First commit

pkg/obiformats/fastseq_write_fasta.go

@@ -0,0 +1,164 @@
+package obiformats
+
+import (
+	"bytes"
+	"fmt"
+	"io"
+	"log"
+	"os"
+	"strings"
+	"sync"
+	"time"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func min(x, y int) int {
+	if x < y {
+		return x
+	}
+	return y
+}
+
+func FormatFasta(seq obiseq.BioSequence, formater FormatHeader) string {
+	var fragments strings.Builder
+
+	s := seq.Sequence()
+	l := len(s)
+
+	fragments.Grow(l + int(l/60) + 10)
+
+	for i := 0; i < l; i += 60 {
+		to := min(i+60, l)
+		fmt.Fprintf(&fragments, "%s\n", string(s[i:to]))
+	}
+
+	folded := fragments.String()
+	folded = folded[:fragments.Len()-1]
+	info := formater(seq)
+	return fmt.Sprintf(">%s %s %s\n%s",
+		seq.Id(), info,
+		seq.Definition(),
+		folded)
+}
+
+func FormatFastaBatch(batch obiseq.BioSequenceBatch, formater FormatHeader) []byte {
+	var bs bytes.Buffer
+	for _, seq := range batch.Slice() {
+		bs.WriteString(FormatFasta(seq, formater))
+		bs.WriteString("\n")
+	}
+	return bs.Bytes()
+}
+
+func WriteFasta(iterator obiseq.IBioSequence, file io.Writer, options ...WithOption) error {
+	opt := MakeOptions(options)
+
+	header_format := opt.FormatFastSeqHeader()
+
+	for iterator.Next() {
+		seq := iterator.Get()
+		fmt.Fprintln(file, FormatFasta(seq, header_format))
+	}
+
+	return nil
+}
+
+func WriteFastaToFile(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 WriteFasta(iterator, file, options...)
+}
+
+func WriteFastaToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
+	return WriteFasta(iterator, os.Stdout, options...)
+}
+
+func WriteFastaBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) error {
+	buffsize := iterator.BufferSize()
+	new_iter := obiseq.MakeIBioSequenceBatch(buffsize)
+
+	opt := MakeOptions(options)
+	nwriters := 4
+
+	chunkchan := make(chan FileChunck)
+	chunkwait := sync.WaitGroup{}
+
+	header_format := opt.FormatFastSeqHeader()
+
+	chunkwait.Add(nwriters)
+
+	go func() {
+		chunkwait.Wait()
+		for len(chunkchan) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(chunkchan)
+	}()
+
+	ff := func(iterator obiseq.IBioSequenceBatch) {
+		for iterator.Next() {
+			batch := iterator.Get()
+			chunkchan <- FileChunck{
+				FormatFastaBatch(batch, header_format),
+				batch.Order(),
+			}
+			new_iter.Channel() <- batch
+		}
+		new_iter.Done()
+	}
+
+	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 nil
+}
+
+func WriteFastaBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) error {
+	return WriteFastaBatch(iterator, os.Stdout, options...)
+}
+
+func WriteFastaBatchToFile(iterator obiseq.IBioSequenceBatch,
+	filename string,
+	options ...WithOption) error {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return err
+	}
+
+	return WriteFastaBatch(iterator, file, options...)
+}