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Adds to every obitools the ability to save in gzip compressed files

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This commit is contained in:
Eric Coissac
2023-02-18 12:06:52 +01:00
parent 1a08ad4254
commit 56722895e4
9 changed files with 85 additions and 66 deletions
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25
pkg/obiformats/fastseq_write_fasta.go
View File

@@ -65,10 +65,12 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []b
}
func WriteFasta(iterator obiiter.IBioSequence,
file io.Writer,
file io.WriteCloser,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
file,_ = goutils.CompressStream(file,opt.CompressedFile(),opt.CloseFile())
buffsize := iterator.BufferSize()
newIter := obiiter.MakeIBioSequence(buffsize)
@@ -133,15 +135,8 @@ func WriteFasta(iterator obiiter.IBioSequence,
}
if opt.CloseFile() {
switch file := file.(type) {
case *os.File:
file.Close()
case *goutils.Wfile:
file.Close()
}
}
file.Close()
log.Debugln("End of the fasta file writing")
obiiter.UnregisterPipe()
waitWriter.Done()
@@ -163,11 +158,13 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
opt := MakeOptions(options)
flags := os.O_WRONLY | os.O_CREATE
file,err := goutils.OpenWritingFile(filename,
opt.CompressedFile(),
opt.AppendFile(),
)
if opt.AppendFile() {
flags |= os.O_APPEND
}
file, err := os.OpenFile(filename, flags, 0660)
if err != nil {
log.Fatalf("open file error: %v", err)

24
pkg/obiformats/fastseq_write_fastq.go
View File

@@ -54,10 +54,12 @@ type FileChunck struct {
}
func WriteFastq(iterator obiiter.IBioSequence,
file io.Writer,
file io.WriteCloser,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
file,_ = goutils.CompressStream(file,opt.CompressedFile(),opt.CloseFile())
buffsize := iterator.BufferSize()
newIter := obiiter.MakeIBioSequence(buffsize)
@@ -123,14 +125,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
}
if opt.CloseFile() {
switch file := file.(type) {
case *os.File:
file.Close()
case *goutils.Wfile:
file.Close()
}
}
file.Close()
log.Debugln("End of the fastq file writing")
obiiter.UnregisterPipe()
@@ -151,12 +146,13 @@ func WriteFastqToFile(iterator obiiter.IBioSequence,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
flags := os.O_WRONLY | os.O_CREATE
file, err := goutils.OpenWritingFile(filename,
opt.CompressedFile(),
opt.AppendFile(),
)
if opt.AppendFile() {
flags |= os.O_APPEND
}
file, err := os.OpenFile(filename, flags, 0660)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err

8
pkg/obiformats/options.go
View File

@@ -110,17 +110,17 @@ func OptionDontCloseFile() WithOption {
return f
}
func OptionsAppendFile() WithOption {
func OptionsAppendFile(append bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.appendfile = true
opt.pointer.appendfile = append
})
return f
}
func OptionsCompressed() WithOption {
func OptionsCompressed(compressed bool) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.compressed = true
opt.pointer.compressed = compressed
})
return f

13
pkg/obiformats/universal_write.go
View File

@@ -7,12 +7,11 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
)
func WriteSequence(iterator obiiter.IBioSequence,
file io.Writer,
file io.WriteCloser,
options ...WithOption) (obiiter.IBioSequence, error) {
iterator = iterator.Rebatch(1000)
@@ -56,13 +55,13 @@ func WriteSequencesToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
flags := os.O_WRONLY | os.O_CREATE
file, err := goutils.OpenWritingFile(filename,
opt.CompressedFile(),
opt.AppendFile(),
)
if opt.AppendFile() {
flags |= os.O_APPEND
}
file, err := os.OpenFile(filename, flags, 0660)
if err != nil {
log.Fatalf("open file error: %v", err)