mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-11-09 09:24:41 +00:00
Eric Coissac
8cc02aa9c1
This commit introduces significant changes to the sequence processing pipeline, implementing parallel loading, k-mer budget control, explicit memory management, and refined logic for pair evaluation and resolution.
79 lines
2.6 KiB
Go
79 lines
2.6 KiB
Go
package obiprimer
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import (
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"math/rand"
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"reflect"
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"strings"
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"testing"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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)
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func TestAmpBatches(t *testing.T) {
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cases := []struct {
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count []int
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budget int
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want [][2]int
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}{
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{[]int{3, 3, 3}, 0, [][2]int{{0, 3}}},
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{[]int{3, 3, 3}, 100, [][2]int{{0, 3}}},
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{[]int{3, 3, 3}, 6, [][2]int{{0, 2}, {2, 3}}},
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{[]int{3, 3, 3}, 1, [][2]int{{0, 1}, {1, 2}, {2, 3}}}, // a pair above the budget goes alone
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{[]int{9, 1, 1}, 5, [][2]int{{0, 1}, {1, 3}}},
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{nil, 5, nil},
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{[]int{0, 0}, 5, [][2]int{{0, 2}}},
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}
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for _, c := range cases {
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if got := ampBatches(c.count, c.budget); !reflect.DeepEqual(got, c.want) {
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t.Errorf("ampBatches(%v, %d) = %v, want %v", c.count, c.budget, got, c.want)
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}
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}
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}
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// The batches of phase 2 only bound the memory: whatever their size, the pairs,
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// their indices and their sites on the reference are the same.
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func TestAmpBudgetDoesNotChangeTheResult(t *testing.T) {
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s := newSynthetic(10, -1, 5)
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// non-targets sharing barcodes with targets, and counterexamples
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for k, role := range []Role{Other, Other, CounterExample, Other, CounterExample} {
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cp := append([]byte(nil), s.corpus.Seqs[k*2].Sequence()...)
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if role == CounterExample {
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for i := s.pos; i < s.pos+10; i++ { // no forward site: not amplified
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cp[i] = "cgta"[strings.IndexByte("acgt", cp[i])]
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}
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}
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s.corpus.Seqs = append(s.corpus.Seqs, obiseq.NewBioSequence(strings.Repeat("x", k+1), cp, ""))
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s.corpus.Roles = append(s.corpus.Roles, role)
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s.taxa.Of = append(s.taxa.Of, int32(100+k%3))
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}
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// a few unrelated sequences, with a taxon of their own or none
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rng := rand.New(rand.NewSource(9))
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for k := 0; k < 3; k++ {
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s.corpus.Seqs = append(s.corpus.Seqs, obiseq.NewBioSequence("u"+strings.Repeat("y", k), []byte(strings.ToLower(randDNA(rng, 300))), ""))
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s.corpus.Roles = append(s.corpus.Roles, Other)
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s.taxa.Of = append(s.taxa.Of, int32(k-1))
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}
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run := func(budget int) []PairStats {
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p := s.params()
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p.MinSpecificity = 0 // keep every pair: the stress case of the batches
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p.FalsePositive = 1
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p.Reference = "s3"
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p.AmpBudget = budget
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pairs, info, err := Search(s.corpus, s.taxa, p)
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if err != nil {
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t.Fatal(err)
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}
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if info.Pair.Candidates < 2 {
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t.Fatalf("budget %d: only %d pairs reach phase 2b, the test needs several", budget, info.Pair.Candidates)
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}
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return pairs
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}
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want := run(0)
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for _, budget := range []int{1, 7, 50, 1000} {
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if got := run(budget); !reflect.DeepEqual(got, want) {
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t.Errorf("budget %d changes the result:\n got %d pairs\nwant %d pairs", budget, len(got), len(want))
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}
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}
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}
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