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
@@ -1,19 +1,105 @@
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package obiformats
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import (
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"bufio"
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"bytes"
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"io"
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"os"
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"path"
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"slices"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
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log "github.com/sirupsen/logrus"
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"golang.org/x/exp/slices"
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)
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func _EndOfLastFastqEntry(buffer []byte) int {
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var i int
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imax := len(buffer)
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state := 0
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restart := imax - 1
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cut := imax
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for i = imax - 1; i >= 0 && state < 7; i-- {
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C := buffer[i]
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is_end_of_line := C == '\r' || C == '\n'
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is_space := C == ' ' || C == '\t'
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is_sep := is_space || is_end_of_line
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switch state {
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case 0:
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if C == '+' {
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// Potential start of quality part step 1
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state = 1
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restart = i
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}
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case 1:
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if is_end_of_line {
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// Potential start of quality part step 2
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state = 2
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} else {
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// it was not the start of quality part
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state = 0
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i = restart
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}
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case 2:
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if is_sep {
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// Potential start of quality part step 2 (stay in the same state)
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state = 2
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} else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
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// End of the sequence
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state = 3
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} else {
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// it was not the start of quality part
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state = 0
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i = restart
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}
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case 3:
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if is_end_of_line {
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// Entrering in the header line
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state = 4
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} else if (C >= 'a' && C <= 'z') || (C >= 'A' && C <= 'Z') || C == '-' || C == '.' || C == '[' || C == ']' {
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// progressing along of the sequence
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state = 3
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} else {
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// it was not the sequence part
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state = 0
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i = restart
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}
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case 4:
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if is_end_of_line {
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state = 4
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} else {
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state = 5
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}
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case 5:
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if is_end_of_line {
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// It was not the header line
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state = 0
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i = restart
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} else if C == '@' {
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state = 6
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cut = i
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}
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case 6:
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if is_end_of_line {
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state = 7
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} else {
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state = 0
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i = restart
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}
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}
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}
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if i == 0 || state != 7 {
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return -1
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}
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return cut
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}
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func lastFastqCut(buffer []byte) ([]byte, []byte) {
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imax := len(buffer)
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cut := imax
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@@ -95,212 +181,154 @@ func lastFastqCut(buffer []byte) ([]byte, []byte) {
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return []byte{}, buffer
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}
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func FastqChunkReader(r io.Reader, size int) (chan FastxChunk, error) {
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out := make(chan FastxChunk)
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buff := make([]byte, size)
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func _ParseFastqFile(source string,
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input ChannelSeqFileChunk,
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out obiiter.IBioSequence,
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quality_shift byte) {
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n, err := io.ReadFull(r, buff)
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if err == io.ErrUnexpectedEOF {
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err = nil
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}
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if n > 0 && err == nil {
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if n < size {
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buff = buff[:n]
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}
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go func(buff []byte) {
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idx := 0
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end := []byte{}
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for err == nil && n > 0 {
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buff = Concatenate(end, buff)
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// fmt.Println("------------buff--pasted----------------")
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// fmt.Println(string(buff))
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buff, end = lastFastqCut(buff)
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// fmt.Println("----------------buff--cutted------------")
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// fmt.Println(string(buff))
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// fmt.Println("------------------end-------------------")
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// fmt.Println(string(end))
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// fmt.Println("========================================")
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if len(buff) > 0 {
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out <- FastxChunk{
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Bytes: bytes.Clone(buff),
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index: idx,
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}
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idx++
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} else {
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size = size * 2
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}
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buff = slices.Grow(buff[:0], size)[0:size]
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n, err = io.ReadFull(r, buff)
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if n < size {
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buff = buff[:n]
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}
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if err == io.ErrUnexpectedEOF {
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err = nil
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}
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// fmt.Printf("n = %d, err = %v\n", n, err)
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}
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if len(end) > 0 {
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out <- FastxChunk{
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Bytes: bytes.Clone(end),
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index: idx,
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}
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}
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close(out)
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}(buff)
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}
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return out, nil
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}
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func ParseFastqChunk(source string, ch FastxChunk, quality_shift byte) *obiiter.BioSequenceBatch {
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slice := make(obiseq.BioSequenceSlice, 0, obioptions.CLIBatchSize())
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state := 0
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start := 0
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current := 0
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var identifier string
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var definition string
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for i := 0; i < len(ch.Bytes); i++ {
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C := ch.Bytes[i]
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is_end_of_line := C == '\r' || C == '\n'
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is_space := C == ' ' || C == '\t'
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is_sep := is_space || is_end_of_line
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state := 0
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// log.Infof("%s : state = %d pos = %d character = %c (%d)", source, state, i, C, C)
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idBytes := new(bytes.Buffer)
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defBytes := new(bytes.Buffer)
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qualBytes := new(bytes.Buffer)
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seqBytes := new(bytes.Buffer)
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switch state {
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case 0: // Beginning of sequence chunk must start with @
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for chunks := range input {
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scanner := bufio.NewReader(chunks.raw)
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sequences := make(obiseq.BioSequenceSlice, 0, 100)
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for C, err := scanner.ReadByte(); err != io.EOF; C, err = scanner.ReadByte() {
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if C == '@' {
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// Beginning of sequence
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state = 1
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} else {
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log.Errorf("%s : sequence entry is not starting with @", source)
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return nil
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}
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case 1: // Beginning of identifier (Mandatory)
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if is_sep {
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// No identifier -> ERROR
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log.Errorf("%s : sequence identifier is empty", source)
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return nil
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} else {
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// Beginning of identifier
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state = 2
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start = i
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}
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case 2: // Following of the identifier
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if is_sep {
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// End of identifier
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identifier = string(ch.Bytes[start:i])
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state = 3
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}
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if is_end_of_line {
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// Definition empty
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definition = ""
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state = 5
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}
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case 3: // Beginning of definition
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if is_end_of_line {
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// Definition empty
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definition = ""
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state = 5
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} else if !is_space {
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// Beginning of definition
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start = i
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state = 4
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}
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case 4: // Following of the definition
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if is_end_of_line {
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definition = string(ch.Bytes[start:i])
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state = 5
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}
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case 5: // Beginning of sequence
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if !is_end_of_line {
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// Beginning of sequence
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start = i
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if C >= 'A' && C <= 'Z' {
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ch.Bytes[current] = C + 'a' - 'A'
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is_end_of_line := C == '\r' || C == '\n'
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is_space := C == ' ' || C == '\t'
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is_sep := is_space || is_end_of_line
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switch state {
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case 0: // Beginning of sequence chunk must start with @
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if C == '@' {
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// Beginning of sequence
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state = 1
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} else {
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log.Errorf("%s : sequence entry is not starting with @", source)
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}
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current = i + 1
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state = 6
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}
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case 6:
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if is_end_of_line {
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// End of sequence
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s := obiseq.NewBioSequence(identifier, bytes.Clone(ch.Bytes[start:current]), definition)
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s.SetSource(source)
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slice = append(slice, s)
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state = 7
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} else {
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if C >= 'A' && C <= 'Z' {
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ch.Bytes[current] = C + 'a' - 'A'
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case 1: // Beginning of identifier (Mandatory)
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if is_sep {
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// No identifier -> ERROR
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log.Errorf("%s : sequence identifier is empty", source)
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} else {
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// Beginning of identifier
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state = 2
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idBytes.Reset()
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idBytes.WriteByte(C)
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}
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case 2: // Following of the identifier
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if is_sep {
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// End of identifier
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identifier = idBytes.String()
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state = 3
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}
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if is_end_of_line {
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// Definition empty
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definition = ""
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state = 5
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}
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case 3: // Beginning of definition
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if is_end_of_line {
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// Definition empty
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definition = ""
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state = 5
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} else if !is_space {
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// Beginning of definition
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defBytes.Reset()
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defBytes.WriteByte(C)
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state = 4
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}
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case 4: // Following of the definition
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if is_end_of_line {
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definition = defBytes.String()
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state = 5
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}
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case 5: // Beginning of sequence
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if !is_end_of_line {
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// Beginning of sequence
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if C >= 'A' && C <= 'Z' {
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C = C + 'a' - 'A'
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}
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seqBytes.Reset()
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seqBytes.WriteByte(C)
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state = 6
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}
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case 6:
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if is_end_of_line {
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// End of sequence
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s := obiseq.NewBioSequence(identifier, slices.Clone(seqBytes.Bytes()), definition)
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s.SetSource(source)
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sequences = append(sequences, s)
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state = 7
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} else {
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if C >= 'A' && C <= 'Z' {
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C = C + 'a' - 'A'
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}
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seqBytes.WriteByte(C)
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}
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case 7:
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if is_end_of_line {
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state = 7
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} else if C == '+' {
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state = 8
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} else {
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log.Errorf("@%s[%s] : sequence data not followed by a line starting with + but a %c", identifier, source, C)
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}
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case 8:
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if is_end_of_line {
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state = 9
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}
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case 9:
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if is_end_of_line {
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state = 9
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} else {
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// beginning of quality
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state = 10
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qualBytes.Reset()
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qualBytes.WriteByte(C)
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}
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case 10:
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if is_end_of_line {
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// End of quality
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q := qualBytes.Bytes()
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if len(q) != sequences[len(sequences)-1].Len() {
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log.Errorf("%s[%s] : sequence data and quality lenght not equal (%d/%d)",
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identifier, source, len(q), sequences[len(sequences)-1].Len())
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}
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for i := 0; i < len(q); i++ {
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q[i] = q[i] - quality_shift
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}
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sequences[len(sequences)-1].SetQualities(q)
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state = 11
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}
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case 11:
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if is_end_of_line {
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state = 11
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} else if C == '@' {
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state = 1
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} else {
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log.Errorf("%s[%s] : sequence record not followed by a line starting with @", identifier, source)
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}
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current = i + 1
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}
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case 7:
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if is_end_of_line {
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state = 7
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} else if C == '+' {
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state = 8
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} else {
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log.Info(ch.Bytes[0:i])
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log.Info(string(ch.Bytes[0:i]))
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log.Info(C)
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log.Errorf("@%s[%s] : sequence data not followed by a line starting with +", identifier, source)
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return nil // Error
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}
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case 8:
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if is_end_of_line {
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state = 9
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}
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case 9:
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if is_end_of_line {
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state = 9
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} else {
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// beginning of quality
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state = 10
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start = i
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}
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case 10:
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if is_end_of_line {
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// End of quality
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q := ch.Bytes[start:i]
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if len(q) != slice[len(slice)-1].Len() {
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log.Errorf("%s[%s] : sequence data and quality lenght not equal (%d/%d)",
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identifier, source, len(q), slice[len(slice)-1].Len())
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return nil // Error quality lenght not equal to sequence length
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}
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for i := 0; i < len(q); i++ {
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q[i] = q[i] - quality_shift
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}
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slice[len(slice)-1].SetQualities(q)
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state = 11
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}
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case 11:
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if is_end_of_line {
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state = 11
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} else if C == '@' {
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state = 1
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} else {
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log.Errorf("%s[%s] : sequence record not followed by a line starting with @", identifier, source)
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return nil
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}
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}
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if len(sequences) > 0 {
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log.Debugln("Pushing sequences")
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out.Push(obiiter.MakeBioSequenceBatch(chunks.order, sequences))
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}
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}
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batch := obiiter.MakeBioSequenceBatch(ch.index, slice)
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return &batch
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out.Done()
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}
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func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
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@@ -310,37 +338,22 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
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source := opt.Source()
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nworker := obioptions.CLIReadParallelWorkers()
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out.Add(nworker)
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chkchan := ReadSeqFileChunk(reader, _EndOfLastFastqEntry)
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chkchan, err := FastqChunkReader(reader, 1024*500)
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if err != nil {
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return obiiter.NilIBioSequence, err
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for i := 0; i < nworker; i++ {
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out.Add(1)
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go _ParseFastqFile(source, chkchan, out,
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byte(obioptions.InputQualityShift()))
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}
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go func() {
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out.WaitAndClose()
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}()
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parser := func() {
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defer out.Done()
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for chk := range chkchan {
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seqs := ParseFastqChunk(source, chk, byte(obioptions.InputQualityShift()))
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if seqs != nil {
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out.Push(*seqs)
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} else {
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log.Fatalf("error parsing %s", source)
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}
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}
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}
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for i := 0; i < nworker; i++ {
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go parser()
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}
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newIter := out.SortBatches().Rebatch(opt.BatchSize())
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log.Debugln("Full file batch mode : ", opt.FullFileBatch())
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if opt.FullFileBatch() {
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newIter = newIter.CompleteFileIterator()
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}
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Reference in New Issue
Block a user