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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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9
pkg/obitools/obiconvert/options.go
View File

@@ -25,6 +25,7 @@ var __output_fastobi_format__ = false
var __output_solexa_quality__ = false
var __no_progress_bar__ = false
var __compressed__ = false
func InputOptionSet(options *getoptions.GetOpt) {
// options.IntVar(&__skipped_entries__, "skip", __skipped_entries__,
@@ -72,6 +73,10 @@ func OutputOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
options.Description("Disable the progress bar printing"))
options.BoolVar(&__compressed__, "--compress", false,
options.Alias("Z"),
options.Description("Output is compressed"))
}
func OptionSet(options *getoptions.GetOpt) {
@@ -110,6 +115,10 @@ func CLIOutputFormat() string {
}
}
func CLICompressed() bool {
return __compressed__
}
func CLIInputFastHeaderFormat() string {
switch {
case __input_fastjson_format__:

2
pkg/obitools/obiconvert/sequence_writer.go
View File

@@ -41,6 +41,8 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
opts = append(opts, obiformats.OptionsQualityShift(CLIOutputQualityShift()))
opts = append(opts, obiformats.OptionsCompressed(CLICompressed()))
var err error
if len(filenames) == 0 {

18
pkg/obitools/obidistribute/distribute.go
View File

@@ -30,19 +30,13 @@ func DistributeSequence(sequences obiiter.IBioSequence) {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers),
obiformats.OptionsBufferSize(obioptions.CLIBufferSize()),
obiformats.OptionsBatchSize(obioptions.CLIBatchSize()),
obiformats.OptionsQualityShift(obiconvert.CLIOutputQualityShift()),
obiformats.OptionsAppendFile(CLIAppendSequences()),
obiformats.OptionsCompressed(obiconvert.CLICompressed()))
opts = append(opts, obiformats.OptionsQualityShift(obiconvert.CLIOutputQualityShift()))
if CLIAppendSequences() {
opts = append(opts, obiformats.OptionsAppendFile())
}
if CLICompressed() {
opts = append(opts, obiformats.OptionsCompressed())
}
var formater obiformats.SequenceBatchWriterToFile
switch obiconvert.CLIOutputFormat() {

8
pkg/obitools/obidistribute/options.go
View File

@@ -18,7 +18,6 @@ var _BatchCount = 0
var _HashSize = 0
var _NAValue = "NA"
var _append = false
var _compressed = false
func DistributeOptionSet(options *getoptions.GetOpt) {
options.StringVar(&_FilenamePattern, "pattern", _FilenamePattern,
@@ -52,10 +51,6 @@ func DistributeOptionSet(options *getoptions.GetOpt) {
options.Alias("A"),
options.Description("Indicates to append sequence to files if they already exist."))
options.BoolVar(&_compressed, "--compress", false,
options.Alias("Z"),
options.Description("Output is compressed"))
options.IntVar(&_HashSize, "hash", 0,
options.Alias("H"),
options.Description("Indicates to split the input into at most <n> batch based on a hash code of the seequence."))
@@ -71,9 +66,6 @@ func CLIAppendSequences() bool {
return _append
}
func CLICompressed() bool {
return _compressed
}
func CLISequenceClassifier() *obiseq.BioSequenceClassifier {
switch {