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Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools

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This commit is contained in:
Eric Coissac
2022-02-24 07:08:40 +01:00
parent 2e7c1834b0
commit eaf65fbcce
39 changed files with 1225 additions and 241 deletions
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8
pkg/obiformats/dispatcher.go
View File

@@ -5,15 +5,15 @@ import (
"log"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
)
type SequenceBatchWriterToFile func(iterator obiseq.IBioSequenceBatch,
type SequenceBatchWriterToFile func(iterator obiiter.IBioSequenceBatch,
filename string,
options ...WithOption) (obiseq.IBioSequenceBatch, error)
options ...WithOption) (obiiter.IBioSequenceBatch, error)
func WriterDispatcher(prototypename string,
dispatcher obiseq.IDistribute,
dispatcher obiiter.IDistribute,
formater SequenceBatchWriterToFile,
options ...WithOption) {

17
pkg/obiformats/ecopcr_read.go
View File

@@ -10,6 +10,7 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@@ -117,7 +118,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error)
return bseq, nil
}
func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenceBatch {
func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
tag := make([]byte, 11)
n, _ := reader.Read(tag)
@@ -163,7 +164,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
opt := MakeOptions(options)
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter.Add(1)
go func() {
@@ -181,7 +182,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
slice = append(slice, seq)
ii++
if ii >= opt.BatchSize() {
newIter.Push(obiseq.MakeBioSequenceBatch(i, slice))
newIter.Push(obiiter.MakeBioSequenceBatch(i, slice))
slice = obiseq.MakeBioSequenceSlice()
i++
ii = 0
@@ -191,7 +192,7 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
}
if len(slice) > 0 {
newIter.Push(obiseq.MakeBioSequenceBatch(i, slice))
newIter.Push(obiiter.MakeBioSequenceBatch(i, slice))
}
newIter.Done()
@@ -205,12 +206,12 @@ func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenc
return newIter
}
func ReadEcoPCR(reader io.Reader, options ...WithOption) obiseq.IBioSequence {
func ReadEcoPCR(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
ib := ReadEcoPCRBatch(reader, options...)
return ib.SortBatches().IBioSequence()
}
func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
var reader io.Reader
var greader io.Reader
var err error
@@ -218,7 +219,7 @@ func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBi
reader, err = os.Open(filename)
if err != nil {
log.Printf("open file error: %+v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
// Test if the flux is compressed by gzip
@@ -230,7 +231,7 @@ func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBi
return ReadEcoPCRBatch(reader, options...), nil
}
func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
ib, err := ReadEcoPCRBatchFromFile(filename, options...)
return ib.SortBatches().IBioSequence(), err

17
pkg/obiformats/embl_read.go
View File

@@ -10,6 +10,7 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@@ -80,7 +81,7 @@ func _EndOfLastEntry(buff []byte) int {
return -1
}
func _ParseEmblFile(input <-chan _FileChunk, out obiseq.IBioSequenceBatch) {
func _ParseEmblFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
for chunks := range input {
scanner := bufio.NewScanner(chunks.raw)
@@ -139,7 +140,7 @@ func _ParseEmblFile(input <-chan _FileChunk, out obiseq.IBioSequenceBatch) {
seqBytes = new(bytes.Buffer)
}
}
out.Push(obiseq.MakeBioSequenceBatch(order, sequences))
out.Push(obiiter.MakeBioSequenceBatch(order, sequences))
}
out.Done()
@@ -176,11 +177,11 @@ func _ReadFlatFileChunk(reader io.Reader, readers chan _FileChunk) {
// 6 5 43 2 1
// <CR>?<LF>//<CR>?<LF>
func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenceBatch {
func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
opt := MakeOptions(options)
entry_channel := make(chan _FileChunk, opt.BufferSize())
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
nworkers := opt.ParallelWorkers()
newIter.Add(nworkers)
@@ -199,12 +200,12 @@ func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenceB
return newIter
}
func ReadEMBL(reader io.Reader, options ...WithOption) obiseq.IBioSequence {
func ReadEMBL(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
ib := ReadEMBLBatch(reader, options...)
return ib.SortBatches().IBioSequence()
}
func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
var reader io.Reader
var greader io.Reader
var err error
@@ -212,7 +213,7 @@ func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiseq.IBioS
reader, err = os.Open(filename)
if err != nil {
log.Printf("open file error: %+v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
// Test if the flux is compressed by gzip
@@ -224,7 +225,7 @@ func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiseq.IBioS
return ReadEMBLBatch(reader, options...), nil
}
func ReadEMBLFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
func ReadEMBLFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
ib, err := ReadEMBLBatchFromFile(filename, options...)
return ib.SortBatches().IBioSequence(), err

9
pkg/obiformats/fastseq_header.go
View File

@@ -3,6 +3,7 @@ package obiformats
import (
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@@ -14,14 +15,16 @@ func ParseGuessedFastSeqHeader(sequence *obiseq.BioSequence) {
}
}
func IParseFastSeqHeaderBatch(iterator obiseq.IBioSequenceBatch, options ...WithOption) obiseq.IBioSequenceBatch {
func IParseFastSeqHeaderBatch(iterator obiiter.IBioSequenceBatch,
options ...WithOption) obiiter.IBioSequenceBatch {
opt := MakeOptions(options)
return iterator.MakeIWorker(obiseq.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
return iterator.MakeIWorker(obiiter.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
opt.ParallelWorkers(),
opt.BufferSize())
}
func IParseFastSeqHeader(iterator obiseq.IBioSequence, options ...WithOption) obiseq.IBioSequence {
func IParseFastSeqHeader(iterator obiiter.IBioSequence,
options ...WithOption) obiiter.IBioSequence {
opt := MakeOptions(options)
return IParseFastSeqHeaderBatch(iterator.IBioSequenceBatch(opt.BatchSize(),

24
pkg/obiformats/fastseq_read.go
View File

@@ -13,11 +13,12 @@ import (
"unsafe"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func _FastseqReader(seqfile C.fast_kseq_p,
iterator obiseq.IBioSequenceBatch,
iterator obiiter.IBioSequenceBatch,
batch_size int) {
var comment string
i := 0
@@ -63,7 +64,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
// log.Printf("\n==> Pushing sequence batch\n")
// start := time.Now()
iterator.Push(obiseq.MakeBioSequenceBatch(i, slice))
iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
// elapsed := time.Since(start)
// log.Printf("\n==>sequences pushed after %s\n", elapsed)
@@ -73,13 +74,13 @@ func _FastseqReader(seqfile C.fast_kseq_p,
}
}
if len(slice) > 0 {
iterator.Push(obiseq.MakeBioSequenceBatch(i, slice))
iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
}
iterator.Done()
}
func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
opt := MakeOptions(options)
name := C.CString(filename)
@@ -92,7 +93,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
if pointer == nil {
err = fmt.Errorf("cannot open file %s", filename)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
size := int64(-1)
@@ -104,7 +105,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
size = -1
}
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter.Add(1)
go func() {
@@ -124,14 +125,14 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
return newIter, err
}
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
ib, err := ReadFastSeqBatchFromFile(filename, options...)
return ib.SortBatches().IBioSequence(), err
}
func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
func ReadFastSeqBatchFromStdin(options ...WithOption) obiiter.IBioSequenceBatch {
opt := MakeOptions(options)
newIter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter.Add(1)
@@ -139,12 +140,13 @@ func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
newIter.WaitAndClose()
}()
go _FastseqReader(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())), newIter, opt.BatchSize())
go _FastseqReader(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())),
newIter, opt.BatchSize())
return newIter
}
func ReadFastSeqFromStdin(options ...WithOption) obiseq.IBioSequence {
func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
ib := ReadFastSeqBatchFromStdin(options...)
return ib.SortBatches().IBioSequence()
}

28
pkg/obiformats/fastseq_write_fasta.go
View File

@@ -8,6 +8,7 @@ import (
"os"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@@ -21,7 +22,7 @@ func min(x, y int) int {
func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
var fragments strings.Builder
if seq==nil {
if seq == nil {
log.Panicln("try to format a nil BioSequence")
}
@@ -44,7 +45,7 @@ func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
folded)
}
func FormatFastaBatch(batch obiseq.BioSequenceBatch, formater FormatHeader) []byte {
func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []byte {
var bs bytes.Buffer
for _, seq := range batch.Slice() {
bs.WriteString(FormatFasta(seq, formater))
@@ -53,7 +54,7 @@ func FormatFastaBatch(batch obiseq.BioSequenceBatch, formater FormatHeader) []by
return bs.Bytes()
}
func WriteFasta(iterator obiseq.IBioSequence, file io.Writer, options ...WithOption) error {
func WriteFasta(iterator obiiter.IBioSequence, file io.Writer, options ...WithOption) error {
opt := MakeOptions(options)
header_format := opt.FormatFastSeqHeader()
@@ -73,7 +74,7 @@ func WriteFasta(iterator obiseq.IBioSequence, file io.Writer, options ...WithOpt
return nil
}
func WriteFastaToFile(iterator obiseq.IBioSequence,
func WriteFastaToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) error {
@@ -89,16 +90,18 @@ func WriteFastaToFile(iterator obiseq.IBioSequence,
return WriteFasta(iterator, file, options...)
}
func WriteFastaToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
func WriteFastaToStdout(iterator obiiter.IBioSequence, options ...WithOption) error {
options = append(options, OptionDontCloseFile())
return WriteFasta(iterator, os.Stdout, options...)
}
func WriteFastaBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
file io.Writer,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
opt := MakeOptions(options)
buffsize := iterator.BufferSize()
newIter := obiseq.MakeIBioSequenceBatch(buffsize)
newIter := obiiter.MakeIBioSequenceBatch(buffsize)
nwriters := opt.ParallelWorkers()
@@ -113,7 +116,7 @@ func WriteFastaBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
close(chunkchan)
}()
ff := func(iterator obiseq.IBioSequenceBatch) {
ff := func(iterator obiiter.IBioSequenceBatch) {
for iterator.Next() {
batch := iterator.Get()
chunkchan <- FileChunck{
@@ -164,20 +167,21 @@ func WriteFastaBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
return newIter, nil
}
func WriteFastaBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteFastaBatchToStdout(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
options = append(options, OptionDontCloseFile())
return WriteFastaBatch(iterator, os.Stdout, options...)
}
func WriteFastaBatchToFile(iterator obiseq.IBioSequenceBatch,
func WriteFastaBatchToFile(iterator obiiter.IBioSequenceBatch,
filename string,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
file, err := os.Create(filename)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
options = append(options, OptionCloseFile())

26
pkg/obiformats/fastseq_write_fastq.go
View File

@@ -8,6 +8,7 @@ import (
"os"
"time"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@@ -34,7 +35,7 @@ func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHead
)
}
func FormatFastqBatch(batch obiseq.BioSequenceBatch, quality_shift int,
func FormatFastqBatch(batch obiiter.BioSequenceBatch, quality_shift int,
formater FormatHeader) []byte {
var bs bytes.Buffer
for _, seq := range batch.Slice() {
@@ -44,7 +45,7 @@ func FormatFastqBatch(batch obiseq.BioSequenceBatch, quality_shift int,
return bs.Bytes()
}
func WriteFastq(iterator obiseq.IBioSequence, file io.Writer, options ...WithOption) error {
func WriteFastq(iterator obiiter.IBioSequence, file io.Writer, options ...WithOption) error {
opt := MakeOptions(options)
header_format := opt.FormatFastSeqHeader()
@@ -65,7 +66,7 @@ func WriteFastq(iterator obiseq.IBioSequence, file io.Writer, options ...WithOpt
return nil
}
func WriteFastqToFile(iterator obiseq.IBioSequence,
func WriteFastqToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) error {
@@ -80,7 +81,7 @@ func WriteFastqToFile(iterator obiseq.IBioSequence,
return WriteFastq(iterator, file, options...)
}
func WriteFastqToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
func WriteFastqToStdout(iterator obiiter.IBioSequence, options ...WithOption) error {
options = append(options, OptionDontCloseFile())
return WriteFastq(iterator, os.Stdout, options...)
}
@@ -90,11 +91,13 @@ type FileChunck struct {
order int
}
func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
file io.Writer,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
opt := MakeOptions(options)
buffsize := iterator.BufferSize()
newIter := obiseq.MakeIBioSequenceBatch(buffsize)
newIter := obiiter.MakeIBioSequenceBatch(buffsize)
nwriters := opt.ParallelWorkers()
@@ -113,7 +116,7 @@ func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
close(chunkchan)
}()
ff := func(iterator obiseq.IBioSequenceBatch) {
ff := func(iterator obiiter.IBioSequenceBatch) {
for iterator.Next() {
batch := iterator.Get()
chunk := FileChunck{
@@ -165,20 +168,21 @@ func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options
return newIter, nil
}
func WriteFastqBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteFastqBatchToStdout(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
options = append(options, OptionDontCloseFile())
return WriteFastqBatch(iterator, os.Stdout, options...)
}
func WriteFastqBatchToFile(iterator obiseq.IBioSequenceBatch,
func WriteFastqBatchToFile(iterator obiiter.IBioSequenceBatch,
filename string,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
file, err := os.Create(filename)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
options = append(options, OptionCloseFile())

7
pkg/obiformats/options.go
View File

@@ -1,11 +1,12 @@
package obiformats
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type __options__ struct {
fastseq_header_parser obiseq.SeqAnnotator
fastseq_header_parser obiiter.SeqAnnotator
fastseq_header_writer func(*obiseq.BioSequence) string
with_progress_bar bool
buffer_size int
@@ -58,7 +59,7 @@ func (opt Options) ParallelWorkers() int {
return opt.pointer.parallel_workers
}
func (opt Options) ParseFastSeqHeader() obiseq.SeqAnnotator {
func (opt Options) ParseFastSeqHeader() obiiter.SeqAnnotator {
return opt.pointer.fastseq_header_parser
}
@@ -123,7 +124,7 @@ func OptionsQualitySolexa() WithOption {
return OptionsQualityShift(64)
}
func OptionsFastSeqHeaderParser(parser obiseq.SeqAnnotator) WithOption {
func OptionsFastSeqHeaderParser(parser obiiter.SeqAnnotator) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.fastseq_header_parser = parser
})

14
pkg/obiformats/universal_read.go
View File

@@ -8,7 +8,7 @@ import (
"os"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
)
func GuessSeqFileType(firstline string) string {
@@ -36,7 +36,8 @@ func GuessSeqFileType(firstline string) string {
}
}
func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func ReadSequencesBatchFromFile(filename string,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
var file *os.File
var reader io.Reader
var greader io.Reader
@@ -46,7 +47,7 @@ func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.
if err != nil {
log.Fatalf("open file error: %v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
reader = file
@@ -65,7 +66,7 @@ func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.
tag, _ := breader.Peek(30)
if len(tag) < 30 {
newIter := obiseq.MakeIBioSequenceBatch()
newIter := obiiter.MakeIBioSequenceBatch()
newIter.Close()
return newIter, nil
}
@@ -89,10 +90,11 @@ func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.
filename, filetype)
}
return obiseq.NilIBioSequenceBatch, nil
return obiiter.NilIBioSequenceBatch, nil
}
func ReadSequencesFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
func ReadSequencesFromFile(filename string,
options ...WithOption) (obiiter.IBioSequence, error) {
ib, err := ReadSequencesBatchFromFile(filename, options...)
return ib.SortBatches().IBioSequence(), err

26
pkg/obiformats/universal_write.go
View File

@@ -6,10 +6,10 @@ import (
"log"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
)
func WriteSequences(iterator obiseq.IBioSequence,
func WriteSequences(iterator obiiter.IBioSequence,
file io.Writer,
options ...WithOption) error {
@@ -34,7 +34,7 @@ func WriteSequences(iterator obiseq.IBioSequence,
return nil
}
func WriteSequencesToFile(iterator obiseq.IBioSequence,
func WriteSequencesToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) error {
@@ -48,13 +48,13 @@ func WriteSequencesToFile(iterator obiseq.IBioSequence,
return WriteSequences(iterator, file, options...)
}
func WriteSequencesToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
func WriteSequencesToStdout(iterator obiiter.IBioSequence, options ...WithOption) error {
return WriteSequences(iterator, os.Stdout, options...)
}
func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
func WriteSequenceBatch(iterator obiiter.IBioSequenceBatch,
file io.Writer,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
iterator = iterator.Rebatch(1000)
@@ -64,7 +64,7 @@ func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
batch := iterator.Get()
iterator.PushBack()
var newIter obiseq.IBioSequenceBatch
var newIter obiiter.IBioSequenceBatch
var err error
if len(batch.Slice()) > 0 {
@@ -84,24 +84,24 @@ func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
return iterator, nil
}
return obiseq.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready")
return obiiter.NilIBioSequenceBatch, fmt.Errorf("input iterator not ready")
}
func WriteSequencesBatchToStdout(iterator obiseq.IBioSequenceBatch,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func WriteSequencesBatchToStdout(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
options = append(options, OptionDontCloseFile())
return WriteSequenceBatch(iterator, os.Stdout, options...)
}
func WriteSequencesBatchToFile(iterator obiseq.IBioSequenceBatch,
func WriteSequencesBatchToFile(iterator obiiter.IBioSequenceBatch,
filename string,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
file, err := os.Create(filename)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
options = append(options, OptionCloseFile())