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rename the iterator class

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This commit is contained in:
Eric Coissac
2023-01-22 22:04:17 +01:00
parent 4592855095
commit f97f92df72
37 changed files with 399 additions and 354 deletions
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2
pkg/obitools/obiannotate/obiannotate.go Normal file
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@@ -0,0 +1,2 @@
package obiannotate

11
pkg/obitools/obiclean/obiclean.go
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@@ -19,7 +19,7 @@ type seqPCR struct {
SonCount int
AddedSons int
Edges []Edge
Cluster map[int]bool // used as the set of head sequences associated to that sequence
Cluster map[int]bool // used as the set of head sequences associated to that sequence
}
// buildSamples sorts the sequences by samples
@@ -58,7 +58,7 @@ func buildSamples(dataset obiseq.BioSequenceSlice,
func annotateOBIClean(dataset obiseq.BioSequenceSlice,
sample map[string]*([]*seqPCR),
tag, NAValue string) obiiter.IBioSequenceBatch {
tag, NAValue string) obiiter.IBioSequence {
batchsize := 1000
var annot = func(data obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
@@ -207,7 +207,6 @@ func GetCluster(sequence *obiseq.BioSequence) map[string]string {
return cluster
}
// func Cluster(sample map[string]*([]*seqPCR)) {
// for _, graph := range sample {
// for _, s := range *graph {
@@ -215,7 +214,7 @@ func GetCluster(sequence *obiseq.BioSequence) map[string]string {
// if len(s.Edges) > 0 {
// for _, f := range s.Edges {
// }
// }
// } else {
// cluster
// }
@@ -286,7 +285,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
return weight
}
func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
func IOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
db := itertator.Load()
@@ -318,7 +317,6 @@ func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
}
}
Mutation(samples)
pbopt := make([]progressbar.Option, 0, 5)
@@ -352,7 +350,6 @@ func IOBIClean(itertator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
EmpiricalDistCsv(RatioTableFilename(), all_ratio)
}
iter := annotateOBIClean(db, samples, SampleAttribute(), "NA")
if OnlyHead() {

10
pkg/obitools/obiconvert/sequence_reader.go
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@@ -67,9 +67,9 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
return list_of_files, nil
}
func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
var iterator obiiter.IBioSequenceBatch
var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequenceBatch, error)
func ReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
var iterator obiiter.IBioSequence
var reader func(string, ...obiformats.WithOption) (obiiter.IBioSequence, error)
opts := make([]obiformats.WithOption, 0, 10)
@@ -109,7 +109,7 @@ func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
list_of_files, err := _ExpandListOfFiles(false, filenames...)
if err != nil {
return obiiter.NilIBioSequenceBatch, err
return obiiter.NilIBioSequence, err
}
switch CLIInputFormat() {
@@ -140,7 +140,7 @@ func ReadBioSequences(filenames ...string) (obiiter.IBioSequenceBatch, error) {
iterator, err = reader(list_of_files[0], opts...)
if err != nil {
return obiiter.NilIBioSequenceBatch, err
return obiiter.NilIBioSequence, err
}
}

10
pkg/obitools/obiconvert/sequence_writer.go
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@@ -8,10 +8,10 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func WriteBioSequences(iterator obiiter.IBioSequenceBatch,
terminalAction bool, filenames ...string) (obiiter.IBioSequenceBatch, error) {
func WriteBioSequences(iterator obiiter.IBioSequence,
terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
var newIter obiiter.IBioSequenceBatch
var newIter obiiter.IBioSequence
opts := make([]obiformats.WithOption, 0, 10)
@@ -62,12 +62,12 @@ func WriteBioSequences(iterator obiiter.IBioSequenceBatch,
if err != nil {
log.Fatalf("Write file error: %v", err)
return obiiter.NilIBioSequenceBatch, err
return obiiter.NilIBioSequence, err
}
if terminalAction {
newIter.Recycle()
return obiiter.NilIBioSequenceBatch, nil
return obiiter.NilIBioSequence, nil
}
return newIter, nil

2
pkg/obitools/obidistribute/distribute.go
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@@ -9,7 +9,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
)
func DistributeSequence(sequences obiiter.IBioSequenceBatch) {
func DistributeSequence(sequences obiiter.IBioSequence) {
opts := make([]obiformats.WithOption, 0, 10)

6
pkg/obitools/obigrep/grep.go
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@@ -8,14 +8,14 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
)
func IFilterSequence(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
var newIter obiiter.IBioSequenceBatch
func IFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {
var newIter obiiter.IBioSequence
predicate := CLISequenceSelectionPredicate()
if predicate != nil {
if CLISaveDiscardedSequences() {
var discarded obiiter.IBioSequenceBatch
var discarded obiiter.IBioSequence
log.Printf("Discarded sequences saved in file: %s\n", CLIDiscardedFileName())
newIter, discarded = iterator.DivideOn(predicate,

4
pkg/obitools/obimultiplex/demultiplex.go
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@@ -10,7 +10,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
)
func IExtractBarcode(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
opts := make([]obingslibrary.WithOption, 0, 10)
@@ -37,7 +37,7 @@ func IExtractBarcode(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBa
newIter = newIter.Rebatch(obioptions.CLIBatchSize())
}
var unidentified obiiter.IBioSequenceBatch
var unidentified obiiter.IBioSequence
if CLIUnidentifiedFileName() != "" {
log.Printf("Unassigned sequences saved in file: %s\n", CLIUnidentifiedFileName())
unidentified, newIter = newIter.DivideOn(obiseq.HasAttribute("demultiplex_error"),

4
pkg/obitools/obipairing/pairing.go
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@@ -206,7 +206,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
func IAssemblePESequencesBatch(iterator obiiter.IPairedBioSequenceBatch,
gap float64, delta, minOverlap int,
minIdentity float64,
withStats bool, sizes ...int) obiiter.IBioSequenceBatch {
withStats bool, sizes ...int) obiiter.IBioSequence {
nworkers := runtime.NumCPU() * 3 / 2
buffsize := iterator.BufferSize()
@@ -219,7 +219,7 @@ func IAssemblePESequencesBatch(iterator obiiter.IPairedBioSequenceBatch,
buffsize = sizes[1]
}
newIter := obiiter.MakeIBioSequenceBatch(buffsize)
newIter := obiiter.MakeIBioSequence(buffsize)
newIter.Add(nworkers)

2
pkg/obitools/obipcr/pcr.go
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@@ -9,7 +9,7 @@ import (
// PCR iterates over sequences provided by a obiseq.IBioSequenceBatch
// and returns an other obiseq.IBioSequenceBatch distributing
// obiseq.BioSequenceBatch containing the selected amplicon sequences.
func PCR(iterator obiiter.IBioSequenceBatch) (obiiter.IBioSequenceBatch, error) {
func PCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
opts := make([]obiapat.WithOption, 0, 10)

6
pkg/obitools/obirefidx/obirefidx.go
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@@ -32,7 +32,7 @@ func IndexSequence(seqidx int,
// r := 0
// w := 0
for i, ref := range references {
lcs, alilength := obialign.FastLCSScore(sequence, ref, -1 , &matrix)
lcs, alilength := obialign.FastLCSScore(sequence, ref, -1, &matrix)
score[i] = alilength - lcs
}
@@ -88,7 +88,7 @@ func IndexSequence(seqidx int,
return obitag_index
}
func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
references := iterator.Load()
refcounts := make(
@@ -118,7 +118,7 @@ func IndexReferenceDB(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBa
bar := progressbar.NewOptions(len(references), pbopt...)
limits := make(chan [2]int)
indexed := obiiter.MakeIBioSequenceBatch()
indexed := obiiter.MakeIBioSequence()
go func() {
for i := 0; i < len(references); i += 10 {
limits <- [2]int{i, goutils.MinInt(i+10, len(references))}

2
pkg/obitools/obitag/obitag.go
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@@ -171,7 +171,7 @@ func IdentifySeqWorker(references obiseq.BioSequenceSlice,
}
}
func AssignTaxonomy(iterator obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
func AssignTaxonomy(iterator obiiter.IBioSequence) obiiter.IBioSequence {
references := CLIRefDB()
refcounts := make(

2
pkg/obitools/obiuniq/unique.go
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@@ -8,7 +8,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func Unique(sequences obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
func Unique(sequences obiiter.IBioSequence) obiiter.IBioSequence {
options := make([]obichunk.WithOption, 0, 30)