obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Change the API of workers

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files

4
pkg/obitax/lca.go
View File

@ -147,14 +147,14 @@ func AddLCAWorker(taxonomy *Taxonomy, slot_name string, threshold float64) obise
lca_name = "scientific_name"
}
f := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
f := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
lca, rans, _ := taxonomy.LCA(sequence, threshold)
sequence.SetAttribute(slot_name, lca.Taxid())
sequence.SetAttribute(lca_name, lca.ScientificName())
sequence.SetAttribute(lca_error, math.Round((1-rans)*1000)/1000)
return sequence
return obiseq.BioSequenceSlice{sequence}, nil
}
return f

22
pkg/obitax/sequence_workers.go
View File

@ -14,9 +14,9 @@ func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiseq.SeqWorker
taxonomy.RankList())
}
w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
w := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetTaxonAtRank(sequence, rank)
return sequence
return obiseq.BioSequenceSlice{sequence}, nil
}
return w
@ -24,9 +24,9 @@ func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiseq.SeqWorker
func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiseq.SeqWorker {
w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
w := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetSpecies(sequence)
return sequence
return obiseq.BioSequenceSlice{sequence}, nil
}
return w
@ -34,9 +34,9 @@ func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiseq.SeqWorker {
func (taxonomy *Taxonomy) MakeSetGenusWorker() obiseq.SeqWorker {
w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
w := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetGenus(sequence)
return sequence
return obiseq.BioSequenceSlice{sequence}, nil
}
return w
@ -44,9 +44,9 @@ func (taxonomy *Taxonomy) MakeSetGenusWorker() obiseq.SeqWorker {
func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiseq.SeqWorker {
w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
w := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetFamily(sequence)
return sequence
return obiseq.BioSequenceSlice{sequence}, nil
}
return w
@ -54,9 +54,9 @@ func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiseq.SeqWorker {
func (taxonomy *Taxonomy) MakeSetPathWorker() obiseq.SeqWorker {
w := func(s *obiseq.BioSequence) *obiseq.BioSequence {
taxonomy.SetPath(s)
return s
w := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetPath(sequence)
return obiseq.BioSequenceSlice{sequence}, nil
}
return w