mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-12-08 16:50:27 +00:00
Refactor sequence file reading
Former-commit-id: 3dcb96e68da648d72bb585da047e3496427d7851
This commit is contained in:
Eric Coissac
@@ -1,250 +1,155 @@
|
||||
package obiformats
|
||||
|
||||
import (
|
||||
"bufio"
|
||||
"bytes"
|
||||
"fmt"
|
||||
"io"
|
||||
"os"
|
||||
"path"
|
||||
"slices"
|
||||
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
|
||||
"golang.org/x/exp/slices"
|
||||
|
||||
log "github.com/sirupsen/logrus"
|
||||
)
|
||||
|
||||
// lastFastaCut extracts the up to the last sequence cut from a given buffer.
|
||||
//
|
||||
// It takes a parameter:
|
||||
// - buffer []byte: the buffer to extract the sequence cut from.
|
||||
//
|
||||
// It returns two values:
|
||||
// - []byte: the extracted sequences.
|
||||
// - []byte: the remaining buffer after the sequence cut (the last sequence).
|
||||
func lastFastaCut(buffer []byte) ([]byte, []byte) {
|
||||
func _EndOfLastFastaEntry(buffer []byte) int {
|
||||
var i int
|
||||
|
||||
imax := len(buffer)
|
||||
last := 0
|
||||
state := 0
|
||||
for i := imax - 1; i >= 0 && state < 2; i-- {
|
||||
if state == 0 && buffer[i] == '>' {
|
||||
|
||||
for i = imax - 1; i >= 0 && state < 2; i-- {
|
||||
C := buffer[i]
|
||||
if C == '>' && state == 0 {
|
||||
state = 1
|
||||
last = i
|
||||
} else if state == 1 && (buffer[i] == '\r' || buffer[i] == '\n') {
|
||||
} else if state == 1 && (C == '\n' || C == '\r') {
|
||||
state = 2
|
||||
} else {
|
||||
state = 0
|
||||
}
|
||||
}
|
||||
|
||||
if state == 2 {
|
||||
return buffer[:last], bytes.Clone(buffer[last:])
|
||||
if i == 0 || state != 2 {
|
||||
return -1
|
||||
}
|
||||
return []byte{}, buffer
|
||||
return last
|
||||
}
|
||||
|
||||
// firstFastaCut cuts the input buffer at the first occurrence of a ">" character
|
||||
// following a sequence of "\r" or "\n" characters.
|
||||
//
|
||||
// It takes a byte slice as input, representing the buffer to be cut.
|
||||
// It returns two byte slices: the first slice contains the part of the buffer before the cut,
|
||||
// and the second slice contains the part of the buffer after the cut.
|
||||
func firstFastaCut(buffer []byte) ([]byte, []byte) {
|
||||
imax := len(buffer)
|
||||
last := 0
|
||||
state := 0
|
||||
for i := 0; i < imax && state < 2; i++ {
|
||||
if (state == 0 || state == 1) && (buffer[i] == '\r' || buffer[i] == '\n') {
|
||||
state = 1
|
||||
} else if (state == 1 || i == 0) && buffer[i] == '>' {
|
||||
state = 2
|
||||
last = i
|
||||
} else {
|
||||
state = 0
|
||||
}
|
||||
}
|
||||
func _ParseFastaFile(source string,
|
||||
input ChannelSeqFileChunk,
|
||||
out obiiter.IBioSequence) {
|
||||
|
||||
if state == 2 {
|
||||
return bytes.Clone(buffer[:last]), buffer[last:]
|
||||
}
|
||||
return buffer, []byte{}
|
||||
|
||||
}
|
||||
|
||||
func Concatenate[S ~[]E, E any](s1, s2 S) S {
|
||||
if len(s1) > 0 {
|
||||
if len(s2) > 0 {
|
||||
return append(s1[:len(s1):len(s1)], s2...)
|
||||
}
|
||||
return s1
|
||||
}
|
||||
return s2
|
||||
}
|
||||
|
||||
type FastxChunk struct {
|
||||
Bytes []byte
|
||||
index int
|
||||
}
|
||||
|
||||
func FastaChunkReader(r io.Reader, size int, cutHead bool) (chan FastxChunk, error) {
|
||||
out := make(chan FastxChunk)
|
||||
buff := make([]byte, size)
|
||||
|
||||
n, err := io.ReadFull(r, buff)
|
||||
|
||||
if err == io.ErrUnexpectedEOF {
|
||||
err = nil
|
||||
}
|
||||
|
||||
if n > 0 && err == nil {
|
||||
if n < size {
|
||||
buff = buff[:n]
|
||||
}
|
||||
|
||||
begin, buff := firstFastaCut(buff)
|
||||
|
||||
if len(begin) > 0 && !cutHead {
|
||||
return out, fmt.Errorf("begin is not empty : %s", string(begin))
|
||||
}
|
||||
|
||||
go func(buff []byte) {
|
||||
idx := 0
|
||||
end := []byte{}
|
||||
|
||||
for err == nil && n > 0 {
|
||||
buff = Concatenate(end, buff)
|
||||
buff, end = lastFastaCut(buff)
|
||||
if len(buff) > 0 {
|
||||
out <- FastxChunk{
|
||||
Bytes: bytes.Clone(buff),
|
||||
index: idx,
|
||||
}
|
||||
idx++
|
||||
} else {
|
||||
size = size * 2
|
||||
}
|
||||
|
||||
buff = slices.Grow(buff[:0], size)[0:size]
|
||||
n, err = io.ReadFull(r, buff)
|
||||
if n < size {
|
||||
buff = buff[:n]
|
||||
}
|
||||
|
||||
if err == io.ErrUnexpectedEOF {
|
||||
err = nil
|
||||
}
|
||||
|
||||
// fmt.Printf("n = %d, err = %v\n", n, err)
|
||||
}
|
||||
|
||||
if len(end) > 0 {
|
||||
out <- FastxChunk{
|
||||
Bytes: bytes.Clone(end),
|
||||
index: idx,
|
||||
}
|
||||
}
|
||||
|
||||
close(out)
|
||||
}(buff)
|
||||
}
|
||||
|
||||
return out, nil
|
||||
}
|
||||
|
||||
func ParseFastaChunk(source string, ch FastxChunk) *obiiter.BioSequenceBatch {
|
||||
slice := make(obiseq.BioSequenceSlice, 0, obioptions.CLIBatchSize())
|
||||
|
||||
state := 0
|
||||
start := 0
|
||||
current := 0
|
||||
var identifier string
|
||||
var definition string
|
||||
|
||||
for i := 0; i < len(ch.Bytes); i++ {
|
||||
C := ch.Bytes[i]
|
||||
is_end_of_line := C == '\r' || C == '\n'
|
||||
is_space := C == ' ' || C == '\t'
|
||||
is_sep := is_space || is_end_of_line
|
||||
state := 0
|
||||
|
||||
switch state {
|
||||
case 0:
|
||||
if C == '>' {
|
||||
// Beginning of sequence
|
||||
state = 1
|
||||
}
|
||||
case 1:
|
||||
if is_sep {
|
||||
// No identifier -> ERROR
|
||||
log.Errorf("%s : sequence entry does not have an identifier", source)
|
||||
return nil
|
||||
} else {
|
||||
// Beginning of identifier
|
||||
state = 2
|
||||
start = i
|
||||
}
|
||||
case 2:
|
||||
if is_sep {
|
||||
// End of identifier
|
||||
identifier = string(ch.Bytes[start:i])
|
||||
state = 3
|
||||
}
|
||||
if is_end_of_line {
|
||||
// Definition empty
|
||||
definition = ""
|
||||
state = 5
|
||||
}
|
||||
case 3:
|
||||
if is_end_of_line {
|
||||
// Definition empty
|
||||
definition = ""
|
||||
state = 5
|
||||
} else if !is_space {
|
||||
// Beginning of definition
|
||||
start = i
|
||||
state = 4
|
||||
}
|
||||
case 4:
|
||||
if is_end_of_line {
|
||||
definition = string(ch.Bytes[start:i])
|
||||
state = 5
|
||||
idBytes := new(bytes.Buffer)
|
||||
defBytes := new(bytes.Buffer)
|
||||
seqBytes := new(bytes.Buffer)
|
||||
|
||||
}
|
||||
case 5:
|
||||
if !is_end_of_line {
|
||||
// Beginning of sequence
|
||||
start = i
|
||||
if C >= 'A' && C <= 'Z' {
|
||||
ch.Bytes[current] = C + 'a' - 'A'
|
||||
for chunks := range input {
|
||||
scanner := bufio.NewReader(chunks.raw)
|
||||
sequences := make(obiseq.BioSequenceSlice, 0, 100)
|
||||
for C, err := scanner.ReadByte(); err != io.EOF; C, err = scanner.ReadByte() {
|
||||
|
||||
is_end_of_line := C == '\r' || C == '\n'
|
||||
is_space := C == ' ' || C == '\t'
|
||||
is_sep := is_space || is_end_of_line
|
||||
|
||||
switch state {
|
||||
case 0:
|
||||
if C == '>' {
|
||||
// Beginning of sequence
|
||||
state = 1
|
||||
}
|
||||
current = i + 1
|
||||
state = 6
|
||||
}
|
||||
case 6:
|
||||
if C == '>' {
|
||||
// End of sequence
|
||||
s := obiseq.NewBioSequence(identifier, bytes.Clone(ch.Bytes[start:current]), definition)
|
||||
s.SetSource(source)
|
||||
slice = append(slice, s)
|
||||
state = 1
|
||||
|
||||
} else if !is_sep {
|
||||
if C >= 'A' && C <= 'Z' {
|
||||
C = C + 'a' - 'A'
|
||||
case 1:
|
||||
if is_sep {
|
||||
// No identifier -> ERROR
|
||||
log.Errorf("%s : sequence entry does not have an identifier", source)
|
||||
} else {
|
||||
// Beginning of identifier
|
||||
idBytes.Reset()
|
||||
state = 2
|
||||
idBytes.WriteByte(C)
|
||||
}
|
||||
// Removing white space from the sequence
|
||||
if (C >= 'a' && C <= 'z') || C == '-' || C == '.' || C == '[' || C == ']' {
|
||||
ch.Bytes[current] = C
|
||||
current++
|
||||
case 2:
|
||||
if is_sep {
|
||||
// End of identifier
|
||||
identifier = idBytes.String()
|
||||
idBytes.Reset()
|
||||
state = 3
|
||||
} else {
|
||||
idBytes.WriteByte(C)
|
||||
}
|
||||
if is_end_of_line {
|
||||
// Definition empty
|
||||
definition = ""
|
||||
state = 5
|
||||
}
|
||||
case 3:
|
||||
if is_end_of_line {
|
||||
// Definition empty
|
||||
definition = ""
|
||||
state = 5
|
||||
} else if !is_space {
|
||||
// Beginning of definition
|
||||
defBytes.Reset()
|
||||
defBytes.WriteByte(C)
|
||||
state = 4
|
||||
}
|
||||
case 4:
|
||||
if is_end_of_line {
|
||||
definition = defBytes.String()
|
||||
state = 5
|
||||
}
|
||||
case 5:
|
||||
if !is_end_of_line {
|
||||
// Beginning of sequence
|
||||
seqBytes.Reset()
|
||||
if C >= 'A' && C <= 'Z' {
|
||||
C = C + 'a' - 'A'
|
||||
}
|
||||
|
||||
if (C >= 'a' && C <= 'z') || C == '-' || C == '.' || C == '[' || C == ']' {
|
||||
seqBytes.WriteByte(C)
|
||||
}
|
||||
state = 6
|
||||
}
|
||||
case 6:
|
||||
if C == '>' {
|
||||
// End of sequence
|
||||
s := obiseq.NewBioSequence(identifier, slices.Clone(seqBytes.Bytes()), definition)
|
||||
s.SetSource(source)
|
||||
sequences = append(sequences, s)
|
||||
state = 1
|
||||
|
||||
} else if !is_sep {
|
||||
if C >= 'A' && C <= 'Z' {
|
||||
C = C + 'a' - 'A'
|
||||
}
|
||||
// Removing white space from the sequence
|
||||
if (C >= 'a' && C <= 'z') || C == '-' || C == '.' || C == '[' || C == ']' {
|
||||
seqBytes.WriteByte(C)
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if len(sequences) > 0 {
|
||||
log.Debugln("Pushing sequences")
|
||||
out.Push(obiiter.MakeBioSequenceBatch(chunks.order, sequences))
|
||||
}
|
||||
}
|
||||
|
||||
slice = append(slice, obiseq.NewBioSequence(identifier, bytes.Clone(ch.Bytes[start:current]), definition))
|
||||
batch := obiiter.MakeBioSequenceBatch(ch.index, slice)
|
||||
return &batch
|
||||
out.Done()
|
||||
|
||||
}
|
||||
|
||||
func ReadFasta(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
|
||||
@@ -254,35 +159,21 @@ func ReadFasta(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
|
||||
source := opt.Source()
|
||||
|
||||
nworker := obioptions.CLIReadParallelWorkers()
|
||||
out.Add(nworker)
|
||||
chkchan := ReadSeqFileChunk(reader, _EndOfLastFastaEntry)
|
||||
|
||||
chkchan, err := FastaChunkReader(reader, 1024*500, false)
|
||||
|
||||
if err != nil {
|
||||
return obiiter.NilIBioSequence, err
|
||||
for i := 0; i < nworker; i++ {
|
||||
out.Add(1)
|
||||
go _ParseFastaFile(source, chkchan, out)
|
||||
}
|
||||
|
||||
go func() {
|
||||
out.WaitAndClose()
|
||||
}()
|
||||
|
||||
parser := func() {
|
||||
defer out.Done()
|
||||
for chk := range chkchan {
|
||||
seqs := ParseFastaChunk(source, chk)
|
||||
if seqs != nil {
|
||||
out.Push(*seqs)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for i := 0; i < nworker; i++ {
|
||||
go parser()
|
||||
}
|
||||
|
||||
newIter := out.SortBatches().Rebatch(opt.BatchSize())
|
||||
|
||||
log.Debugln("Full file batch mode : ", opt.FullFileBatch())
|
||||
|
||||
if opt.FullFileBatch() {
|
||||
newIter = newIter.CompleteFileIterator()
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user