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Change the API of workers

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Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
This commit is contained in:
Eric Coissac
2024-03-02 16:03:46 -04:00
parent 4a0b20484f
commit 0f3871d203
19 changed files with 194 additions and 120 deletions
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48
pkg/obitools/obiannotate/obiannotate.go
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@@ -15,11 +15,11 @@ import (
)
func DeleteAttributesWorker(toBeDeleted []string) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
for _, k := range toBeDeleted {
s.DeleteAttribute(k)
}
return s
return obiseq.BioSequenceSlice{s}, nil
}
return f
@@ -48,7 +48,7 @@ func MatchPatternWorker(pattern, name string, errormax int, allowsIndel bool) ob
slot_error := fmt.Sprintf("%s_error", name)
slot_location := fmt.Sprintf("%s_location", name)
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
apats, err := obiapat.MakeApatSequence(s, false)
if err != nil {
log.Fatalf("error in preparing sequence %s : %v", s.Id(), err)
@@ -59,6 +59,11 @@ func MatchPatternWorker(pattern, name string, errormax int, allowsIndel bool) ob
if matched {
annot := s.Annotations()
annot[slot] = pattern
if start < 0 {
start = 0
}
match, err := s.Subsequence(start, end, false)
if err != nil {
log.Fatalf("Error in extracting pattern of sequence %s [%d;%d[ : %v",
@@ -83,7 +88,7 @@ func MatchPatternWorker(pattern, name string, errormax int, allowsIndel bool) ob
annot[slot_location] = fmt.Sprintf("complement(%d..%d)", start+1, end)
}
}
return s
return obiseq.BioSequenceSlice{s}, nil
}
return f
@@ -97,14 +102,14 @@ func ToBeKeptAttributesWorker(toBeKept []string) obiseq.SeqWorker {
d[v] = true
}
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
annot := s.Annotations()
for key := range annot {
if _, ok := d[key]; !ok {
s.DeleteAttribute(key)
}
}
return s
return obiseq.BioSequenceSlice{s}, nil
}
return f
@@ -112,7 +117,7 @@ func ToBeKeptAttributesWorker(toBeKept []string) obiseq.SeqWorker {
func CutSequenceWorker(from, to int, breakOnError bool) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
var f, t int
switch {
@@ -142,16 +147,15 @@ func CutSequenceWorker(from, to int, breakOnError bool) obiseq.SeqWorker {
if breakOnError {
log.Fatalf("Cannot cut sequence %s (%v)", s.Id(), err)
} else {
log.Warnf("Cannot cut sequence %s (%v), sequence discarded", s.Id(), err)
return nil
err = fmt.Errorf("Cannot cut sequence %s (%v), sequence discarded", s.Id(), err)
}
}
return rep
return obiseq.BioSequenceSlice{rep}, err
}
if from == 0 && to == 0 {
f = func(s *obiseq.BioSequence) *obiseq.BioSequence {
return s
f = func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
return obiseq.BioSequenceSlice{s}, nil
}
}
@@ -163,23 +167,23 @@ func CutSequenceWorker(from, to int, breakOnError bool) obiseq.SeqWorker {
}
func ClearAllAttributesWorker() obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
annot := s.Annotations()
for key := range annot {
s.DeleteAttribute(key)
}
return s
return obiseq.BioSequenceSlice{s}, nil
}
return f
}
func RenameAttributeWorker(toBeRenamed map[string]string) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
for newName, oldName := range toBeRenamed {
s.RenameAttribute(newName, oldName)
}
return s
return obiseq.BioSequenceSlice{s}, nil
}
return f
@@ -201,20 +205,20 @@ func EvalAttributeWorker(expression map[string]string) obiseq.SeqWorker {
}
func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
for _, r := range ranks {
taxonomy.SetTaxonAtRank(s, r)
}
return s
return obiseq.BioSequenceSlice{s}, nil
}
return f
}
func AddSeqLengthWorker() obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
s.SetAttribute("seq_length", s.Len())
return s
return obiseq.BioSequenceSlice{s}, nil
}
return f
@@ -309,8 +313,8 @@ func CLIAnnotationPipeline() obiiter.Pipeable {
predicate := obigrep.CLISequenceSelectionPredicate()
worker := CLIAnnotationWorker()
annotator := obiseq.SeqToSliceConditionalWorker(worker, predicate, true, false)
f := obiiter.SliceWorkerPipe(annotator, obioptions.CLIParallelWorkers())
annotator := obiseq.SeqToSliceConditionalWorker(predicate, worker, true, false)
f := obiiter.SliceWorkerPipe(annotator, false, obioptions.CLIParallelWorkers())
return f
}