change the model for representing paired reads and extend its usage to other commands

pkg/obitools/obiconvert/options.go

@@ -27,6 +27,9 @@ var __output_solexa_quality__ = false
 var __no_progress_bar__ = false
 var __compressed__ = false
 
+var __output_file_name__ = "-"
+var __paired_file_name__ = ""
+
 func InputOptionSet(options *getoptions.GetOpt) {
 	// options.IntVar(&__skipped_entries__, "skip", __skipped_entries__,
 	// 	options.Description("The N first sequence records of the file are discarded from the analysis and not reported to the output file."))
@@ -73,15 +76,29 @@ func OutputOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
 		options.Description("Disable the progress bar printing"))
 
-	options.BoolVar(&__compressed__, "--compress", false,
+	options.BoolVar(&__compressed__, "compress", false,
 		options.Alias("Z"),
 		options.Description("Output is compressed"))
 
+	options.StringVar(&__output_file_name__, "out", __output_file_name__,
+		options.Alias("o"),
+		options.ArgName("FILENAME"),
+		options.Description("Filename used for saving the output"),
+	)
+
+}
+
+func PairedFilesOptionSet(options *getoptions.GetOpt) {
+	options.StringVar(&__paired_file_name__, "paired-with", __paired_file_name__,
+		options.ArgName("FILENAME"),
+		options.Description("Filename containing the paired reads"),
+	)
 }
 
 func OptionSet(options *getoptions.GetOpt) {
 	InputOptionSet(options)
 	OutputOptionSet(options)
+	PairedFilesOptionSet(options)
 }
 
 // Returns true if the number of reads described in the
@@ -170,3 +187,14 @@ func CLIOutputQualityShift() int {
 func CLIProgressBar() bool {
 	return !__no_progress_bar__
 }
+
+func CLIOutPutFileName() string {
+	return __output_file_name__
+}
+
+func CLIHasPairedFile() bool {
+	return __paired_file_name__ != ""
+}
+func CLIPairedFileName() string {
+	return __paired_file_name__
+}

pkg/obitools/obiconvert/sequence_reader.go

@@ -67,7 +67,7 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 	return list_of_files, nil
 }
 
-func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
+func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 	var iterator obiiter.IBioSequence
 	var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequence, error)
 
@@ -142,6 +142,17 @@ func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 			if err != nil {
 				return obiiter.NilIBioSequence, err
 			}
+
+			if CLIPairedFileName() != "" {
+				ip, err := reader(CLIPairedFileName(), opts...)
+
+				if err != nil {
+					return obiiter.NilIBioSequence, err
+				}
+
+				iterator = iterator.PairTo(ip)
+			}
+
 		}
 
 		// list_of_files = list_of_files[1:]

pkg/obitools/obiconvert/sequence_writer.go

@@ -1,6 +1,9 @@
 package obiconvert
 
 import (
+	"path/filepath"
+	"strings"
+
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
@@ -8,6 +11,27 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 )
 
+func BuildPairedFileNames(filename string) (string, string) {
+
+	dir, name := filepath.Split(filename)
+	parts := strings.SplitN(name, ".", 2)
+
+	forward := parts[0] + "_R1"
+	reverse := parts[0] + "_R2"
+
+	if parts[1] != "" {
+		suffix := "." + parts[1]
+		forward += suffix
+		reverse += suffix
+	}
+
+	if dir != "" {
+		forward = filepath.Join(dir, forward)
+		reverse = filepath.Join(dir, reverse)
+	}
+
+	return forward, reverse
+}
 func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 	terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
 
@@ -45,7 +69,32 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 
 	var err error
 
-	if len(filenames) == 0 {
+	// No file names are specified or it is "-" : the output is done on stdout
+
+	if CLIOutPutFileName() != "-" || (len(filenames) > 0 && filenames[0] != "-") {
+		var fn string
+
+		if len(filenames) == 0 {
+			fn = CLIOutPutFileName()
+		} else {
+			fn = filenames[0]
+		}
+
+		if iterator.IsPaired() {
+			var reverse string
+			fn, reverse = BuildPairedFileNames(fn)
+			opts = append(opts, obiformats.WritePairedReadsTo(reverse))
+		}
+
+		switch CLIOutputFormat() {
+		case "fastq":
+			newIter, err = obiformats.WriteFastqToFile(iterator, fn, opts...)
+		case "fasta":
+			newIter, err = obiformats.WriteFastaToFile(iterator, fn, opts...)
+		default:
+			newIter, err = obiformats.WriteSequencesToFile(iterator, fn, opts...)
+		}
+	} else {
 		switch CLIOutputFormat() {
 		case "fastq":
 			newIter, err = obiformats.WriteFastqToStdout(iterator, opts...)
@@ -54,15 +103,6 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 		default:
 			newIter, err = obiformats.WriteSequencesToStdout(iterator, opts...)
 		}
-	} else {
-		switch CLIOutputFormat() {
-		case "fastq":
-			newIter, err = obiformats.WriteFastqToFile(iterator, filenames[0], opts...)
-		case "fasta":
-			newIter, err = obiformats.WriteFastaToFile(iterator, filenames[0], opts...)
-		default:
-			newIter, err = obiformats.WriteSequencesToFile(iterator, filenames[0], opts...)
-		}
 	}
 
 	if err != nil {