mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
Eric Coissac
3cd8aabd83
Changes to be committed: modified: pkg/obitools/obiclean/options.go modified: pkg/obitools/obiconvert/options.go
114 lines
3.3 KiB
Go
114 lines
3.3 KiB
Go
package obiclean
|
|
|
|
import (
|
|
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
|
|
"github.com/DavidGamba/go-getoptions"
|
|
)
|
|
|
|
var _distStepMax = 1
|
|
var _sampleAttribute = "sample"
|
|
|
|
var _ratioMax = 1.0
|
|
var _minEvalRate = 1000
|
|
|
|
var _clusterMode = false
|
|
var _onlyHead = false
|
|
|
|
var _saveGraph = "__@@NOSAVE@@__"
|
|
var _saveRatio = "__@@NOSAVE@@__"
|
|
|
|
func ObicleanOptionSet(options *getoptions.GetOpt) {
|
|
options.StringVar(&_sampleAttribute, "sample", _sampleAttribute,
|
|
options.Alias("s"),
|
|
options.Description("Attribute containing sample descriptions (default %s)."))
|
|
|
|
options.IntVar(&_distStepMax, "distance", _distStepMax,
|
|
options.Alias("d"),
|
|
options.Description("Maximum numbers of differences between two variant sequences (default: %d)."))
|
|
|
|
options.Float64Var(&_ratioMax, "ratio", _ratioMax,
|
|
options.Alias("r"),
|
|
options.Description("Threshold ratio between counts (rare/abundant counts)"+
|
|
" of two sequence records so that the less abundant one is a variant of "+
|
|
"the more abundant (default: %3.2f)."))
|
|
|
|
options.IntVar(&_minEvalRate, "min-eval-rate", _minEvalRate,
|
|
options.Description("Minimum abundance of a sequence to be used to evaluate mutation rate."))
|
|
|
|
// options.BoolVar(&_clusterMode, "cluster", _clusterMode,
|
|
// options.Alias("C"),
|
|
// options.Description("Switch obiclean into its clustering mode. This adds information to each sequence about the true."),
|
|
// )
|
|
|
|
options.BoolVar(&_onlyHead, "head", _onlyHead,
|
|
options.Alias("H"),
|
|
options.Description("Select only sequences with the head status in at least one sample."),
|
|
)
|
|
|
|
options.StringVar(&_saveGraph, "save-graph", _saveGraph,
|
|
options.Description("Creates a directory containing the set of DAG used by the obiclean clustering algorithm. "+
|
|
"The graph files follow the graphml format."),
|
|
)
|
|
|
|
options.StringVar(&_saveRatio, "save-ratio", _saveRatio,
|
|
options.Description("Creates a file containing the set of abundance ratio on the graph edge. "+
|
|
"The ratio file follows the csv format."),
|
|
)
|
|
|
|
}
|
|
|
|
func OptionSet(options *getoptions.GetOpt) {
|
|
obiconvert.InputOptionSet(options)
|
|
obiconvert.OutputOptionSet(options)
|
|
ObicleanOptionSet(options)
|
|
}
|
|
|
|
func DistStepMax() int {
|
|
return _distStepMax
|
|
}
|
|
|
|
// It returns the name of the attibute used to store sample name
|
|
func SampleAttribute() string {
|
|
return _sampleAttribute
|
|
}
|
|
|
|
// Return the maximum abundance ratio between read counts to consider sequences as error.
|
|
func RatioMax() float64 {
|
|
return _ratioMax
|
|
}
|
|
|
|
// > The function `MinCountToEvalMutationRate()` returns the minimum number of reads that must be
|
|
// observed before the mutation rate can be evaluated
|
|
func MinCountToEvalMutationRate() int {
|
|
return _minEvalRate
|
|
}
|
|
|
|
func ClusterMode() bool {
|
|
return _clusterMode
|
|
}
|
|
|
|
// `OnlyHead()` returns a boolean value that indicates whether the `-h` flag was passed to the program
|
|
func OnlyHead() bool {
|
|
return _onlyHead
|
|
}
|
|
|
|
// Returns true it the obliclean graphs must be saved
|
|
func SaveGraphToFiles() bool {
|
|
return _saveGraph != "__@@NOSAVE@@__"
|
|
}
|
|
|
|
// It returns the directory where the graph files are saved
|
|
func GraphFilesDirectory() string {
|
|
return _saveGraph
|
|
}
|
|
|
|
// Returns true it the table of ratio must be saved
|
|
func IsSaveRatioTable() bool {
|
|
return _saveRatio != "__@@NOSAVE@@__"
|
|
}
|
|
|
|
// It returns the filename of the file that stores the ratio table
|
|
func RatioTableFilename() string {
|
|
return _saveRatio
|
|
}
|