Adds information on the new github address

Former-commit-id: 2c47d88724102b115aac5641abccb880dfbec64d

README.md

@@ -5,7 +5,7 @@ They are implemented in *GO* and are tens of times faster than OBITools2.
 
 The git for *OBITools4* is available at :
 
-> https://metabarcoding.org/obitools4
+> https://github.com/metabarcoding/obitools4
 
 ## Installing *OBITools V4*
 
@@ -13,7 +13,7 @@ An installation script that compiles the new *OBITools* on your Unix-like system
 The easiest way to run it is to copy and paste the following command into your terminal
 
 ```{bash}
-curl -L https://metabarcoding.org/obitools4/install.sh | bash
+curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
 ```
 
 By default, the script installs the *OBITools* commands and other associated files into the `/usr/local` directory.
@@ -33,7 +33,7 @@ available on your system, the installation script offers two options:
 You can use these options by following the installation command:
 
 ```{bash}
-curl -L https://metabarcoding.org/obitools4/install.sh | \
+curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
       bash -s -- --install-dir test_install --obitools-prefix k
 ```
 

Release-notes.md

@@ -2,6 +2,26 @@
 
 ## Latest changes
 
+## August 2nd, 2024. Release 4.3.0
+
+### Change of git repositiory
+
+-   The OBITools4 git repository has been moved to the github repository. 
+    The new address is: https://github.com/metabarcoding/obitools4.
+    Take care for using the new install script for retrieving the new version.
+
+    ```bash
+    curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh \
+      | bash
+    ```
+
+    or with options:
+
+    ```bash
+    curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh \
+      | bash -s -- --install-dir test_install --obitools-prefix k
+    ```
+    
 ### CPU limitation
 
 -   By default, *OBITools4* tries to use all the computing power available on
@@ -20,6 +40,37 @@
 
 ### New features
 
+-   The output of the obitools will evolve to produce results only in standard
+    formats such as fasta and fastq. For non-sequential data, the output will be
+    in CSV format, with the separator `,`, the decimal separator `.`, and a
+    header line with the column names. It is more convenient to use the output
+    in other programs. For example, you can use the `csvtomd` command to
+    reformat the csv output into a markdown table. The first command to initiate
+    this change is `obicount`, which now produces a 3-line CSV output.
+
+    ```bash
+    obicount data.csv | csvtomd 
+    ```
+
+-   Adds the new experimental `obicleandb` utility to clean up reference
+    database files created with `obipcr`. An easy way to create a reference
+    database for `obitag` is to use `obipcr` on a local copy of Genbank or EMBL.
+    However, these sequence databases are known to contain many taxonomic
+    errors, such as bacterial sequences annotated with the taxid of their host
+    species. obicleandb tries to detect these errors. To do this, it first keeps
+    only sequences annotated with the taxid to which a species, genus, and
+    family taxid can be assigned. Then, for each sequence, it compares the
+    distance of the sequence to the other sequences belonging to the same genus
+    to the same number of distances between the considered sequence and a
+    randomly selected set of sequences belonging to another family using a
+    Mann-Whitney U test. The alternative hypothesis is that out-of-family
+    distances are greater than intrageneric distances. Sequences are annotated
+    with the p-value of the Mann-Whitney U test in the **obicleandb_trusted**
+    slot. Later, the distribution of this p-value can be analyzed to determine a
+    threshold. Empirically, a threshold of 0.05 is a good compromise and allows
+    to filter out less than 1‰ of the sequences. These sequences can then be
+    removed using `obigrep`.
+
 -   Adds a new `obijoin` utility to join information contained in a sequence
     file with that contained in another sequence or CSV file. The command allows
     you to specify the names of the keys in the main sequence file and in the

cmd/obitools/obicount/main.go

@@ -4,7 +4,8 @@ import (
 	"fmt"
 	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiblackboard"
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicount"
 
@@ -34,28 +35,28 @@ func main() {
 
 	_, args := optionParser(os.Args)
 
-	black := obiblackboard.NewBlackBoard(obioptions.CLIParallelWorkers())
+	obioptions.SetStrictReadWorker(min(4, obioptions.CLIParallelWorkers()))
+	fs, err := obiconvert.CLIReadBioSequences(args...)
 
-	black.ReadSequences(args)
+	if err != nil {
+		log.Errorf("Cannot open file (%v)", err)
+		os.Exit(1)
+	}
 
-	counter := obiblackboard.CountSequenceAggregator("to_delete")
+	nvariant, nread, nsymbol := fs.Count(true)
 
-	black.RegisterRunner("sequences", counter.Runner)
-	black.RegisterRunner("to_delete", obiblackboard.RecycleSequences(true, "final"))
-
-	black.Run()
-
-	fmt.Print("entity,n\n")
+	fmt.Print("entites,n\n")
 
 	if obicount.CLIIsPrintingVariantCount() {
-		fmt.Printf("variants,%d\n", counter.Variants)
+		fmt.Printf("variants,%d\n", nvariant)
 	}
 
 	if obicount.CLIIsPrintingReadCount() {
-		fmt.Printf("reads,%d\n", counter.Reads)
+		fmt.Printf("reads,%d\n", nread)
 	}
 
 	if obicount.CLIIsPrintingSymbolCount() {
-		fmt.Printf("nucleotides,%d\n", counter.Nucleotides)
+		fmt.Printf("symbols,%d\n", nsymbol)
 	}
+
 }

cmd/obitools/obitag2/main.go

@@ -0,0 +1,65 @@
+package main
+
+import (
+	"fmt"
+	"os"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag2"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+)
+
+func main() {
+
+	// go tool pprof -http=":8000" ./build/obitag ./cpu.pprof
+	// f, err := os.Create("cpu.pprof")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// pprof.StartCPUProfile(f)
+	// defer pprof.StopCPUProfile()
+
+	// go tool trace cpu.trace
+	// ftrace, err := os.Create("cpu.trace")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// trace.Start(ftrace)
+	// defer trace.Stop()
+
+	obioptions.SetWorkerPerCore(2)
+	obioptions.SetStrictReadWorker(1)
+	obioptions.SetStrictWriteWorker(1)
+	obioptions.SetBatchSize(10)
+
+	optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)
+
+	_, args := optionParser(os.Args)
+
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)", err)
+		os.Exit(1)
+	}
+
+	taxo, error := obifind.CLILoadSelectedTaxonomy()
+	if error != nil {
+		log.Panicln(error)
+	}
+
+	references := obitag.CLIRefDB()
+
+	identified := obitag2.CLIAssignTaxonomy(fs, references, taxo)
+
+	obiconvert.CLIWriteBioSequences(identified, true)
+	obiiter.WaitForLastPipe()
+
+	fmt.Println("")
+}

cmd/test/main.go

@@ -1,29 +1,38 @@
 package main
 
 import (
-	"fmt"
+	"os"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiblackboard"
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 )
 
-func r2(bb *obiblackboard.Blackboard, task *obiblackboard.Task) *obiblackboard.Task {
-	fmt.Printf("value : %v\n", task.Body)
-	return obiblackboard.NewInitialTask()
-}
-
-func rmul(bb *obiblackboard.Blackboard, task *obiblackboard.Task) *obiblackboard.Task {
-	nt := task.GetNext()
-	nt.Body = task.Body.(int) * 2
-	return nt
-}
-
 func main() {
+	optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
 
-	black := obiblackboard.NewBlackBoard(20)
+	_, args := optionParser(os.Args)
 
-	black.RegisterRunner("todisplay", "final", r2)
-	black.RegisterRunner("multiply", "todisplay", rmul)
-	black.RegisterRunner("initial", "multiply", obiblackboard.DoCount(1000).RepeatTask(4))
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)", err)
+		os.Exit(1)
+	}
+
+	frags := obiiter.IFragments(
+		1000,
+		100,
+		10,
+		100,
+		obioptions.CLIParallelWorkers(),
+	)
+
+	obiconvert.CLIWriteBioSequences(fs.Pipe(frags), true)
+
+	obiiter.WaitForLastPipe()
 
-	black.Run()
 }

install_obitools.sh

@@ -4,7 +4,7 @@ INSTALL_DIR="/usr/local"
 OBITOOLS_PREFIX=""
 # default values
 URL="https://go.dev/dl/"
-OBIURL4="https://git.metabarcoding.org/obitools/obitools4/obitools4/-/archive/master/obitools4-master.tar.gz"
+OBIURL4="https://github.com/metabarcoding/obitools4/archive/refs/heads/master.zip"
 INSTALL_DIR="/usr/local"
 OBITOOLS_PREFIX=""
 
@@ -106,8 +106,10 @@ curl "$GOURL" \
 PATH="$(pwd)/go/bin:$PATH"
 export PATH
 
-curl -L "$OBIURL4" \
-    | tar zxf - 
+curl -L "$OBIURL4" > master.zip
+unzip master.zip
+
+echo "Install OBITOOLS from : $OBIURL4"
 
 cd obitools4-master || exit
 

pkg/obiblackboard/blackboard.go

@@ -1,204 +0,0 @@
-package obiblackboard
-
-import (
-	"slices"
-	"sync"
-	"time"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
-)
-
-type DoTask func(*Blackboard, *Task) *Task
-
-type Blackboard struct {
-	Board      map[int]Queue
-	BoardLock  *sync.Mutex
-	Runners    map[string]DoTask
-	Running    *obiutils.Counter
-	TargetSize int
-	Size       int
-}
-
-func doFinal(bb *Blackboard, task *Task) *Task {
-	if task.SavedTask != nil {
-		return task.SavedTask
-	}
-
-	return NewInitialTask()
-}
-
-func NewBlackBoard(size int) *Blackboard {
-	board := make(map[int]Queue, 0)
-	runners := make(map[string]DoTask, 0)
-
-	if size < 2 {
-		size = 2
-	}
-
-	bb := &Blackboard{
-		Board:      board,
-		BoardLock:  &sync.Mutex{},
-		Runners:    runners,
-		Running:    obiutils.NewCounter(),
-		TargetSize: size,
-		Size:       0,
-	}
-
-	for i := 0; i < size; i++ {
-		bb.PushTask(NewInitialTask())
-	}
-
-	bb.RegisterRunner("final", doFinal)
-
-	return bb
-}
-
-func (bb *Blackboard) RegisterRunner(target string, runner DoTask) {
-	bb.Runners[target] = runner
-}
-
-func (bb *Blackboard) MaxQueue() Queue {
-	max_priority := -1
-	max_queue := Queue(nil)
-	for priority, queue := range bb.Board {
-		if priority > max_priority {
-			max_queue = queue
-		}
-	}
-
-	return max_queue
-}
-
-func (bb *Blackboard) PopTask() *Task {
-	bb.BoardLock.Lock()
-	defer bb.BoardLock.Unlock()
-
-	q := bb.MaxQueue()
-
-	if q != nil {
-		next_task := (*q)[0]
-		(*q) = (*q)[1:]
-		if len(*q) == 0 {
-			delete(bb.Board, next_task.Priority)
-		}
-		bb.Size--
-		return next_task
-	}
-
-	return (*Task)(nil)
-}
-
-func (bb *Blackboard) PushTask(task *Task) {
-	bb.BoardLock.Lock()
-	defer bb.BoardLock.Unlock()
-
-	if task != nil {
-		priority := task.Priority
-		queue, ok := bb.Board[priority]
-
-		if !ok {
-			queue = NewQueue()
-			bb.Board[priority] = queue
-		}
-
-		*queue = slices.Grow(*queue, 1)
-		*queue = append((*queue), task)
-
-		bb.Size++
-	}
-}
-
-func (bb *Blackboard) Run() {
-
-	ctask := make(chan *Task)
-	lock := &sync.WaitGroup{}
-
-	launcher := func() {
-		for task := range ctask {
-			runner, ok := bb.Runners[task.Role]
-
-			if ok {
-				task = runner(bb, task)
-			}
-
-			bb.PushTask(task)
-			bb.Running.Dec()
-		}
-
-		lock.Done()
-	}
-
-	parallel := bb.TargetSize - 1
-	lock.Add(parallel)
-
-	for i := 0; i < parallel; i++ {
-		go launcher()
-	}
-
-	go func() {
-
-		for {
-			bb.Running.Inc()
-			task := bb.PopTask()
-
-			if task != nil {
-				ctask <- task
-			} else {
-				bb.Running.Dec()
-				if bb.Running.Value()+bb.Len() <= 0 {
-					break
-				}
-				time.Sleep(time.Millisecond)
-			}
-
-		}
-
-		close(ctask)
-	}()
-
-	lock.Wait()
-}
-
-// func (bb *Blackboard) Run() {
-// 	lock := &sync.WaitGroup{}
-
-// 	launcher := func(runner DoTask, task *Task) {
-// 		task = runner(bb, task)
-
-// 		if task != nil {
-// 			for bb.Len() > bb.TargetSize {
-// 				time.Sleep(time.Millisecond)
-// 			}
-// 			bb.PushTask(task)
-// 		}
-
-// 		bb.Running.Dec()
-// 		lock.Done()
-// 	}
-
-// 	lock.Add(1)
-
-// 	func() {
-// 		for bb.Len()+bb.Running.Value() > 0 {
-// 			bb.Running.Inc()
-// 			task := bb.PopTask()
-
-// 			if task != nil {
-// 				lock.Add(1)
-// 				go launcher(bb.Runners[task.Role], task)
-// 			} else {
-// 				bb.Running.Dec()
-// 			}
-// 		}
-
-// 		lock.Done()
-// 	}()
-
-// 	lock.Wait()
-// }
-
-func (bb *Blackboard) Len() int {
-	return bb.Size
-}
-
-// 151431044 151431044 15083822152

pkg/obiblackboard/count_sequences.go

@@ -1,50 +0,0 @@
-package obiblackboard
-
-import (
-	"sync"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-)
-
-type SequenceCounter struct {
-	Variants    int
-	Reads       int
-	Nucleotides int
-	Runner      DoTask
-}
-
-func CountSequenceAggregator(target string) *SequenceCounter {
-	cc := &SequenceCounter{
-		Variants:    0,
-		Reads:       0,
-		Nucleotides: 0,
-		Runner:      nil,
-	}
-
-	mutex := sync.Mutex{}
-
-	runner := func(bb *Blackboard, task *Task) *Task {
-		body := task.Body.(obiiter.BioSequenceBatch)
-
-		mutex.Lock()
-		cc.Variants += body.Len()
-		cc.Reads += body.Slice().Count()
-		cc.Nucleotides += body.Slice().Size()
-		mutex.Unlock()
-
-		nt := task.GetNext(target, true, false)
-		return nt
-	}
-
-	cc.Runner = runner
-	return cc
-}
-
-func RecycleSequences(rescycleSequence bool, target string) DoTask {
-	return func(bb *Blackboard, task *Task) *Task {
-		body := task.Body.(obiiter.BioSequenceBatch)
-		// log.Warningf("With priority %d, Recycling %s[%d]", task.Priority, body.Source(), body.Order())
-		body.Recycle(rescycleSequence)
-		return task.GetNext(target, false, false)
-	}
-}

pkg/obiblackboard/display_task.go

@@ -1,17 +0,0 @@
-package obiblackboard
-
-import "fmt"
-
-func DisplayTask(bb *Blackboard, task *Task) *Task {
-	if task == nil {
-		return nil
-	}
-
-	fmt.Printf("Task: %s:\n%v\n\n", task.Role, task.Body)
-
-	return task
-}
-
-func (runner DoTask) Display() DoTask {
-	return runner.CombineWith(DisplayTask)
-}

pkg/obiblackboard/doIterate.go

@@ -1,70 +0,0 @@
-package obiblackboard
-
-import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
-
-type Iteration[T any] struct {
-	Index int
-	Value T
-}
-
-// DoIterateSlice generates a DoTask function that iterates over a given slice and
-// creates a new InitialTask for each element. The function takes in a slice of type
-// T and a target string. It returns a DoTask function that can be used to execute
-// the iteration. The DoTask function takes a Blackboard and a Task as input and
-// returns a new Task. The Task's Role is set to the target string and its Body is
-// set to an Iteration struct containing the index i and the element s[i] from the
-// input slice. The iteration stops when the index i is equal to or greater than
-// the length of the input slice.
-//
-// Parameters:
-// - s: The slice of type T to iterate over.
-// - target: The target string to set as the Task's Role.
-//
-// Return type:
-// - DoTask: The DoTask function that can be used to execute the iteration.
-func DoIterateSlice[T any](s []T, target string) DoTask {
-	n := len(s)
-	idx := obiutils.AtomicCounter()
-
-	dt := func(bb *Blackboard, t *Task) *Task {
-		i := idx()
-		if i < n {
-			nt := t.GetNext(target, false, false)
-			nt.Body = Iteration[T]{i, s[i]}
-			return nt
-		}
-		return nil
-	}
-
-	return dt
-}
-
-// DoCount generates a DoTask function that iterates over a given integer n and
-// creates a new InitialTask for each iteration. The function takes in an integer n
-// and a target string. It returns a DoTask function that can be used to execute
-// the iteration. The DoTask function takes a Blackboard and a Task as input and
-// returns a new Task. The Task's Role is set to the target string and its Body is
-// set to the current iteration index i. The iteration stops when the index i is
-// equal to or greater than the input integer n.
-//
-// Parameters:
-// - n: The integer to iterate over.
-// - target: The target string to set as the Task's Role.
-//
-// Return type:
-// - DoTask: The DoTask function that can be used to execute the iteration.
-func DoCount(n int, target string) DoTask {
-	idx := obiutils.AtomicCounter()
-
-	dt := func(bb *Blackboard, t *Task) *Task {
-		i := idx()
-		if i < n {
-			nt := t.GetNext(target, false, false)
-			nt.Body = i
-			return nt
-		}
-		return nil
-	}
-
-	return dt
-}

pkg/obiblackboard/queue.go

@@ -1,8 +0,0 @@
-package obiblackboard
-
-type Queue *[]*Task
-
-func NewQueue() Queue {
-	q := make([]*Task, 0)
-	return &q
-}

pkg/obiblackboard/read_sequences.go

@@ -1,534 +0,0 @@
-package obiblackboard
-
-import (
-	"bufio"
-	"bytes"
-	"fmt"
-	"io"
-	"os"
-	"path"
-	"path/filepath"
-	"regexp"
-	"strings"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
-
-	"github.com/gabriel-vasile/mimetype"
-	"github.com/goombaio/orderedset"
-	log "github.com/sirupsen/logrus"
-)
-
-func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
-	res, err := _ExpandListOfFiles(check_ext, filenames...)
-
-	if err != nil {
-		log.Infof("Found %d files to process", len(res))
-	}
-
-	return res, err
-}
-
-func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
-	var err error
-	list_of_files := orderedset.NewOrderedSet()
-	for _, fn := range filenames {
-		// Special case for stdin
-		if fn == "-" {
-			list_of_files.Add(fn)
-			continue
-		}
-
-		err = filepath.Walk(fn,
-			func(path string, info os.FileInfo, err error) error {
-				var e error
-				if info == nil {
-					return fmt.Errorf("cannot open path")
-				}
-				for info.Mode()&os.ModeSymlink == os.ModeSymlink {
-					path, e = filepath.EvalSymlinks(path)
-					if e != nil {
-						return e
-					}
-
-					info, e = os.Stat(path)
-					if e != nil {
-						return e
-					}
-				}
-
-				if info.IsDir() {
-					if path != fn {
-						subdir, e := ExpandListOfFiles(true, path)
-						if e != nil {
-							return e
-						}
-						for _, f := range subdir {
-							list_of_files.Add(f)
-						}
-					} else {
-						check_ext = true
-					}
-				} else {
-					if !check_ext ||
-						strings.HasSuffix(path, "csv") ||
-						strings.HasSuffix(path, "csv.gz") ||
-						strings.HasSuffix(path, "fasta") ||
-						strings.HasSuffix(path, "fasta.gz") ||
-						strings.HasSuffix(path, "fastq") ||
-						strings.HasSuffix(path, "fastq.gz") ||
-						strings.HasSuffix(path, "seq") ||
-						strings.HasSuffix(path, "seq.gz") ||
-						strings.HasSuffix(path, "gb") ||
-						strings.HasSuffix(path, "gb.gz") ||
-						strings.HasSuffix(path, "dat") ||
-						strings.HasSuffix(path, "dat.gz") ||
-						strings.HasSuffix(path, "ecopcr") ||
-						strings.HasSuffix(path, "ecopcr.gz") {
-						log.Debugf("Appending %s file\n", path)
-						list_of_files.Add(path)
-					}
-				}
-				return nil
-			})
-
-		if err != nil {
-			return nil, err
-		}
-	}
-
-	res := make([]string, 0, list_of_files.Size())
-	for _, v := range list_of_files.Values() {
-		res = append(res, v.(string))
-	}
-
-	return res, nil
-}
-
-// OBIMimeTypeGuesser is a function that takes an io.Reader as input and guesses the MIME type of the data.
-// It uses several detectors to identify specific file formats, such as FASTA, FASTQ, ecoPCR2, GenBank, and EMBL.
-// The function reads data from the input stream and analyzes it using the mimetype library.
-// It then returns the detected MIME type, a modified reader with the read data, and any error encountered during the process.
-//
-// The following file types are recognized:
-// - "text/ecopcr": if the first line starts with "#@ecopcr-v2".
-// - "text/fasta": if the first line starts with ">".
-// - "text/fastq": if the first line starts with "@".
-// - "text/embl": if the first line starts with "ID   ".
-// - "text/genbank": if the first line starts with "LOCUS       ".
-// - "text/genbank" (special case): if the first line "Genetic Sequence Data Bank" (for genbank release files).
-// - "text/csv"
-//
-// Parameters:
-// - stream: An io.Reader representing the input stream to read data from.
-//
-// Returns:
-// - *mimetype.MIME: The detected MIME type of the data.
-// - io.Reader: A modified reader with the read data.
-// - error: Any error encountered during the process.
-func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
-	fastaDetector := func(raw []byte, limit uint32) bool {
-		ok, err := regexp.Match("^>[^ ]", raw)
-		return ok && err == nil
-	}
-
-	fastqDetector := func(raw []byte, limit uint32) bool {
-		ok, err := regexp.Match("^@[^ ].*\n[^ ]+\n\\+", raw)
-		return ok && err == nil
-	}
-
-	ecoPCR2Detector := func(raw []byte, limit uint32) bool {
-		ok := bytes.HasPrefix(raw, []byte("#@ecopcr-v2"))
-		return ok
-	}
-
-	genbankDetector := func(raw []byte, limit uint32) bool {
-		ok2 := bytes.HasPrefix(raw, []byte("LOCUS       "))
-		ok1, err := regexp.Match("^[^ ]* +Genetic Sequence Data Bank *\n", raw)
-		return ok2 || (ok1 && err == nil)
-	}
-
-	emblDetector := func(raw []byte, limit uint32) bool {
-		ok := bytes.HasPrefix(raw, []byte("ID   "))
-		return ok
-	}
-
-	mimetype.Lookup("text/plain").Extend(fastaDetector, "text/fasta", ".fasta")
-	mimetype.Lookup("text/plain").Extend(fastqDetector, "text/fastq", ".fastq")
-	mimetype.Lookup("text/plain").Extend(ecoPCR2Detector, "text/ecopcr2", ".ecopcr")
-	mimetype.Lookup("text/plain").Extend(genbankDetector, "text/genbank", ".seq")
-	mimetype.Lookup("text/plain").Extend(emblDetector, "text/embl", ".dat")
-
-	mimetype.Lookup("application/octet-stream").Extend(fastaDetector, "text/fasta", ".fasta")
-	mimetype.Lookup("application/octet-stream").Extend(fastqDetector, "text/fastq", ".fastq")
-	mimetype.Lookup("application/octet-stream").Extend(ecoPCR2Detector, "text/ecopcr2", ".ecopcr")
-	mimetype.Lookup("application/octet-stream").Extend(genbankDetector, "text/genbank", ".seq")
-	mimetype.Lookup("application/octet-stream").Extend(emblDetector, "text/embl", ".dat")
-
-	// Create a buffer to store the read data
-	buf := make([]byte, 1024*128)
-	n, err := io.ReadFull(stream, buf)
-
-	if err != nil && err != io.ErrUnexpectedEOF {
-		return nil, nil, err
-	}
-
-	// Detect the MIME type using the mimetype library
-	mimeType := mimetype.Detect(buf)
-	if mimeType == nil {
-		return nil, nil, err
-	}
-
-	// Create a new reader based on the read data
-	newReader := io.Reader(bytes.NewReader(buf[:n]))
-
-	if err == nil {
-		newReader = io.MultiReader(newReader, stream)
-	}
-
-	return mimeType, newReader, nil
-}
-
-func TextChunkParser(parser obiformats.SeqFileChunkParser, target string) DoTask {
-
-	return func(bb *Blackboard, task *Task) *Task {
-		chunk := task.Body.(obiformats.SeqFileChunk)
-		sequences, err := parser(chunk.Source, chunk.Raw)
-
-		if err != nil {
-			return nil
-		}
-
-		nt := task.GetNext(target, false, false)
-		nt.Body = obiiter.MakeBioSequenceBatch(
-			chunk.Source,
-			chunk.Order,
-			sequences)
-
-		return nt
-	}
-}
-
-func SeqAnnotParser(parser obiseq.SeqAnnotator, target string) DoTask {
-	worker := obiseq.SeqToSliceWorker(obiseq.AnnotatorToSeqWorker(parser), false)
-
-	return func(bb *Blackboard, task *Task) *Task {
-		batch := task.Body.(obiiter.BioSequenceBatch)
-		sequences, err := worker(batch.Slice())
-
-		if err != nil {
-			log.Errorf("SeqAnnotParser on %s[%d]: %v", batch.Source(), batch.Order(), err)
-			return nil
-		}
-
-		nt := task.GetNext(target, false, false)
-		nt.Body = obiiter.MakeBioSequenceBatch(
-			batch.Source(),
-			batch.Order(),
-			sequences,
-		)
-		return nt
-	}
-
-}
-
-// OpenStream opens a file specified by the given filename and returns a reader for the file,
-// the detected MIME type of the file, and any error encountered during the process.
-//
-// Parameters:
-//   - filename: A string representing the path to the file to be opened. If the filename is "-",
-//     the function opens the standard input stream.
-//
-// Returns:
-// - io.Reader: A reader for the file.
-// - *mimetype.MIME: The detected MIME type of the file.
-// - error: Any error encountered during the process.
-func OpenStream(filename string) (io.Reader, *mimetype.MIME, error) {
-	var stream io.Reader
-	var err error
-	if filename == "-" {
-		stream, err = obiformats.Buf(os.Stdin)
-	} else {
-		stream, err = obiformats.Ropen(filename)
-	}
-
-	if err != nil {
-		return nil, nil, err
-	}
-
-	// Detect the MIME type using the mimetype library
-	mimeType, newReader, err := OBIMimeTypeGuesser(stream)
-	if err != nil {
-		return nil, nil, err
-	}
-
-	log.Infof("%s mime type: %s", filename, mimeType.String())
-
-	return bufio.NewReader(newReader), mimeType, nil
-}
-
-type OpenedStreamBody struct {
-	Stream     io.Reader
-	Filename   string
-	Source     string
-	Mime       *mimetype.MIME
-	ToBeClosed bool
-}
-
-func FilenameToStream(target string) DoTask {
-
-	return func(bb *Blackboard, task *Task) *Task {
-		filename := task.Body.(Iteration[string]).Value
-		stream, mimetype, err := OpenStream(filename)
-
-		if err != nil {
-			log.Errorf("Error opening %s: %v", filename, err)
-			return nil
-		}
-
-		tobeclosed := filename != "-"
-
-		switch mimetype.String() {
-		case "text/fasta", "text/fastq", "text/ecopcr2", "text/genbank", "text/embl", "text/csv":
-			nt := task.GetNext(target+":"+mimetype.String(), false, false)
-			nt.Body = OpenedStreamBody{
-				Stream:     stream,
-				Mime:       mimetype,
-				Filename:   filename,
-				Source:     obiutils.RemoveAllExt((path.Base(filename))),
-				ToBeClosed: tobeclosed,
-			}
-
-			return nt
-
-		default:
-			log.Errorf("File %s (mime type %s) is an unsupported format", filename, mimetype.String())
-			return nil
-		}
-	}
-}
-
-type TextChunkIteratorBody struct {
-	Chunks     obiformats.ChannelSeqFileChunk
-	Stream     io.Reader
-	Source     string
-	ToBeClosed bool
-}
-
-func StreamToTextChunkReader(lastEntry obiformats.LastSeqRecord, target string) DoTask {
-	return func(bb *Blackboard, task *Task) *Task {
-
-		body := task.Body.(OpenedStreamBody)
-		iterator := obiformats.ReadSeqFileChunk(
-			body.Source,
-			body.Stream,
-			make([]byte, 64*1024*1024),
-			lastEntry,
-		)
-
-		nt := task.GetNext(target, false, false)
-		nt.Body = TextChunkIteratorBody{
-			Chunks:     iterator,
-			Stream:     body.Stream,
-			Source:     body.Source,
-			ToBeClosed: body.ToBeClosed,
-		}
-
-		return nt
-	}
-}
-
-func TextChuckIterator(endTask *Task, target string) DoTask {
-	return func(bb *Blackboard, task *Task) *Task {
-		body := task.Body.(TextChunkIteratorBody)
-
-		chunk, ok := <-body.Chunks
-
-		if !ok {
-			return endTask
-		}
-
-		var nt *Task
-
-		if bb.Len() > bb.TargetSize {
-			nt = task.GetNext(target, false, true)
-		} else {
-			nt = task.GetNext(target, false, false)
-			bb.PushTask(task)
-		}
-
-		nt.Body = chunk
-		return nt
-	}
-}
-
-type SequenceIteratorBody struct {
-	Iterator   obiiter.IBioSequence
-	Stream     io.Reader
-	Source     string
-	ToBeClosed bool
-}
-
-func StreamToSequenceReader(
-	reader obiformats.SequenceReader,
-	options []obiformats.WithOption,
-	target string) DoTask {
-	return func(bb *Blackboard, task *Task) *Task {
-		body := task.Body.(OpenedStreamBody)
-		iterator, err := reader(body.Stream, options...)
-
-		if err != nil {
-			log.Errorf("Error opening %s: %v", body.Filename, err)
-			return nil
-		}
-
-		nt := task.GetNext(target, false, false)
-		nt.Body = SequenceIteratorBody{
-			Iterator:   iterator,
-			Stream:     body.Stream,
-			Source:     body.Source,
-			ToBeClosed: body.ToBeClosed,
-		}
-
-		return nt
-	}
-}
-
-func SequenceIterator(endTask *Task, target string) DoTask {
-	return func(bb *Blackboard, task *Task) *Task {
-		body := task.Body.(SequenceIteratorBody)
-
-		if body.Iterator.Next() {
-			batch := body.Iterator.Get()
-
-			var nt *Task
-			if bb.Len() > bb.TargetSize {
-				nt = task.GetNext(target, false, true)
-			} else {
-				nt = task.GetNext(target, false, false)
-				bb.PushTask(task)
-			}
-
-			nt.Body = batch
-
-			return nt
-		} else {
-			return endTask
-		}
-	}
-}
-
-func (bb *Blackboard) ReadSequences(filepath []string, options ...obiformats.WithOption) {
-
-	var err error
-
-	opts := obiformats.MakeOptions(options)
-
-	if len(filepath) == 0 {
-		filepath = []string{"-"}
-	}
-
-	filepath, err = ExpandListOfFiles(false, filepath...)
-
-	if err != nil {
-		log.Fatalf("Cannot expand list of files : %v", err)
-	}
-
-	bb.RegisterRunner(
-		"initial",
-		DoIterateSlice(filepath, "filename"),
-	)
-
-	bb.RegisterRunner(
-		"filename",
-		FilenameToStream("stream"),
-	)
-
-	bb.RegisterRunner("stream:text/fasta",
-		StreamToTextChunkReader(
-			obiformats.EndOfLastFastaEntry,
-			"fasta_text_reader",
-		))
-
-	bb.RegisterRunner("fasta_text_reader",
-		TextChuckIterator(NewInitialTask(), "fasta_text_chunk"),
-	)
-
-	bb.RegisterRunner(
-		"fasta_text_chunk",
-		TextChunkParser(
-			obiformats.FastaChunkParser(),
-			"unannotated_sequences",
-		),
-	)
-
-	bb.RegisterRunner("stream:text/fastq",
-		StreamToTextChunkReader(obiformats.EndOfLastFastqEntry,
-			"fastq_text_reader"))
-
-	bb.RegisterRunner("fastq_text_reader",
-		TextChuckIterator(NewInitialTask(), "fastq_text_chunk"),
-	)
-
-	bb.RegisterRunner(
-		"fastq_text_chunk",
-		TextChunkParser(
-			obiformats.FastqChunkParser(obioptions.InputQualityShift()),
-			"unannotated_sequences",
-		),
-	)
-
-	bb.RegisterRunner("stream:text/embl",
-		StreamToTextChunkReader(obiformats.EndOfLastFlatFileEntry,
-			"embl_text_reader"))
-
-	bb.RegisterRunner("embl_text_reader",
-		TextChuckIterator(NewInitialTask(), "embl_text_chunk"),
-	)
-
-	bb.RegisterRunner(
-		"embl_text_chunk",
-		TextChunkParser(
-			obiformats.EmblChunkParser(opts.WithFeatureTable()),
-			"sequences",
-		),
-	)
-
-	bb.RegisterRunner("stream:text/genbank",
-		StreamToTextChunkReader(obiformats.EndOfLastFlatFileEntry,
-			"genbank_text_reader"))
-
-	bb.RegisterRunner("genbank_text_reader",
-		TextChuckIterator(NewInitialTask(), "genbank_text_chunk"),
-	)
-
-	bb.RegisterRunner(
-		"genbank_text_chunk",
-		TextChunkParser(
-			obiformats.GenbankChunkParser(opts.WithFeatureTable()),
-			"sequences",
-		),
-	)
-
-	bb.RegisterRunner(
-		"unannotated_sequences",
-		SeqAnnotParser(
-			opts.ParseFastSeqHeader(),
-			"sequences",
-		),
-	)
-
-	bb.RegisterRunner("stream:text/csv",
-		StreamToSequenceReader(obiformats.ReadCSV, options, "sequence_reader"))
-
-	bb.RegisterRunner("stream:text/ecopcr2",
-		StreamToSequenceReader(obiformats.ReadEcoPCR, options, "sequence_reader"))
-
-	bb.RegisterRunner("sequence_reader",
-		SequenceIterator(NewInitialTask(), "sequences"),
-	)
-
-}

pkg/obiblackboard/subtask.go

@@ -1,108 +0,0 @@
-package obiblackboard
-
-import (
-	"sync"
-
-	log "github.com/sirupsen/logrus"
-)
-
-// RepeatTask creates a new DoTask function that repeats the given task n times.
-//
-// It takes an integer n as input, which specifies the number of times the task should be repeated.
-// It returns a new DoTask function that can be used to execute the repeated task.
-//
-// The returned DoTask function maintains a map of tasks to their counts and tasks.
-// When a task is executed, it checks if the task has been executed before.
-// If it has, it increments the count and returns the previously executed task.
-// If it has not been executed before, it executes the task using the provided runner function.
-// If the runner function returns nil, the task is not added to the task memory and nil is returned.
-// If the runner function returns a non-nil task, it is added to the task memory with a count of 0.
-// After executing the task, the function checks if the count is less than (n-1).
-// If it is, the task is added back to the blackboard to be executed again.
-// If the count is equal to (n-1), the task is removed from the task memory.
-// Finally, the function returns the executed task.
-func (runner DoTask) RepeatTask(n int) DoTask {
-	type memtask struct {
-		count int
-		task  *Task
-	}
-	taskMemory := make(map[*Task]*memtask)
-	taskMemoryLock := sync.Mutex{}
-
-	if n < 1 {
-		log.Fatalf("Cannot repeat a task less than once (n=%d)", n)
-	}
-
-	st := func(bb *Blackboard, task *Task) *Task {
-		taskMemoryLock.Lock()
-
-		mem, ok := taskMemory[task]
-
-		if !ok {
-			nt := runner(bb, task)
-
-			if nt == nil {
-				taskMemoryLock.Unlock()
-				return nt
-			}
-
-			mem = &memtask{
-				count: 0,
-				task:  nt,
-			}
-
-			taskMemory[task] = mem
-		} else {
-			mem.count++
-		}
-
-		taskMemoryLock.Unlock()
-
-		if mem.count < (n - 1) {
-			bb.PushTask(task)
-		}
-
-		if mem.count == (n - 1) {
-			taskMemoryLock.Lock()
-			delete(taskMemory, task)
-			taskMemoryLock.Unlock()
-		}
-
-		return mem.task
-	}
-
-	return st
-}
-
-// CombineWith returns a new DoTask function that combines the given DoTask
-// functions. The returned function applies the `other` function to the result
-// of the `runner` function. The `bb` parameter is the Blackboard instance,
-// and the `task` parameter is the Task instance.
-//
-// Parameters:
-// - bb: The Blackboard instance.
-// - task: The Task instance.
-//
-// Returns:
-//   - *Task: The result of applying the `other` function to the result of the
-//     `runner` function.
-func (runner DoTask) CombineWith(other DoTask) DoTask {
-	return func(bb *Blackboard, task *Task) *Task {
-		return other(bb, runner(bb, task))
-	}
-}
-
-// SetTarget sets the target role for the task.
-//
-// Parameters:
-// - target: The target role to set.
-//
-// Returns:
-// - DoTask: The modified DoTask function.
-func (runner DoTask) SetTarget(target string) DoTask {
-	return func(bb *Blackboard, task *Task) *Task {
-		nt := runner(bb, task)
-		nt.Role = target
-		return nt
-	}
-}

pkg/obiblackboard/task.go

@@ -1,34 +0,0 @@
-package obiblackboard
-
-type Task struct {
-	Role      string
-	SavedTask *Task
-	Priority  int
-	Body      interface{}
-}
-
-func NewInitialTask() *Task {
-	return &Task{
-		Role:      "initial",
-		SavedTask: nil,
-		Priority:  0,
-		Body:      nil,
-	}
-}
-
-func (task *Task) GetNext(target string, copy bool, save bool) *Task {
-	t := NewInitialTask()
-	t.Priority = task.Priority + 1
-	t.Role = target
-	if copy {
-		t.Body = task.Body
-	}
-
-	if save {
-		t.SavedTask = task
-	} else {
-		t.SavedTask = task.SavedTask
-	}
-
-	return t
-}

pkg/obiformats/fastseq_write_fasta.go

@@ -74,7 +74,7 @@ func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
 // - skipEmpty: a boolean indicating whether empty sequences should be skipped or not.
 //
 // It returns a byte array containing the formatted sequences.
-func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) []byte {
+func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) *bytes.Buffer {
 	// Create a buffer to store the formatted sequences
 	var bs bytes.Buffer
 
@@ -114,7 +114,7 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, ski
 	}
 
 	// Return the byte array representation of the buffer
-	return bs.Bytes()
+	return &bs
 }
 
 // WriteFasta writes a given iterator of bio sequences to a file in FASTA format.
@@ -154,7 +154,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 
 			chunkchan <- SeqFileChunk{
 				Source: batch.Source(),
-				Raw:    bytes.NewBuffer(FormatFastaBatch(batch, header_format, opt.SkipEmptySequence())),
+				Raw:    FormatFastaBatch(batch, header_format, opt.SkipEmptySequence()),
 				Order:  batch.Order(),
 			}
 

pkg/obiformats/fastseq_write_fastq.go

@@ -14,6 +14,8 @@ import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
+type FormatSeqBatch func(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) *bytes.Buffer
+
 func _formatFastq(buff *bytes.Buffer, seq *obiseq.BioSequence, formater FormatHeader) {
 
 	info := ""
@@ -49,7 +51,7 @@ func FormatFastq(seq *obiseq.BioSequence, formater FormatHeader) string {
 }
 
 func FormatFastqBatch(batch obiiter.BioSequenceBatch,
-	formater FormatHeader, skipEmpty bool) []byte {
+	formater FormatHeader, skipEmpty bool) *bytes.Buffer {
 	var bs bytes.Buffer
 
 	lt := 0
@@ -82,9 +84,7 @@ func FormatFastqBatch(batch obiiter.BioSequenceBatch,
 
 	}
 
-	chunk := bs.Bytes()
-
-	return chunk
+	return &bs
 }
 
 type FileChunk struct {
@@ -127,7 +127,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
 			batch := iterator.Get()
 			chunk := SeqFileChunk{
 				Source: batch.Source(),
-				Raw:    bytes.NewBuffer(FormatFastqBatch(batch, header_format, opt.SkipEmptySequence())),
+				Raw:    FormatFastqBatch(batch, header_format, opt.SkipEmptySequence()),
 				Order:  batch.Order(),
 			}
 			chunkchan <- chunk

pkg/obiformats/options.go

@@ -7,7 +7,8 @@ import (
 
 type __options__ struct {
 	fastseq_header_parser obiseq.SeqAnnotator
-	fastseq_header_writer func(*obiseq.BioSequence) string
+	fastseq_header_writer BioSequenceFormater
+	seqBatchFormater      FormatSeqBatch
 	with_progress_bar     bool
 	buffer_size           int
 	batch_size            int
@@ -44,6 +45,7 @@ func MakeOptions(setters []WithOption) Options {
 	o := __options__{
 		fastseq_header_parser: ParseGuessedFastSeqHeader,
 		fastseq_header_writer: FormatFastSeqJsonHeader,
+		seqBatchFormater:      nil,
 		with_progress_bar:     false,
 		buffer_size:           2,
 		parallel_workers:      obioptions.CLIReadParallelWorkers(),
@@ -103,6 +105,10 @@ func (opt Options) FormatFastSeqHeader() func(*obiseq.BioSequence) string {
 	return opt.pointer.fastseq_header_writer
 }
 
+func (opt Options) SequenceFormater() FormatSeqBatch {
+	return opt.pointer.seqBatchFormater
+}
+
 func (opt Options) NoOrder() bool {
 	return opt.pointer.no_order
 }
@@ -219,8 +225,6 @@ func OptionNoOrder(no_order bool) WithOption {
 	return f
 }
 
-
-
 func OptionsCompressed(compressed bool) WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.compressed = compressed
@@ -271,6 +275,14 @@ func OptionsFastSeqHeaderFormat(format func(*obiseq.BioSequence) string) WithOpt
 	return f
 }
 
+func OptionsSequenceFormater(formater FormatSeqBatch) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.seqBatchFormater = formater
+	})
+
+	return f
+}
+
 func OptionsParallelWorkers(nworkers int) WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.parallel_workers = nworkers

pkg/obioptions/options.go

@@ -14,7 +14,7 @@ import (
 )
 
 var _Debug = false
-var _WorkerPerCore = 1.0
+var _WorkerPerCore = 2.0
 var _ReadWorkerPerCore = 0.5
 var _WriteWorkerPerCore = 0.25
 var _StrictReadWorker = 0

pkg/obioptions/version.go

@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "776b8f7"
+var _Commit = "1b1cd41"
 var _Version = ""
 
 // Version returns the version of the obitools package.

pkg/obiseq/biosequenceslice.go

@@ -186,21 +186,6 @@ func (s BioSequenceSlice) Size() int {
 	return size
 }
 
-// Count calculates the total count of all BioSequence elements in the BioSequenceSlice.
-//
-// It iterates over each BioSequence in the slice and adds the count of each BioSequence to the total count.
-//
-// Returns the total count as an integer.
-func (s BioSequenceSlice) Count() int {
-	size := 0
-
-	for _, s := range s {
-		size += s.Count()
-	}
-
-	return size
-}
-
 func (s BioSequenceSlice) AttributeKeys(skip_map bool) obiutils.Set[string] {
 	keys := obiutils.MakeSet[string]()
 

pkg/obitools/obiconsensus/obiconsensus.go

@@ -51,7 +51,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 				0,
 				seqs,
 			),
-				obiformats.FormatFastSeqJsonHeader, false))
+				obiformats.FormatFastSeqJsonHeader, false).Bytes())
 			fasta.Close()
 		}
 

pkg/obitools/obipcr/pcr.go

@@ -52,7 +52,7 @@ func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
 			100,
 			obioptions.CLIParallelWorkers(),
 		)
-		log.Infof("Fragmenting sequence longer than %dbp into chunks of %dbp",
+		log.Infof("Fragmenting sequence longer than %dbp into chuncks of %dbp",
 			CLIMaxLength()*1000,
 			CLIMaxLength()*100,
 		)