obitools/obitools4
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Change path of the obitools pkg

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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
This commit is contained in:
Eric Coissac
2023-11-29 12:14:37 +01:00
parent 72ad84c2d4
commit 8d77cc4133
122 changed files with 1004 additions and 544 deletions
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2
pkg/obiiter/batch.go
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@ -1,6 +1,6 @@
package obiiter
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
type BioSequenceBatch struct {
slice obiseq.BioSequenceSlice

6
pkg/obiiter/batchiterator.go
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@ -10,9 +10,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"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/tevino/abool/v2"
)

4
pkg/obiiter/distribute.go
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@ -4,7 +4,7 @@ import (
"fmt"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
type IDistribute struct {
@ -46,8 +46,6 @@ func (iterator IBioSequence) Distribute(class *obiseq.BioSequenceClassifier, siz
batchsize = sizes[0]
}
jobDone := sync.WaitGroup{}
lock := sync.Mutex{}

10
pkg/obiiter/fragment.go
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@ -3,8 +3,8 @@ package obiiter
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
@ -25,19 +25,19 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
news := obiseq.MakeBioSequenceSlice()
sl := iterator.Get()
for _, s := range sl.Slice() {
if s.Len() <= minsize {
news = append(news, s)
} else {
for i := 0; i < s.Len(); i += step {
end := obiutils.MinInt(i+length, s.Len())
fusion:=false
fusion := false
if (s.Len() - end) < step {
end = s.Len()
fusion = true
}
frg, err := s.Subsequence(i, end, false)
if err != nil {
log.Panicln(err)
}

2
pkg/obiiter/merge.go
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@ -1,6 +1,6 @@
package obiiter
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
func (iterator IBioSequence) IMergeSequenceBatch(na string, statsOn []string, sizes ...int) IBioSequence {
batchsize := 100

48
pkg/obiiter/workers.go
View File

@ -3,8 +3,8 @@ package obiiter
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// That method allows for applying a SeqWorker function on every sequences.
@ -56,6 +56,16 @@ func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker, sizes ...int)
return newIter
}
// MakeIConditionalWorker applies a given worker function to each sequence in the iterator that satisfies the given predicate.
// It creates a new iterator with the modified sequences and returns it.
//
// Parameters:
// - predicate: A function that takes a sequence and returns a boolean value indicating whether the sequence satisfies a certain condition.
// - worker: A function that takes a sequence and returns a modified version of the sequence.
// - sizes: Optional. One or more integers representing the number of workers to be used for parallel processing. If not provided, the number of workers will be determined by the obioptions.CLIReadParallelWorkers() function.
//
// Return:
// - newIter: A new IBioSequence iterator with the modified sequences.
func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
worker obiseq.SeqWorker, sizes ...int) IBioSequence {
nworkers := obioptions.CLIReadParallelWorkers()
@ -100,6 +110,16 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
return newIter
}
// MakeISliceWorker applies a SeqSliceWorker function to each slice in the IBioSequence iterator,
// creating a new IBioSequence with the modified slices.
//
// The worker function takes a slice as input and returns a modified slice. It is applied to each
// slice in the iterator.
//
// The sizes argument is optional and specifies the number of workers to use. If sizes is not
// provided, the default number of workers is used.
//
// The function returns a new IBioSequence containing the modified slices.
func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, sizes ...int) IBioSequence {
nworkers := obioptions.CLIParallelWorkers()
@ -119,12 +139,12 @@ func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, size
f := func(iterator IBioSequence) {
for iterator.Next() {
batch := iterator.Get()
bs := len(batch.slice)
batch.slice = worker(batch.slice)
if bs != len(batch.slice) {
log.Warnf("Input size : %d output %d", bs, len(batch.slice))
if batch.slice.Len() > 0 {
newIter.Push(batch)
} else {
batch.Recycle(false)
}
newIter.Push(batch)
}
newIter.Done()
}
@ -142,6 +162,17 @@ func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, size
return newIter
}
// WorkerPipe is a function that takes a SeqWorker and a variadic list of sizes as parameters and returns a Pipeable.
//
// The WorkerPipe function creates a closure that takes an IBioSequence iterator as a parameter and returns an IBioSequence.
// Inside the closure, the MakeIWorker method of the iterator is called with the provided worker and sizes, and the result is returned.
//
// Parameters:
// - worker: A SeqWorker object that represents the worker to be used in the closure.
// - sizes: A variadic list of int values that represents the sizes to be used in the MakeIWorker method.
//
// Return:
// - f: A Pipeable object that represents the closure created by the WorkerPipe function.
func WorkerPipe(worker obiseq.SeqWorker, sizes ...int) Pipeable {
f := func(iterator IBioSequence) IBioSequence {
return iterator.MakeIWorker(worker, sizes...)
@ -150,6 +181,11 @@ func WorkerPipe(worker obiseq.SeqWorker, sizes ...int) Pipeable {
return f
}
// SliceWorkerPipe creates a Pipeable function that applies a SeqSliceWorker to an iterator.
//
// The worker parameter is the SeqSliceWorker to be applied.
// The sizes parameter is a variadic parameter representing the sizes of the slices.
// The function returns a Pipeable function that applies the SeqSliceWorker to the iterator.
func SliceWorkerPipe(worker obiseq.SeqSliceWorker, sizes ...int) Pipeable {
f := func(iterator IBioSequence) IBioSequence {
return iterator.MakeISliceWorker(worker, sizes...)