Change the way sequence definition are managed. They are now when present stored as an attribute

Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c

pkg/obiapat/pattern.go

@@ -298,6 +298,24 @@ func (pattern ApatPattern) FindAllIndex(sequence ApatSequence, begin, length int
 	return loc
 }
 
+// BestMatch finds the best match of a given pattern in a sequence.
+//
+// THe function identify the first occurrence of the pattern in the sequence.
+// The search can be limited to a portion of the sequence using the begin and
+// length parameters to find the next occurrences.
+//
+// The BestMatch methood ins
+// It takes the following parameters:
+// - pattern: the pattern to search for (ApatPattern).
+// - sequence: the sequence to search in (ApatSequence).
+// - begin: the starting index of the search (int).
+// - length: the length of the search (int).
+//
+// It returns the following values:
+// - start: the starting index of the best match (int).
+// - end: the ending index of the best match (int).
+// - nerr: the number of errors in the best match (int).
+// - matched: a boolean indicating whether a match was found (bool).
 func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (start int, end int, nerr int, matched bool) {
 	res := pattern.FindAllIndex(sequence, begin, length)
 

pkg/obiformats/empty_file.go

@@ -0,0 +1,9 @@
+package obiformats
+
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+
+func ReadEmptyFile(options ...WithOption) (obiiter.IBioSequence, error) {
+	out := obiiter.MakeIBioSequence()
+	out.Close()
+	return out, nil
+}

pkg/obiformats/fastaseq_read.go

@@ -294,6 +294,11 @@ func ReadFastaFromFile(filename string, options ...WithOption) (obiiter.IBioSequ
 
 	file, err := Ropen(filename)
 
+	if err == ErrNoContent {
+		log.Infof("file %s is empty", filename)
+		return ReadEmptyFile(options...)
+	}
+
 	if err != nil {
 		return obiiter.NilIBioSequence, err
 	}
@@ -305,6 +310,11 @@ func ReadFastaFromStdin(reader io.Reader, options ...WithOption) (obiiter.IBioSe
 	options = append(options, OptionsSource(obiutils.RemoveAllExt("stdin")))
 	input, err := Buf(os.Stdin)
 
+	if err == ErrNoContent {
+		log.Infof("stdin is empty")
+		return ReadEmptyFile(options...)
+	}
+
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
 		return obiiter.NilIBioSequence, err

pkg/obiformats/fastqseq_read.go

@@ -339,6 +339,11 @@ func ReadFastqFromFile(filename string, options ...WithOption) (obiiter.IBioSequ
 
 	file, err := Ropen(filename)
 
+	if err == ErrNoContent {
+		log.Infof("file %s is empty", filename)
+		return ReadEmptyFile(options...)
+	}
+
 	if err != nil {
 		return obiiter.NilIBioSequence, err
 	}
@@ -350,6 +355,11 @@ func ReadFastqFromStdin(reader io.Reader, options ...WithOption) (obiiter.IBioSe
 	options = append(options, OptionsSource(obiutils.RemoveAllExt("stdin")))
 	input, err := Buf(os.Stdin)
 
+	if err == ErrNoContent {
+		log.Infof("stdin is empty")
+		return ReadEmptyFile(options...)
+	}
+
 	if err != nil {
 		log.Fatalf("open file error: %v", err)
 		return obiiter.NilIBioSequence, err

pkg/obiformats/ngsfilter_read.go

@@ -59,9 +59,13 @@ func _parseMainNGSFilterTags(text string) obingslibrary.TagPair {
 	}
 }
 
-func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.TagPair, string, string, bool) {
+func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.TagPair, string, string, bool, bool) {
 	fields := strings.Fields(text)
 
+	if len(fields) < 6 {
+		return obingslibrary.PrimerPair{}, obingslibrary.TagPair{}, "", "", false, false
+	}
+
 	tags := _parseMainNGSFilterTags(fields[2])
 	partial := fields[5] == "T" || fields[5] == "t"
 
@@ -72,7 +76,8 @@ func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.T
 		tags,
 		fields[0],
 		fields[1],
-		partial
+		partial,
+		true
 }
 
 func ReadNGSFilter(reader io.Reader) (obingslibrary.NGSLibrary, error) {
@@ -89,7 +94,15 @@ func ReadNGSFilter(reader io.Reader) (obingslibrary.NGSLibrary, error) {
 
 		split := strings.SplitN(line, "@", 2)
 
-		primers, tags, experiment, sample, partial := _parseMainNGSFilter(split[0])
+		if len(split) < 1 {
+			return nil, fmt.Errorf("line %d : invalid format", i+1)
+		}
+
+		primers, tags, experiment, sample, partial, ok := _parseMainNGSFilter(split[0])
+
+		if !ok {
+			return nil, fmt.Errorf("line %d : invalid format", i+1)
+		}
 
 		marker, _ := ngsfilter.GetMarker(primers.Forward, primers.Reverse)
 		pcr, ok := marker.GetPCR(tags.Forward, tags.Reverse)

pkg/obingslibrary/match.go

@@ -104,6 +104,16 @@ func (marker *Marker) Compile(forward, reverse string, maxError int, allowsIndel
 	return nil
 }
 
+// Match finds the best matching demultiplex for a given sequence.
+//
+// Parameters:
+//
+//	marker - a pointer to a Marker struct that contains the forward and reverse primers.
+//	sequence - a pointer to a BioSequence struct that represents the input sequence.
+//
+// Returns:
+//
+//	A pointer to a DemultiplexMatch struct that contains the best matching demultiplex.
 func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 	aseq, _ := obiapat.MakeApatSequence(sequence, false)
 
@@ -223,6 +233,15 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 	return nil
 }
 
+// ExtractBarcode extracts the barcode from the given biosequence.
+//
+// Parameters:
+// - sequence: The biosequence from which to extract the barcode.
+// - inplace: A boolean indicating whether the barcode should be extracted in-place or not.
+//
+// Returns:
+// - The biosequence with the extracted barcode.
+// - An error indicating any issues encountered during the extraction process.
 func (match *DemultiplexMatch) ExtractBarcode(sequence *obiseq.BioSequence, inplace bool) (*obiseq.BioSequence, error) {
 	if !inplace {
 		sequence = sequence.Copy()

pkg/obiseq/biosequence.go

@@ -55,8 +55,8 @@ type Annotation map[string]interface{}
 // A BioSequence is a sequence of bytes with an identifier, a definition, a sequence, qualities,
 // features and annotations. It aims to represent a biological sequence
 type BioSequence struct {
-	id          string // The identidier of the sequence (private accessible through the method Id)
+	id string // The identidier of the sequence (private accessible through the method Id)
-	definition  string // The documentation of the sequence (private accessible through the method Definition)
+	//definition  string // The documentation of the sequence (private accessible through the method Definition)
 	source      string // The filename without directory name and extension from where the sequence was read.
 	sequence    []byte // The sequence itself, it is accessible by the methode Sequence
 	qualities   []byte // The quality scores of the sequence.
@@ -80,8 +80,8 @@ func NewEmptyBioSequence(preallocate int) *BioSequence {
 	}
 
 	return &BioSequence{
-		id:          "",
+		id: "",
-		definition:  "",
+		//definition:  "",
 		source:      "",
 		sequence:    seq,
 		qualities:   nil,
@@ -148,7 +148,7 @@ func (s *BioSequence) Copy() *BioSequence {
 	newSeq := NewEmptyBioSequence(0)
 
 	newSeq.id = s.id
-	newSeq.definition = s.definition
+	//newSeq.definition = s.definition
 
 	newSeq.sequence = CopySlice(s.sequence)
 	newSeq.qualities = CopySlice(s.qualities)
@@ -176,7 +176,16 @@ func (s *BioSequence) Id() string {
 // No parameters.
 // Returns a string.
 func (s *BioSequence) Definition() string {
-	return s.definition
+	definition := ""
+	var err error
+	def, ok := s.GetAttribute("definition")
+	if ok {
+		definition, err = obiutils.InterfaceToString(def)
+		if err != nil {
+			definition = ""
+		}
+	}
+	return definition
 }
 
 // Sequence returns the sequence of the BioSequence.
@@ -315,7 +324,7 @@ func (s *BioSequence) SetId(id string) {
 //
 // It takes a string parameter 'definition' and assigns it to the 'definition' field of the BioSequence struct.
 func (s *BioSequence) SetDefinition(definition string) {
-	s.definition = definition
+	s.SetAttribute("definition", definition)
 }
 
 // SetSource sets the source of the BioSequence.

pkg/obiseq/biosequence_test.go

@@ -143,11 +143,10 @@ func TestBioSequence_Recycle(t *testing.T) {
 // Returns: None.
 func TestCopy(t *testing.T) {
 	seq := &BioSequence{
-		id:         "test",
+		id:        "test",
-		definition: "test sequence",
+		sequence:  []byte("ATCG"),
-		sequence:   []byte("ATCG"),
+		qualities: []byte("1234"),
-		qualities:  []byte("1234"),
+		feature:   []byte("feature1...feature2"),
-		feature:    []byte("feature1...feature2"),
 		annotations: Annotation{
 			"annotation1": "value1",
 			"annotation2": "value2",
@@ -161,10 +160,6 @@ func TestCopy(t *testing.T) {
 	if newSeq.id != seq.id {
 		t.Errorf("Expected id to be %v, got %v", seq.id, newSeq.id)
 	}
-	if newSeq.definition != seq.definition {
-		t.Errorf("Expected definition to be %v, got %v", seq.definition, newSeq.definition)
-	}
-
 	// Test if the sequence, qualities, and feature fields are copied correctly
 	if !reflect.DeepEqual(newSeq.sequence, seq.sequence) {
 		t.Errorf("Expected sequence to be %v, got %v", seq.sequence, newSeq.sequence)

pkg/obiseq/subseq.go

@@ -32,7 +32,7 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
 		}
 
 		newSeq.id = fmt.Sprintf("%s_sub[%d..%d]", sequence.Id(), from+1, to)
-		newSeq.definition = sequence.definition
+		//	newSeq.definition = sequence.definition
 	} else {
 		newSeq, _ = sequence.Subsequence(from, sequence.Len(), false)
 		newSeq.Write(sequence.Sequence()[0:to])

pkg/obiutils/cast_interface.go

@@ -1,5 +1,17 @@
 package obiutils
 
+import "fmt"
+
+// InterfaceToString converts an interface value to a string.
+//
+// The function takes an interface{} value as a parameter and returns a string representation of that value.
+// It returns the string representation and an error if any occurred during the conversion process.
+func InterfaceToString(i interface{}) (val string, err error) {
+	err = nil
+	val = fmt.Sprintf("%v", i)
+	return
+}
+
 // CastableToInt checks if the given input can be casted to an integer.
 //
 // i: the value to check for castability.

pkg/obiutils/goutils.go

@@ -4,7 +4,6 @@ import (
 	"bufio"
 	"bytes"
 	"encoding/json"
-	"fmt"
 	"io"
 	"os"
 	"reflect"
@@ -13,15 +12,6 @@ import (
 	"github.com/barkimedes/go-deepcopy"
 )
 
-// InterfaceToInt converts a interface{} to an integer value if possible.
-// If not a "NotAnInteger" error is returned via the err
-// return value and val is set to 0.
-func InterfaceToString(i interface{}) (val string, err error) {
-	err = nil
-	val = fmt.Sprintf("%v", i)
-	return
-}
-
 // NotAnInteger defines a new type of Error : "NotAnInteger"
 type NotAnInteger struct {
 	message string