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Add some code refactoring from the blackboard branch

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This commit is contained in:
Eric Coissac
2024-08-02 12:35:46 +02:00
parent bc1aaaf7d9
commit 1b1cd41fd3
38 changed files with 491 additions and 330 deletions
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8
pkg/obitools/obiclean/obiclean.go
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@@ -57,7 +57,7 @@ func buildSamples(dataset obiseq.BioSequenceSlice,
return samples
}
func annotateOBIClean(dataset obiseq.BioSequenceSlice,
func annotateOBIClean(source string, dataset obiseq.BioSequenceSlice,
sample map[string]*([]*seqPCR),
tag, NAValue string) obiiter.IBioSequence {
batchsize := 1000
@@ -91,7 +91,7 @@ func annotateOBIClean(dataset obiseq.BioSequenceSlice,
return data, nil
}
iter := obiiter.IBatchOver(dataset, batchsize)
iter := obiiter.IBatchOver(source, dataset, batchsize)
riter := iter.MakeISliceWorker(annot, false)
return riter
@@ -288,7 +288,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
db := itertator.Load()
source, db := itertator.Load()
log.Infof("Sequence dataset of %d sequeences loaded\n", len(db))
@@ -365,7 +365,7 @@ func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
EmpiricalDistCsv(RatioTableFilename(), all_ratio)
}
iter := annotateOBIClean(db, samples, SampleAttribute(), "NA")
iter := annotateOBIClean(source, db, samples, SampleAttribute(), "NA")
if OnlyHead() {
iter = iter.FilterOn(IsHead, 1000)