obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-08 16:50:27 +00:00
Code Issues Packages Projects Releases Wiki Activity

change the model for representing paired reads and extend its usage to other commands

Browse Source
This commit is contained in:
Eric Coissac
2023-02-23 23:35:58 +01:00
parent ebb05fcdf7
commit 072b85e155
23 changed files with 598 additions and 338 deletions
Download Patch File Download Diff File Expand all files Collapse all files

21
pkg/obiformats/fastseq_write_fasta.go
View File

@@ -69,7 +69,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
file,_ = goutils.CompressStream(file,opt.CompressedFile(),opt.CloseFile())
file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
buffsize := iterator.BufferSize()
newIter := obiiter.MakeIBioSequence(buffsize)
@@ -136,7 +136,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
}
file.Close()
log.Debugln("End of the fasta file writing")
obiiter.UnregisterPipe()
waitWriter.Done()
@@ -156,7 +156,6 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
filename string,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
flags := os.O_WRONLY | os.O_CREATE
@@ -164,7 +163,6 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
flags |= os.O_APPEND
}
file, err := os.OpenFile(filename, flags, 0660)
if err != nil {
log.Fatalf("open file error: %v", err)
@@ -173,5 +171,18 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
options = append(options, OptionCloseFile())
return WriteFasta(iterator, file, options...)
iterator, err = WriteFasta(iterator, file, options...)
if opt.HaveToSavePaired() {
var revfile *os.File
revfile, err = os.OpenFile(opt.PairedFileName(), flags, 0660)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err
}
iterator, err = WriteFasta(iterator.PairedWith(), revfile, options...)
}
return iterator, err
}

19
pkg/obiformats/fastseq_write_fastq.go
View File

@@ -58,7 +58,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options)
file,_ = goutils.CompressStream(file,opt.CompressedFile(),opt.CloseFile())
file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
buffsize := iterator.BufferSize()
newIter := obiiter.MakeIBioSequence(buffsize)
@@ -152,7 +152,7 @@ func WriteFastqToFile(iterator obiiter.IBioSequence,
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
@@ -160,5 +160,18 @@ func WriteFastqToFile(iterator obiiter.IBioSequence,
options = append(options, OptionCloseFile())
return WriteFastq(iterator, file, options...)
iterator, err = WriteFastq(iterator, file, options...)
if opt.HaveToSavePaired() {
var revfile *os.File
revfile, err = os.OpenFile(opt.PairedFileName(), flags, 0660)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err
}
iterator, err = WriteFastq(iterator.PairedWith(), revfile, options...)
}
return iterator, err
}

31
pkg/obiformats/options.go
View File

@@ -15,6 +15,11 @@ type __options__ struct {
closefile bool
appendfile bool
compressed bool
csv_ids bool
cvs_sequence bool
csv_definition bool
csv_separator string
paired_filename string
}
type Options struct {
@@ -35,6 +40,11 @@ func MakeOptions(setters []WithOption) Options {
closefile: false,
appendfile: false,
compressed: false,
csv_ids: true,
csv_definition: false,
cvs_sequence: true,
csv_separator: ",",
paired_filename: "",
}
opt := Options{&o}
@@ -86,6 +96,18 @@ func (opt Options) CompressedFile() bool {
return opt.pointer.compressed
}
func (opt Options) CSVIds() bool {
return opt.pointer.csv_ids
}
func (opt Options) HaveToSavePaired() bool {
return opt.pointer.paired_filename != ""
}
func (opt Options) PairedFileName() string {
return opt.pointer.paired_filename
}
func OptionsBufferSize(size int) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.buffer_size = size
@@ -216,3 +238,12 @@ func OptionsWithoutProgressBar() WithOption {
return f
}
func WritePairedReadsTo(filename string) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.paired_filename = filename
})
return f
}

16
pkg/obiformats/universal_write.go
View File

@@ -69,5 +69,19 @@ func WriteSequencesToFile(iterator obiiter.IBioSequence,
}
options = append(options, OptionCloseFile())
return WriteSequence(iterator, file, options...)
iterator, err = WriteSequence(iterator, file, options...)
if opt.HaveToSavePaired() {
var revfile *os.File
revfile, err = os.OpenFile(opt.PairedFileName(), flags, 0660)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err
}
iterator, err = WriteSequence(iterator.PairedWith(), revfile, options...)
}
return iterator, err
}