First commit

pkg/obiformats/universal_write.go

@@ -0,0 +1,79 @@
+package obiformats
+
+import (
+	"fmt"
+	"io"
+	"log"
+	"os"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func WriteSequences(iterator obiseq.IBioSequence,
+	file io.Writer,
+	options ...WithOption) error {
+
+	opts := MakeOptions(options)
+
+	header_format := opts.FormatFastSeqHeader()
+	quality := opts.QualityShift()
+
+	ok := iterator.Next()
+
+	if ok {
+		seq := iterator.Get()
+		if seq.HasQualities() {
+			fmt.Fprintln(file, FormatFastq(seq, quality, header_format))
+			WriteFastq(iterator, file, options...)
+		} else {
+			fmt.Fprintln(file, FormatFasta(seq, header_format))
+			WriteFasta(iterator, file, options...)
+		}
+	}
+
+	return nil
+}
+
+func WriteSequencesToFile(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 WriteSequences(iterator, file, options...)
+}
+
+func WriteSequencesToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
+	return WriteSequences(iterator, os.Stdout, options...)
+}
+
+// func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
+// 	file io.Writer,
+// 	options ...WithOption) error {
+
+// 	opts := MakeOptions(options)
+
+// 	header_format := opts.FormatFastSeqHeader()
+// 	quality := opts.QualityShift()
+
+// 	ok := iterator.Next()
+
+// 	if ok {
+// 		batch := iterator.Get()
+// 		if batch.Slice()[0].HasQualities() {
+// 			file.Write()
+// 			fmt.Fprintln(file, FormatFastq(seq, quality, header_format))
+// 			WriteFastq(iterator, file, options...)
+// 		} else {
+// 			fmt.Fprintln(file, FormatFasta(seq, header_format))
+// 			WriteFasta(iterator, file, options...)
+// 		}
+// 	}
+
+// 	return nil
+// }