First commit

pkg/obiformats/fastseq_write_fastq.go

@@ -0,0 +1,168 @@
+package obiformats
+
+import (
+	"bytes"
+	"fmt"
+	"io"
+	"log"
+	"os"
+	"time"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func FormatFastq(seq obiseq.BioSequence, quality_shift int, formater FormatHeader) string {
+
+	l := seq.Length()
+	q := seq.Qualities()
+	ascii := make([]byte, seq.Length())
+
+	for j := 0; j < l; j++ {
+		ascii[j] = uint8(q[j]) + uint8(quality_shift)
+	}
+
+	info := ""
+	if formater != nil {
+		info = formater(seq)
+	}
+
+	return fmt.Sprintf("@%s %s %s\n%s\n+\n%s",
+		seq.Id(), info,
+		seq.Definition(),
+		string(seq.Sequence()),
+		string(ascii),
+	)
+}
+
+func FormatFastqBatch(batch obiseq.BioSequenceBatch, quality_shift int,
+	formater FormatHeader) []byte {
+	var bs bytes.Buffer
+	for _, seq := range batch.Slice() {
+		bs.WriteString(FormatFastq(seq, quality_shift, formater))
+		bs.WriteString("\n")
+	}
+	return bs.Bytes()
+}
+
+func WriteFastq(iterator obiseq.IBioSequence, file io.Writer, options ...WithOption) error {
+	opt := MakeOptions(options)
+
+	header_format := opt.FormatFastSeqHeader()
+	quality := opt.QualityShift()
+
+	for iterator.Next() {
+		seq := iterator.Get()
+		fmt.Fprintln(file, FormatFastq(seq, quality, header_format))
+	}
+
+	return nil
+}
+
+func WriteFastqToFile(iterator obiseq.IBioSequence,
+	filename string,
+	options ...WithOption) error {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return err
+	}
+
+	return WriteFastq(iterator, file, options...)
+}
+
+func WriteFastqToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
+	return WriteFastq(iterator, os.Stdout, options...)
+}
+
+type FileChunck struct {
+	text  []byte
+	order int
+}
+
+func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	buffsize := iterator.BufferSize()
+	new_iter := obiseq.MakeIBioSequenceBatch(buffsize)
+
+	opt := MakeOptions(options)
+	nwriters := 4
+
+	chunkchan := make(chan FileChunck)
+
+	header_format := opt.FormatFastSeqHeader()
+	quality := opt.QualityShift()
+
+	new_iter.Add(nwriters)
+
+	go func() {
+		new_iter.Wait()
+		for len(chunkchan) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(chunkchan)
+		for len(new_iter.Channel()) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(new_iter.Channel())
+	}()
+
+	ff := func(iterator obiseq.IBioSequenceBatch) {
+		for iterator.Next() {
+			batch := iterator.Get()
+			chunkchan <- FileChunck{
+				FormatFastqBatch(batch, quality, header_format),
+				batch.Order(),
+			}
+			new_iter.Channel() <- batch
+		}
+		new_iter.Done()
+	}
+
+	log.Println("Start of the fastq file reading")
+	for i := 0; i < nwriters; i++ {
+		go ff(iterator.Split())
+	}
+
+	next_to_send := 0
+	received := make(map[int]FileChunck, 100)
+
+	go func() {
+		for chunk := range chunkchan {
+			if chunk.order == next_to_send {
+				file.Write(chunk.text)
+				next_to_send++
+				chunk, ok := received[next_to_send]
+				for ok {
+					file.Write(chunk.text)
+					delete(received, next_to_send)
+					next_to_send++
+					chunk, ok = received[next_to_send]
+				}
+			} else {
+				received[chunk.order] = chunk
+			}
+
+		}
+	}()
+
+	return new_iter, nil
+}
+
+func WriteFastqBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	return WriteFastqBatch(iterator, os.Stdout, options...)
+}
+
+func WriteFastqBatchToFile(iterator obiseq.IBioSequenceBatch,
+	filename string,
+	options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	return WriteFastqBatch(iterator, file, options...)
+}