
case aCode:
sequence[i+idSize] = tCode
case tCode:
// handle both tCode and uCode
sequence[i+idSize] = aCode
case cCode:
sequence[i+idSize] = gCode
case gCode:
sequence[i+idSize] = cCode
default:
//case N -> leave it
}
}
// reverse the sequence
for i, j := idSize, len(sequence)-1; i < j; i, j = i+1, j-1 {
sequence[i], sequence[j] = sequence[j], sequence[i]
}
if !alternative {
// Staden convention: Frame -1 is the reverse-complement of the sequence
// having the same codon phase as frame 1. Frame -2 is the same phase as
// frame 2. Frame -3 is the same phase as frame 3
//
// use the matrix to keep track of the forward frame as it depends on the
// length of the sequence
switch nuclSeqLength % 3 {
case 0:
startPosition[0], startPosition[1], startPosition[2] = 0, 2, 1
case 1:
startPosition[0], startPosition[1], startPosition[2] = 1, 0, 2
case 2:
startPosition[0], startPosition[1], startPosition[2] = 2, 1, 0
}
}
// run the same loop, but with the reverse-complemented sequence
goto Translate
}
if w.buf.Len() > maxBufferSize {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
w.buf.Reset()
}
pool.Put(sequence)
}
if w.buf.Len() > 0 {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
}
}()
}
readSequenceFromFasta(ctx, inputSequence, fnaSequences)
wg.Wait()
select {
case err, ok := <-errs:
if ok {
return err
}
default:
}
return nil
}
func readSequenceFromFasta(ctx context.Context, inputSequence io.Reader, fnaSequences chan encodedSequence) {
feeder := &fastaChannelFeeder{
idBuffer: bytes.NewBuffer(nil),
commentBuffer: bytes.NewBuffer(nil),
sequenceBuffer: bytes.NewBuffer(nil),
fastaChan: fnaSequences,
}
// fasta format is:
//
// >sequenceID some comments on sequence
// ACAGGCAGAGACACGACAGACGACGACACAGGAGCAGACAGCAGCAGACGACCACATATT
// TTTGCGGTCACATGACGACTTCGGCAGCGA
//
// see https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp
// section 1 for details
scanner := bufio.NewScanner(inputSequence)
Loop:
for scanner.Scan() {
line := scanner.Bytes()
if len(line) == 0 {
continue
}
if line[0] == '>' {
if feeder.idBuffer.Len() > 0 {
select {
case <-ctx.Done():
break Loop
default:
}
feeder.sendFasta()
}
feeder.reset()
// parse the ID of the sequence. ID is formatted like this:
// >sequenceID comments
seqID := bytes.SplitN(line, byte{' '}, 2)
feeder.idBuffer.Write(seqID[0])
if len(seqID) > 1 {
feeder.commentBuffer.WriteByte(' ')
feeder.commentBuffer.Write(seqID[1])
}
} else {
// if the line doesn't start with '>', then it's a part of the
// nucleotide sequence, so write it to the buffer
feeder.sequenceBuffer.Write(line)
}
}
// don't forget to push last sequence
select {
case <-ctx.Done():
default:
feeder.sendFasta()
}
close(fnaSequences)
}
// a type to hold an encoded fasta sequence
//
// s[0:4] stores the size of the sequence id + the size of the comment as an uint32 (little endian)
// s[4:idSize] stores the sequence id, and the comment id there is one
// s[idSize:] stores the nucl sequence
type encodedSequence byte
var pool = sync.Pool{
New: func() interface{} {
return make(encodedSequence, 512)
},
}
func getSizedSlice(idSize, requiredSize int) encodedSequence {
s := pool.Get().(encodedSequence)
binary.LittleEndian.PutUint32(s[0:4], uint32(idSize))
for len(s) < requiredSize {
s = append(s, byte(0))
}
return s[0:requiredSize]
}
func (f *fastaChannelFeeder) sendFasta() {
idSize := 4 + f.idBuffer.Len() + f.commentBuffer.Len()
requiredSize := idSize + f.sequenceBuffer.Len()
s := getSizedSlice(idSize, requiredSize)
if f.commentBuffer.Len() > 0 {
copy(s[idSize-f.commentBuffer.Len():idSize], f.commentBuffer.Bytes())
}
copy(s[4:4+f.idBuffer.Len()], f.idBuffer.Bytes())
// convert the sequence of bytes to an array of uint8 codes,
// so a codon (3 nucleotides | 3 bytes ) can be represented
// as an uint32
for i, b := range f.sequenceBuffer.Bytes() {
switch b {
case 'A':
s[i+idSize] = aCode
case 'C':
s[i+idSize] = cCode
case 'G':
s[i+idSize] = gCode
case 'T', 'U':
s[i+idSize] = tCode
case 'N':
s[i+idSize] = nCode
default:
fmt.Printf("WARNING: invalid char in sequence %s: %s, ignoring", s[4:4+idSize], string(b))
}
}
f.fastaChan <- s
}
type fastaChannelFeeder struct {
idBuffer, commentBuffer, sequenceBuffer *bytes.Buffer
fastaChan chan encodedSequence
}
func (f *fastaChannelFeeder) reset() {
f.idBuffer.Reset()
f.sequenceBuffer.Reset()
f.commentBuffer.Reset()
}
performance go bioinformatics multiprocessing
asked 11 mins ago
felix
69839
Goal of the program
The goal of the program is to translate a nucleic acid sequence into it's corresponding amino acid sequence. The nucleic sequences
have to be formatted in a specific format called fasta. There is an existing implementation of this program in C here: emboss transeq
Fasta format
A fasta file looks like this:
>sequenceId comment
nucleic sequence
for example:
>Seq1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
>Seq2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GGTAGGTACCGCCCTAAGNCTCCTAATCCGAGCAGAACTANGCCAACCCGGAGCCCTTCTGGGAGACGAC
AATCAACATAAAA
A nucleic sequence is a string composed of the letters A, C, T, G, U, N
Expected output
A combinaison of 3 nucleic acid, named codon, gives a specif amino acid, for exemple GCT is the code for Alanine, symbolised by the letter A
With the Seq1 define above:
codon CCT TTA TCT AAT CTT TGG AGC ATG ...
amino acid P L S N L W S M ...
The expected output is:
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
Specific rules
The program takes 4 parameters:
clean: if true, write STOP codon asXinstead of*
trim: if true, remove allXand*chars from the right end of the amino - acid sequence
alternative: different way to compute reverse frame
frame: a string value in["1", "2", "3", "F", "-1", "-2", "-3", "R", "6" ]
The frame define the position in the nucleic sequence to start from:
-frame 1
|-frame 2
||-frame 3
|||
CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAA
CCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
|||
||-frame -1
|-frame -2
-frame -3
frame "F" = "1", "2", "3"
frame "R" = "-1", "-2", "-3"
frame "6" = "1", "2", "3", "-1", "-2", "-3"
In the output file, we add the frame used to the sequenceId: sequenceId = sequenceId_frame
For example if the program is used with frame=6, the expected output is
>Seq1_1 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
PLSNLWSMSWHSWNRPQPPHPCRTQSCTNTSSDSSAIQKSISSFY
>Seq1_2 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
LYLIFGA*AGIVGTALSLLIRAEPSPVPTPLLILRPSRSLYPHFT
>Seq1_3 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
FI*SLEHELA*LEPPSASSSVQNPVLYQHLF*FFGHPEVYILILX
>Seq1_4 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
VK*GYRLLDGRRIRRGVGTGLGSARMRRLRAVPTMPAHAPKIR*R
>Seq1_5 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
KMRI*TSGWPKNQKRCWYRTGFCTDEEAEGGSNYASSCSKD*IKX
>Seq1_6 [organism=Carpodacus mexicanus] [clone=6b] actin (act) mRNA, partial cds
*NEDIDFWMAEESEEVLVQDWVLHG*GG*GRFQLCQLMLQRLDKG
>Seq2_1 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
GRYRPKXPNPSRTXPTRSPSGRRQST*X
>Seq2_2 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
VGTALXLLIRAELXQPGALLGDDNQHKX
>Seq2_3 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
*VPP*XS*SEQNXANPEPFWETTINIK
>Seq2_4 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
LC*LSSPRRAPGWXSSARIRXLRAVPT
>Seq2_5 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FMLIVVSQKGSGLA*FCSD*EX*GGTYX
>Seq2_6 [organism=uncultured bacillus sp.] [isolate=A2] corticotropin (CT) gene
FYVDCRLPEGLRVGXVLLGLGXLGRYLP
Improvements
- Is the code easy to read / understand ?
- Is the code idiomatic ?
- Any other improvements (performance, doc...)
( full project with tests + flags handling is avaible on github: gotranseq)
code :
package transeq
import (
"bufio"
"bytes"
"context"
"encoding/binary"
"fmt"
"io"
"runtime"
"sync"
)
var (
letterCode = map[byte]uint8{
'A': aCode,
'C': cCode,
'T': tCode,
'G': gCode,
'N': nCode,
'U': uCode,
}
standard = map[string]byte{
"TTT": 'F',
"TCT": 'S',
"TAT": 'Y',
"TGT": 'C',
"TTC": 'F',
"TCC": 'S',
"TAC": 'Y',
"TGC": 'C',
"TTA": 'L',
"TCA": 'S',
"TAA": '*',
"TGA": '*',
"TTG": 'L',
"TCG": 'S',
"TAG": '*',
"TGG": 'W',
"CTT": 'L',
"CCT": 'P',
"CAT": 'H',
"CGT": 'R',
"CTC": 'L',
"CCC": 'P',
"CAC": 'H',
"CGC": 'R',
"CTA": 'L',
"CCA": 'P',
"CAA": 'Q',
"CGA": 'R',
"CTG": 'L',
"CCG": 'P',
"CAG": 'Q',
"CGG": 'R',
"ATT": 'I',
"ACT": 'T',
"AAT": 'N',
"AGT": 'S',
"ATC": 'I',
"ACC": 'T',
"AAC": 'N',
"AGC": 'S',
"ATA": 'I',
"ACA": 'T',
"AAA": 'K',
"AGA": 'R',
"ATG": 'M',
"ACG": 'T',
"AAG": 'K',
"AGG": 'R',
"GTT": 'V',
"GCT": 'A',
"GAT": 'D',
"GGT": 'G',
"GTC": 'V',
"GCC": 'A',
"GAC": 'D',
"GGC": 'G',
"GTA": 'V',
"GCA": 'A',
"GAA": 'E',
"GGA": 'G',
"GTG": 'V',
"GCG": 'A',
"GAG": 'E',
"GGG": 'G',
}
)
const (
nCode = uint8(0)
aCode = uint8(1)
cCode = uint8(2)
tCode = uint8(3)
uCode = uint8(3)
gCode = uint8(4)
stopByte = '*'
unknown = 'X'
// Length of the array to store code/bytes
// uses gCode because it's the biggest uint8 of all codes
arrayCodeSize = (uint32(gCode) | uint32(gCode)<<8 | uint32(gCode)<<16) + 1
)
func createCodeArray(clean bool) byte {
resultMap := map[uint32]byte{}
twoLetterMap := map[string]byte{}
tmpCode := make(uint8, 4)
for codon, aaCode := range standard {
// generate 3 letter code
for i := 0; i < 3; i++ {
tmpCode[i] = letterCode[codon[i]]
}
// each codon is represented by an unique uint32:
// each possible nucleotide is represented by an uint8 (255 possibility)
// the three first bytes are the the code for each nucleotide
// last byte is unused ( eq to uint8(0) )
// example:
// codon 'ACG' ==> uint32(aCode) | uint32(cCode)<<8 | uint32(gCode)<<16
uint32Code := uint32(tmpCode[0]) | uint32(tmpCode[1])<<8 | uint32(tmpCode[2])<<16
resultMap[uint32Code] = aaCode
// generate 2 letter code
codes, ok := twoLetterMap[codon[0:2]]
if !ok {
twoLetterMap[codon[0:2]] = byte{aaCode}
} else {
twoLetterMap[codon[0:2]] = append(codes, aaCode)
}
}
for twoLetterCodon, codes := range twoLetterMap {
uniqueAA := true
for i := 0; i < len(codes); i++ {
if codes[i] != codes[0] {
uniqueAA = false
}
}
if uniqueAA {
first := letterCode[twoLetterCodon[0]]
second := letterCode[twoLetterCodon[1]]
uint32Code := uint32(first) | uint32(second)<<8
resultMap[uint32Code] = codes[0]
}
}
// if clean is specified, we want to replace all '*' by 'X' in the output
// sequence, so replace all occurrences of '*' directly in the ref map
if clean {
for k, v := range resultMap {
if v == stopByte {
resultMap[k] = unknown
}
}
}
r := make(byte, arrayCodeSize)
for k, v := range resultMap {
r[k] = v
}
return r
}
func computeFrames(frameName string) (frames int, reverse bool, err error) {
frames = make(int, 6)
reverse = false
switch frameName {
case "1":
frames[0] = 1
case "2":
frames[1] = 1
case "3":
frames[2] = 1
case "F":
for i := 0; i < 3; i++ {
frames[i] = 1
}
case "-1":
frames[3] = 1
reverse = true
case "-2":
frames[4] = 1
reverse = true
case "-3":
frames[5] = 1
reverse = true
case "R":
for i := 3; i < 6; i++ {
frames[i] = 1
}
reverse = true
case "6":
for i := range frames {
frames[i] = 1
}
reverse = true
default:
err = fmt.Errorf("wrong value for -f | --frame parameter: %s", frameName)
}
return frames, reverse, err
}
type writer struct {
buf *bytes.Buffer
currentLineLen int
bytesToTrim int
}
func (w *writer) addByte(b byte) {
w.buf.WriteByte(b)
w.currentLineLen++
if b == stopByte || b == unknown {
w.bytesToTrim++
} else {
w.bytesToTrim = 0
}
}
func (w *writer) addUnknown() {
w.buf.WriteByte(unknown)
w.currentLineLen++
w.bytesToTrim++
}
func (w *writer) newLine() {
w.buf.WriteByte('n')
w.currentLineLen = 0
w.bytesToTrim++
}
const (
// size of the buffer for writing to file
maxBufferSize = 1024 * 1024 * 30
// max line size for sequence
maxLineSize = 60
// suffixes ta add to sequence id for each frame
suffixes = "123456"
)
// Translate read a fata file, translate each sequence to the corresponding prot sequence in the specified frame
func Translate(inputSequence io.Reader, out io.Writer, frame string, clean, trim, alternative bool) error {
arrayCode := createCodeArray(clean)
framesToGenerate, reverse, err := computeFrames(frame)
if err != nil {
return err
}
fnaSequences := make(chan encodedSequence, 10)
errs := make(chan error, 1)
var wg sync.WaitGroup
ctx, cancel := context.WithCancel(context.Background())
defer cancel()
for nWorker := 0; nWorker < runtime.NumCPU(); nWorker++ {
wg.Add(1)
go func() {
defer wg.Done()
startPosition := make(int, 3)
w := &writer{
buf: bytes.NewBuffer(nil),
bytesToTrim: 0,
currentLineLen: 0,
}
for sequence := range fnaSequences {
select {
case <-ctx.Done():
return
default:
}
frameIndex := 0
startPosition[0], startPosition[1], startPosition[2] = 0, 1, 2
idSize := int(binary.LittleEndian.Uint32(sequence[0:4]))
nuclSeqLength := len(sequence) - idSize
Translate:
for _, startPos := range startPosition {
if framesToGenerate[frameIndex] == 0 {
frameIndex++
continue
}
// sequence id should look like
// >sequenceID_<frame> comment
idEnd := bytes.IndexByte(sequence[4:idSize], ' ')
if idEnd != -1 {
w.buf.Write(sequence[4 : 4+idEnd])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
w.buf.Write(sequence[4+idEnd : idSize])
} else {
w.buf.Write(sequence[4:idSize])
w.buf.WriteByte('_')
w.buf.WriteByte(suffixes[frameIndex])
}
w.newLine()
// if in trim mode, nb of bytes to trim (nb of successive 'X', '*' and 'n'
// from right end of the sequence)
w.bytesToTrim = 0
w.currentLineLen = 0
// read the sequence 3 letters at a time, starting at a specific position
// corresponding to the frame
for pos := startPos + 2 + idSize; pos < len(sequence); pos += 3 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
// create an uint32 from the codon, to retrieve the corresponding
// AA from the map
codonCode := uint32(sequence[pos-2]) | uint32(sequence[pos-1])<<8 | uint32(sequence[pos])<<16
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 2 nucleotid long, try to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 2 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
codonCode := uint32(sequence[len(sequence)-2]) | uint32(sequence[len(sequence)-1])<<8
b := arrayCode[codonCode]
if b != byte(0) {
w.addByte(b)
} else {
w.addUnknown()
}
}
// the last codon is only 1 nucleotid long, no way to guess
// the corresponding AA
if (nuclSeqLength-startPos)%3 == 1 {
if w.currentLineLen == maxLineSize {
w.newLine()
}
w.addUnknown()
}
if trim && w.bytesToTrim > 0 {
// remove the last bytesToTrim bytes of the buffer
// as they are 'X', '*' or 'n'
w.buf.Truncate(w.buf.Len() - w.bytesToTrim)
w.currentLineLen -= w.bytesToTrim
}
if w.currentLineLen != 0 {
w.newLine()
}
frameIndex++
}
if reverse && frameIndex < 6 {
// get the complementary sequence.
// Basically, switch
// A <-> T
// C <-> G
// N is not modified
for i, n := range sequence[idSize:] {
switch n {
case aCode:
sequence[i+idSize] = tCode
case tCode:
// handle both tCode and uCode
sequence[i+idSize] = aCode
case cCode:
sequence[i+idSize] = gCode
case gCode:
sequence[i+idSize] = cCode
default:
//case N -> leave it
}
}
// reverse the sequence
for i, j := idSize, len(sequence)-1; i < j; i, j = i+1, j-1 {
sequence[i], sequence[j] = sequence[j], sequence[i]
}
if !alternative {
// Staden convention: Frame -1 is the reverse-complement of the sequence
// having the same codon phase as frame 1. Frame -2 is the same phase as
// frame 2. Frame -3 is the same phase as frame 3
//
// use the matrix to keep track of the forward frame as it depends on the
// length of the sequence
switch nuclSeqLength % 3 {
case 0:
startPosition[0], startPosition[1], startPosition[2] = 0, 2, 1
case 1:
startPosition[0], startPosition[1], startPosition[2] = 1, 0, 2
case 2:
startPosition[0], startPosition[1], startPosition[2] = 2, 1, 0
}
}
// run the same loop, but with the reverse-complemented sequence
goto Translate
}
if w.buf.Len() > maxBufferSize {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
w.buf.Reset()
}
pool.Put(sequence)
}
if w.buf.Len() > 0 {
_, err := out.Write(w.buf.Bytes())
if err != nil {
select {
case errs <- fmt.Errorf("fail to write to output file: %v", err):
default:
}
cancel()
return
}
}
}()
}
readSequenceFromFasta(ctx, inputSequence, fnaSequences)
wg.Wait()
select {
case err, ok := <-errs:
if ok {
return err
}
default:
}
return nil
}
func readSequenceFromFasta(ctx context.Context, inputSequence io.Reader, fnaSequences chan encodedSequence) {
feeder := &fastaChannelFeeder{
idBuffer: bytes.NewBuffer(nil),
commentBuffer: bytes.NewBuffer(nil),
sequenceBuffer: bytes.NewBuffer(nil),
fastaChan: fnaSequences,
}
// fasta format is:
//
// >sequenceID some comments on sequence
// ACAGGCAGAGACACGACAGACGACGACACAGGAGCAGACAGCAGCAGACGACCACATATT
// TTTGCGGTCACATGACGACTTCGGCAGCGA
//
// see https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp
// section 1 for details
scanner := bufio.NewScanner(inputSequence)
Loop:
for scanner.Scan() {
line := scanner.Bytes()
if len(line) == 0 {
continue
}
if line[0] == '>' {
if feeder.idBuffer.Len() > 0 {
select {
case <-ctx.Done():
break Loop
default:
}
feeder.sendFasta()
}
feeder.reset()
// parse the ID of the sequence. ID is formatted like this:
// >sequenceID comments
seqID := bytes.SplitN(line, byte{' '}, 2)
feeder.idBuffer.Write(seqID[0])
if len(seqID) > 1 {
feeder.commentBuffer.WriteByte(' ')
feeder.commentBuffer.Write(seqID[1])
}
} else {
// if the line doesn't start with '>', then it's a part of the
// nucleotide sequence, so write it to the buffer
feeder.sequenceBuffer.Write(line)
}
}
// don't forget to push last sequence
select {
case <-ctx.Done():
default:
feeder.sendFasta()
}
close(fnaSequences)
}
// a type to hold an encoded fasta sequence
//
// s[0:4] stores the size of the sequence id + the size of the comment as an uint32 (little endian)
// s[4:idSize] stores the sequence id, and the comment id there is one
// s[idSize:] stores the nucl sequence
type encodedSequence byte
var pool = sync.Pool{
New: func() interface{} {
return make(encodedSequence, 512)
},
}
func getSizedSlice(idSize, requiredSize int) encodedSequence {
s := pool.Get().(encodedSequence)
binary.LittleEndian.PutUint32(s[0:4], uint32(idSize))
for len(s) < requiredSize {
s = append(s, byte(0))
}
return s[0:requiredSize]
}
func (f *fastaChannelFeeder) sendFasta() {
idSize := 4 + f.idBuffer.Len() + f.commentBuffer.Len()
requiredSize := idSize + f.sequenceBuffer.Len()
s := getSizedSlice(idSize, requiredSize)
if f.commentBuffer.Len() > 0 {
copy(s[idSize-f.commentBuffer.Len():idSize], f.commentBuffer.Bytes())
}
copy(s[4:4+f.idBuffer.Len()], f.idBuffer.Bytes())
// convert the sequence of bytes to an array of uint8 codes,
// so a codon (3 nucleotides | 3 bytes ) can be represented
// as an uint32
for i, b := range f.sequenceBuffer.Bytes() {
switch b {
case 'A':
s[i+idSize] = aCode
case 'C':
s[i+idSize] = cCode
case 'G':
s[i+idSize] = gCode
case 'T', 'U':
s[i+idSize] = tCode
case 'N':
s[i+idSize] = nCode
default:
fmt.Printf("WARNING: invalid char in sequence %s: %s, ignoring", s[4:4+idSize], string(b))
}
}
f.fastaChan <- s
}
type fastaChannelFeeder struct {
idBuffer, commentBuffer, sequenceBuffer *bytes.Buffer
fastaChan chan encodedSequence
}
func (f *fastaChannelFeeder) reset() {
f.idBuffer.Reset()
f.sequenceBuffer.Reset()
f.commentBuffer.Reset()
}
performance go bioinformatics multiprocessing
performance go bioinformatics multiprocessing
asked 11 mins ago
felix
69839
asked 11 mins ago
felix
69839
asked 11 mins ago
felix
69839
asked 11 mins ago
felix
69839
asked 11 mins ago
felix
69839
69839
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