Adds to every obitools the ability to save in gzip compressed files

pkg/obiformats/fastseq_write_fasta.go

@@ -65,10 +65,12 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []b
 }
 
 func WriteFasta(iterator obiiter.IBioSequence,
-	file io.Writer,
+	file io.WriteCloser,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
+	file,_ = goutils.CompressStream(file,opt.CompressedFile(),opt.CloseFile())
+
 	buffsize := iterator.BufferSize()
 	newIter := obiiter.MakeIBioSequence(buffsize)
 
@@ -133,15 +135,8 @@ func WriteFasta(iterator obiiter.IBioSequence,
 
 		}
 
-		if opt.CloseFile() {
-			switch file := file.(type) {
-			case *os.File:
-				file.Close()
-			case *goutils.Wfile:
-				file.Close()
-			}
-		}
-
+		file.Close()
+	
 		log.Debugln("End of the fasta file writing")
 		obiiter.UnregisterPipe()
 		waitWriter.Done()
@@ -163,11 +158,13 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
 
 
 	opt := MakeOptions(options)
+	flags := os.O_WRONLY | os.O_CREATE
 
-	file,err := goutils.OpenWritingFile(filename,
-		opt.CompressedFile(),
-		opt.AppendFile(),
-	)
+	if opt.AppendFile() {
+		flags |= os.O_APPEND
+	}
+	file, err := os.OpenFile(filename, flags, 0660)
+	
 
 	if err != nil {
 		log.Fatalf("open file error: %v", err)