obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-13 18:50:26 +00:00
Code Issues Packages Projects Releases Wiki Activity

Patch rev complement and first implementation of --auto in obicsv

Browse Source 
Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
This commit is contained in:
Eric Coissac
2023-11-07 09:37:07 +02:00
parent 6a6a6f6f2c
commit 61c30f9b6a
21 changed files with 270 additions and 107 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
pkg/obitools/obiconvert/options.go
View File

@@ -16,13 +16,10 @@ var __input_ecopcr_format__ = false
var __input_embl_format__ = false
var __input_genbank_format__ = false
var __input_solexa_quality__ = false
var __output_in_fasta__ = false
var __output_in_fastq__ = false
var __output_fastjson_format__ = false
var __output_fastobi_format__ = false
var __output_solexa_quality__ = false
var __no_progress_bar__ = false
var __compressed__ = false
@@ -54,9 +51,6 @@ func InputOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__input_genbank_format__, "genbank", __input_genbank_format__,
options.Description("Read data following the Genbank flatfile format."))
options.BoolVar(&__input_solexa_quality__, "solexa", __input_solexa_quality__,
options.Description("Decodes quality string according to the Solexa specification."))
options.BoolVar(&__no_ordered_input__, "no-order", __no_ordered_input__,
options.Description("When several input files are provided, "+
"indicates that there is no order among them."))
@@ -71,7 +65,7 @@ func OutputModeOptionSet(options *getoptions.GetOpt) {
options.Alias("Z"),
options.Description("Output is compressed"))
options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
options.Description("Sequences of length equal to zero are suppressed from the output"))
options.StringVar(&__output_file_name__, "out", __output_file_name__,
@@ -146,7 +140,7 @@ func CLICompressed() bool {
}
func CLISkipEmpty() bool {
return __skip_empty__
return __skip_empty__
}
func CLIInputFastHeaderFormat() string {
@@ -181,22 +175,6 @@ func CLIAnalyzeOnly() int {
return __read_only_entries__
}
func CLIInputQualityShift() int {
if __input_solexa_quality__ {
return 64
} else {
return 33
}
}
func CLIOutputQualityShift() int {
if __output_solexa_quality__ {
return 64
} else {
return 33
}
}
func CLIProgressBar() bool {
return !__no_progress_bar__
}
@@ -217,4 +195,4 @@ func SetFullFileBatch() {
}
func FullFileBatch() bool {
return __full_file_batch__
}
}

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

@@ -98,10 +98,8 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(CLIInputQualityShift()))
opts = append(opts, obiformats.OptionsFullFileBatch(FullFileBatch()))
if len(filenames) == 0 {
log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
opts = append(opts, obiformats.OptionsSource("stdin"))

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

@@ -59,8 +59,6 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(CLIOutputQualityShift()))
opts = append(opts, obiformats.OptionsCompressed(CLICompressed()))
var err error

3
pkg/obitools/obicsv/obicsv.go
View File

@@ -27,8 +27,6 @@ func CLIWriteCSV(iterator obiiter.IBioSequence,
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(obiconvert.CLIOutputQualityShift()))
opts = append(opts, obiformats.OptionsCompressed(obiconvert.CLICompressed()))
opts = append(opts, obiformats.CSVId(CLIPrintId()),
@@ -37,6 +35,7 @@ func CLIWriteCSV(iterator obiiter.IBioSequence,
obiformats.CSVDefinition(CLIPrintDefinition()),
obiformats.CSVKeys(CLIToBeKeptAttributes()),
obiformats.CSVSequence(CLIPrintSequence()),
obiformats.CSVAutoColumn(CLIAutoColumns()),
)
var err error

1
pkg/obitools/obidistribute/distribute.go
View File

@@ -32,7 +32,6 @@ func DistributeSequence(sequences obiiter.IBioSequence) {
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers),
obiformats.OptionsBatchSize(obioptions.CLIBatchSize()),
obiformats.OptionsQualityShift(obiconvert.CLIOutputQualityShift()),
obiformats.OptionsAppendFile(CLIAppendSequences()),
obiformats.OptionsCompressed(obiconvert.CLICompressed()))

2
pkg/obitools/obitag/options.go
View File

@@ -93,8 +93,6 @@ func CLISaveRefetenceDB(db obiseq.BioSequenceSlice) {
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(obiconvert.CLIOutputQualityShift()))
opts = append(opts, obiformats.OptionsCompressed(obiconvert.CLICompressed()))
var err error