refactor code and change algorithm used to read from many files

pkg/goutils/goutils.go

@@ -6,6 +6,7 @@ import (
 	"encoding/gob"
 	"io"
 	"os"
+	"sync"
 )
 
 // NotAnInteger defines a new type of Error : "NotAnInteger"
@@ -69,7 +70,6 @@ func (m *NotABoolean) Error() string {
 	return m.message
 }
 
-
 // It converts an interface{} to a bool, and returns an error if the interface{} cannot be converted
 // to a bool
 func InterfaceToBool(i interface{}) (val bool, err error) {
@@ -79,27 +79,27 @@ func InterfaceToBool(i interface{}) (val bool, err error) {
 
 	switch t := i.(type) {
 	case int:
-		val = t!=0
+		val = t != 0
 	case int8:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case int16:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case int32:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case int64:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case float32:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case float64:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case uint8:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case uint16:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case uint32:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	case uint64:
-		val = t!=0 // standardizes across systems
+		val = t != 0 // standardizes across systems
 	default:
 		err = &NotABoolean{"value attribute cannot be casted to a boolean"}
 	}
@@ -121,7 +121,7 @@ func CastableToInt(i interface{}) bool {
 }
 
 // "CopyMap copies the contents of a map[string]interface{} to another map[string]interface{}."
-// 
+//
 // The function uses the gob package to encode the source map into a buffer and then decode the buffer
 // into the destination map
 func CopyMap(dest, src map[string]interface{}) {
@@ -161,12 +161,30 @@ func ReadLines(path string) (lines []string, err error) {
 	return
 }
 
-
 func Contains[T comparable](arr []T, x T) bool {
-    for _, v := range arr {
+	for _, v := range arr {
-        if v == x {
+		if v == x {
-            return true
+			return true
-        }
+		}
-    }
+	}
-    return false
+	return false
+}
+
+func AtomicCounter(initial ...int) func() int {
+	counterMutex := sync.Mutex{}
+	counter := 0
+	if len(initial) > 0 {
+		counter = initial[0]
+	}
+
+	nextCounter := func() int {
+		counterMutex.Lock()
+		defer counterMutex.Unlock()
+		val := counter
+		counter++
+
+		return val
+	}
+
+	return nextCounter
 }

pkg/obiformats/batch_of_files_reader.go

@@ -0,0 +1,64 @@
+package obiformats
+
+import (
+	"log"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+)
+
+func ReadSequencesBatchFromFiles(filenames []string,
+	reader IBatchReader,
+	concurrent_readers int,
+	options ...WithOption) obiiter.IBioSequenceBatch {
+
+	if reader == nil {
+		reader = ReadSequencesBatchFromFile
+	}
+
+	batchiter := obiiter.MakeIBioSequenceBatch(0)
+	nextCounter := goutils.AtomicCounter()
+
+	batchiter.Add(concurrent_readers)
+
+	go func() {
+		batchiter.WaitAndClose()
+		log.Println("Finnished to read every files")
+	}()
+
+	filenameChan := make(chan string)
+
+	go func() {
+		for _, filename := range filenames {
+			filenameChan <- filename
+		}
+
+		close(filenameChan)
+	}()
+
+	for i := 0; i < concurrent_readers; i++ {
+		go func() {
+
+			for filename := range filenameChan {
+				iter, err := reader(filename, options...)
+
+				if err != nil {
+					log.Panicf("Cannot open file %s : %v", filename, err)
+				}
+
+				log.Printf("Start reading of file : %s", filename)
+
+				for iter.Next() {
+					batch := iter.Get()
+					batchiter.Push(batch.Reorder(nextCounter()))
+				}
+
+				log.Printf("End of reading of file : %s", filename)
+
+			}
+			batchiter.Done()
+		}()
+	}
+
+	return batchiter
+}

pkg/obiformats/batch_reader_type.go

@@ -0,0 +1,5 @@
+package obiformats
+
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+
+type IBatchReader func(string, ...WithOption) (obiiter.IBioSequenceBatch, error)

pkg/obiformats/fastseq_write_fasta.go

@@ -120,7 +120,9 @@ func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
 
 	ff := func(iterator obiiter.IBioSequenceBatch) {
 		for iterator.Next() {
+
 			batch := iterator.Get()
+
 			chunkchan <- FileChunck{
 				FormatFastaBatch(batch, header_format),
 				batch.Order(),

pkg/obitools/obiconvert/sequence_reader.go

@@ -73,7 +73,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 
 	opts := make([]obiformats.WithOption, 0, 10)
 
-	switch InputFastHeaderFormat() {
+	switch CLIInputFastHeaderFormat() {
 	case "json":
 		opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseFastSeqJsonHeader))
 	case "obi":
@@ -91,15 +91,17 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 	opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
 	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
 
-	opts = append(opts, obiformats.OptionsQualityShift(InputQualityShift()))
+	opts = append(opts, obiformats.OptionsQualityShift(CLIInputQualityShift()))
 
 	if len(filenames) == 0 {
 
-		switch InputFormat() {
+		switch CLIInputFormat() {
 		case "ecopcr":
 			iterator = obiformats.ReadEcoPCRBatch(os.Stdin, opts...)
 		case "embl":
 			iterator = obiformats.ReadEMBLBatch(os.Stdin, opts...)
+		case "genbank":
+			iterator = obiformats.ReadGenbankBatch(os.Stdin, opts...)
 		default:
 			iterator = obiformats.ReadFastSeqBatchFromStdin(opts...)
 		}
@@ -110,39 +112,56 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 			return obiiter.NilIBioSequenceBatch, err
 		}
 
-		switch InputFormat() {
+		switch CLIInputFormat() {
 		case "ecopcr":
 			reader = obiformats.ReadEcoPCRBatchFromFile
 		case "embl":
 			reader = obiformats.ReadEMBLBatchFromFile
+		case "genbank":
+			reader = obiformats.ReadGenbankBatchFromFile
 		default:
 			reader = obiformats.ReadSequencesBatchFromFile
 		}
 
-		iterator, err = reader(list_of_files[0], opts...)
+		if len(list_of_files) > 1 {
+			nreader := 1
 
-		if err != nil {
+			if CLINoInputOrder() {
-			return obiiter.NilIBioSequenceBatch, err
+				nreader = obioptions.CLIParallelWorkers()
-		}
+			}
+			
+			iterator = obiformats.ReadSequencesBatchFromFiles(
+				filenames,
+				reader,
+				nreader,
+				opts...,
+			)
+		} else {
+			iterator, err = reader(list_of_files[0], opts...)
 
-		list_of_files = list_of_files[1:]
-		others := make([]obiiter.IBioSequenceBatch, 0, len(list_of_files))
-
-		for _, fn := range list_of_files {
-			r, err := reader(fn, opts...)
 			if err != nil {
 				return obiiter.NilIBioSequenceBatch, err
 			}
-			others = append(others, r)
 		}
 
-		if len(others) > 0 {
+		// list_of_files = list_of_files[1:]
-			if NoInputOrder() {
+		// others := make([]obiiter.IBioSequenceBatch, 0, len(list_of_files))
-				iterator = iterator.Pool(others...)
+
-			} else {
+		// for _, fn := range list_of_files {
-				iterator = iterator.Concat(others...)
+		// 	r, err := reader(fn, opts...)
-			}
+		// 	if err != nil {
-		}
+		// 		return obiiter.NilIBioSequenceBatch, err
+		// 	}
+		// 	others = append(others, r)
+		// }
+
+		// if len(others) > 0 {
+		// 	if CLINoInputOrder() {
+		// 		iterator = iterator.Pool(others...)
+		// 	} else {
+		// 		iterator = iterator.Concat(others...)
+		// 	}
+		// }
 
 	}
 

pkg/obitools/obiconvert/sequence_writer.go

@@ -12,7 +12,7 @@ func WriteBioSequences(iterator obiiter.IBioSequence, filenames ...string) error
 
 	opts := make([]obiformats.WithOption, 0, 10)
 
-	switch OutputFastHeaderFormat() {
+	switch CLIOutputFastHeaderFormat() {
 	case "json":
 		log.Println("On output use JSON headers")
 		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
@@ -33,12 +33,12 @@ func WriteBioSequences(iterator obiiter.IBioSequence, filenames ...string) error
 	opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
 	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
 
-	opts = append(opts, obiformats.OptionsQualityShift(OutputQualityShift()))
+	opts = append(opts, obiformats.OptionsQualityShift(CLIOutputQualityShift()))
 
 	var err error
 
 	if len(filenames) == 0 {
-		switch OutputFormat() {
+		switch CLIOutputFormat() {
 		case "fastq":
 			err = obiformats.WriteFastqToStdout(iterator, opts...)
 		case "fasta":
@@ -47,7 +47,7 @@ func WriteBioSequences(iterator obiiter.IBioSequence, filenames ...string) error
 			err = obiformats.WriteSequencesToStdout(iterator, opts...)
 		}
 	} else {
-		switch OutputFormat() {
+		switch CLIOutputFormat() {
 		case "fastq":
 			err = obiformats.WriteFastqToFile(iterator, filenames[0], opts...)
 		case "fasta":
@@ -72,7 +72,7 @@ func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
 
 	opts := make([]obiformats.WithOption, 0, 10)
 
-	switch OutputFastHeaderFormat() {
+	switch CLIOutputFastHeaderFormat() {
 	case "json":
 		log.Println("On output use JSON headers")
 		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
@@ -93,12 +93,12 @@ func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
 	opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
 	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
 
-	opts = append(opts, obiformats.OptionsQualityShift(OutputQualityShift()))
+	opts = append(opts, obiformats.OptionsQualityShift(CLIOutputQualityShift()))
 
 	var err error
 
 	if len(filenames) == 0 {
-		switch OutputFormat() {
+		switch CLIOutputFormat() {
 		case "fastq":
 			newIter, err = obiformats.WriteFastqBatchToStdout(iterator, opts...)
 		case "fasta":
@@ -107,7 +107,7 @@ func WriteBioSequencesBatch(iterator obiiter.IBioSequenceBatch,
 			newIter, err = obiformats.WriteSequencesBatchToStdout(iterator, opts...)
 		}
 	} else {
-		switch OutputFormat() {
+		switch CLIOutputFormat() {
 		case "fastq":
 			newIter, err = obiformats.WriteFastqBatchToFile(iterator, filenames[0], opts...)
 		case "fasta":