mirror of
https://github.com/metabarcoding/obitools4.git
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Refactor primer logic and enhance taxonomy features
This commit introduces refinements to primer design strategies, species identification rules, and performance analysis. It also updates taxonomy handling by implementing methods for setting and dropping taxonomic paths, along with necessary utility improvements for set handling and comprehensive test coverage.
This commit is contained in:
Eric Coissac committed
1 parent
574221df42
commit
d7d63f315c
8 files changed
+886
-9
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@@ -16,6 +16,12 @@ import (
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// loadTutorial reads the Cyprinidae examples of the tutorial data (the opt-in
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// tests need OBIPRIMERS_TUTORIAL, see TestStrictWordsAgainstEcoPrimers).
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func loadTutorial(t *testing.T) (*Corpus, *Taxa, *obitax.Taxonomy) {
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t.Helper()
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return loadTutorialWith(t, nil)
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}
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// loadTutorialWith is loadTutorial with counterexample clades (ecoPrimers -i).
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func loadTutorialWith(t *testing.T, ignore []string) (*Corpus, *Taxa, *obitax.Taxonomy) {
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t.Helper()
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dir := os.Getenv("OBIPRIMERS_TUTORIAL")
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if dir == "" {
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@@ -33,7 +39,11 @@ func loadTutorial(t *testing.T) (*Corpus, *Taxa, *obitax.Taxonomy) {
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if err != nil {
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t.Fatal(err)
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}
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corpus, err := LoadCorpus(seqs, Selection{Restrict: restrict})
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sel := Selection{Restrict: restrict}
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if sel.Ignore, err = BelongingTo(taxonomy, ignore); err != nil {
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t.Fatal(err)
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}
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corpus, err := LoadCorpus(seqs, sel)
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if err != nil {
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t.Fatal(err)
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}
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@@ -173,3 +183,61 @@ func TestReferenceSitesAreRealSites(t *testing.T) {
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})
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}
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}
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// ecoPrimers with counterexamples: -r 7953 -i 1 (the Cyprinidae against all the
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// other sequences of the database, 7497 counterexamples of 7387 species), -e 3
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// -3 2 -l 30 -L 150 -c. ecoPrimers needed 45 minutes and keeps 173 pairs.
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// testdata/ecoprimers_Cyprinidae_I1.pairs.tsv holds for each: the primers, the
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// good flags, the amplified example and counterexample sequences, the amplified
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// example and counterexample taxa, and the identified taxa.
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func TestCounterExamplesAgainstEcoPrimers(t *testing.T) {
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corpus, taxa, _ := loadTutorialWith(t, []string{"1"})
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if c := corpus.Counts(); c.Examples != 325 || c.CounterExamples != 7497 || taxa.CounterExamples != 7387 {
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t.Fatalf("counts %+v, %d counterexample species (ecoPrimers: 325, 7497, 7387)", c, taxa.CounterExamples)
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}
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pairs, info, err := Search(corpus, taxa, tutorialParams(t))
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if err != nil {
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t.Fatal(err)
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}
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t.Logf("%+v", *info)
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f, err := os.Open(filepath.Join("testdata", "ecoprimers_Cyprinidae_I1.pairs.tsv"))
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if err != nil {
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t.Fatal(err)
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}
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defer f.Close()
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type row struct {
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good string
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v [5]int
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}
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want := map[string]row{}
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sc := bufio.NewScanner(f)
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for sc.Scan() {
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var p1, p2 string
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var r row
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if _, err := fmt.Sscanf(sc.Text(), "%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d", &p1, &p2, &r.good,
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&r.v[0], &r.v[1], &r.v[2], &r.v[3], &r.v[4]); err != nil {
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t.Fatal(err)
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}
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want[p1+"/"+p2] = r
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}
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if len(pairs) != len(want) {
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t.Errorf("%d pairs, ecoPrimers reports %d", len(pairs), len(want))
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}
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bad := 0
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for _, g := range pairs {
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w, ok := want[g.Primer1+"/"+g.Primer2]
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if !ok {
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t.Errorf("pair %s/%s is not in the ecoPrimers result", g.Primer1, g.Primer2)
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continue
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}
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good := string("bG"[b2i(g.Good1)]) + string("bG"[b2i(g.Good2)])
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got := [5]int{g.Examples, g.CounterExamples, g.ExampleTaxa, g.CounterTaxa, g.Identified}
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if got != w.v || good != w.good {
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if bad++; bad <= 3 {
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t.Errorf("pair %s/%s: got %s %v, ecoPrimers %s %v", g.Primer1, g.Primer2, good, got, w.good, w.v)
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}
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}
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}
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}
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@@ -0,0 +1,173 @@
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AGCAATCCAGGTCAGTTT TGCCACCCCAGTATGTCC bG 309 454 301 452 197
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GCAATCCAGGTCAGTTTC TGCCACCCCAGTATGTCC bG 309 455 301 453 197
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AGCAATCCAGGTCAGTTT CCACCCCAGTATGTCCTT bG 311 484 302 482 197
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CCACCCCAGTATGTCCTT GCAATCCAGGTCAGTTTC Gb 311 485 302 483 197
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AGCAATCCAGGTCAGTTT GCCACCCCAGTATGTCCT bG 308 445 300 444 196
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GCAATCCAGGTCAGTTTC GCCACCCCAGTATGTCCT bG 308 446 300 445 196
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ACCGGAGCAATCCAGGTC TGCCACCCCAGTATGTCC bG 308 453 300 451 196
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GAGCAATCCAGGTCAGTT TGCCACCCCAGTATGTCC bG 308 453 300 451 196
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AGACCGGAGCAATCCAGG CCACCCCAGTATGTCCTT bG 310 483 301 481 196
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CCACCCCAGTATGTCCTT GAGCAATCCAGGTCAGTT Gb 310 483 301 481 196
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ACCGGAGCAATCCAGGTC CCACCCCAGTATGTCCTT bG 310 484 301 482 196
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CCACCCCAGTATGTCCTT GACCGGAGCAATCCAGGT Gb 310 484 301 482 196
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CCACCCCAGTATGTCCTT GGTCAGTTTCTATCTGTA Gb 309 460 300 459 195
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AGGTCAGTTTCTATCTGT TGCCACCCCAGTATGTCC bG 307 438 299 437 195
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CAGGTCAGTTTCTATCTG TGCCACCCCAGTATGTCC bG 307 440 299 439 195
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GGTCAGTTTCTATCTGTA TGCCACCCCAGTATGTCC bG 307 441 299 440 195
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GAGCAATCCAGGTCAGTT GCCACCCCAGTATGTCCT bG 307 444 299 443 195
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ACCGGAGCAATCCAGGTC GCCACCCCAGTATGTCCT bG 307 445 299 444 195
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GACCGGAGCAATCCAGGT GCCACCCCAGTATGTCCT bG 307 445 299 444 195
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AGGTCAGTTTCTATCTGT CCACCCCAGTATGTCCTT bG 309 469 300 467 195
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CAGGTCAGTTTCTATCTG CCACCCCAGTATGTCCTT bG 309 470 300 468 195
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GGAGCAATCCAGGTCAGT TGCCACCCCAGTATGTCC bG 307 454 299 452 195
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CCAGGTCAGTTTCTATCT TGCCACCCCAGTATGTCC bG 307 455 299 453 195
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AATCCAGGTCAGTTTCTA TGCCACCCCAGTATGTCC bG 307 455 299 453 195
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CAATCCAGGTCAGTTTCT TGCCACCCCAGTATGTCC bG 307 455 299 453 195
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ATCCAGGTCAGTTTCTAT TGCCACCCCAGTATGTCC bG 307 455 299 453 195
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TCCAGGTCAGTTTCTATC TGCCACCCCAGTATGTCC bG 307 455 299 453 195
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CCACCCCAGTATGTCCTT GGAGCAATCCAGGTCAGT Gb 309 484 300 482 195
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CAATCCAGGTCAGTTTCT CCACCCCAGTATGTCCTT bG 309 485 300 483 195
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AATCCAGGTCAGTTTCTA CCACCCCAGTATGTCCTT bG 309 485 300 483 195
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ATCCAGGTCAGTTTCTAT CCACCCCAGTATGTCCTT bG 309 485 300 483 195
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CCACCCCAGTATGTCCTT TCCAGGTCAGTTTCTATC Gb 309 485 300 483 195
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CCACCCCAGTATGTCCTT CCAGGTCAGTTTCTATCT Gb 309 485 300 483 195
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GCCACCCCAGTATGTCCT GGTCAGTTTCTATCTGTA Gb 306 437 298 437 194
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AGGTCAGTTTCTATCTGT GCCACCCCAGTATGTCCT bG 306 440 298 439 194
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CAGGTCAGTTTCTATCTG GCCACCCCAGTATGTCCT bG 306 442 298 441 194
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GCCACCCCAGTATGTCCT GGAGCAATCCAGGTCAGT Gb 306 445 298 444 194
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GCCACCCCAGTATGTCCT TCCAGGTCAGTTTCTATC Gb 306 446 298 445 194
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CCAGGTCAGTTTCTATCT GCCACCCCAGTATGTCCT bG 306 446 298 445 194
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CAATCCAGGTCAGTTTCT GCCACCCCAGTATGTCCT bG 306 446 298 445 194
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AATCCAGGTCAGTTTCTA GCCACCCCAGTATGTCCT bG 306 446 298 445 194
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ATCCAGGTCAGTTTCTAT GCCACCCCAGTATGTCCT bG 306 446 298 445 194
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CGGAGCAATCCAGGTCAG TGCCACCCCAGTATGTCC bG 304 445 296 444 192
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CCGGAGCAATCCAGGTCA TGCCACCCCAGTATGTCC bG 304 445 296 444 192
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TGCCACCCCAGTATGTCC TTTTCCTAGTACGAAAGG Gb 308 453 300 452 192
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CCACCCCAGTATGTCCTT CCGGAGCAATCCAGGTCA Gb 306 476 297 474 192
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CCACCCCAGTATGTCCTT CGGAGCAATCCAGGTCAG Gb 306 476 297 474 192
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GACCGGAGCAATCCAGGT TGCCACCCCAGTATGTCC bG 304 453 296 451 192
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CCACCCCAGTATGTCCTT GTCAGTTTCTATCTGTAA Gb 304 408 295 407 190
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CCACCCCAGTATGTCCTT TTTTCCTAGTACGAAAGG Gb 310 484 301 482 192
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CAGACCGGAGCAATCCAG CCACCCCAGTATGTCCTT bG 306 484 297 482 192
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GTCAGTTTCTATCTGTAA TGCCACCCCAGTATGTCC bG 302 390 294 390 190
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AGCAATCCAGGTCAGTTT CCCAGTATGTCCTTATTT bG 301 310 292 309 187
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CCCAGTATGTCCTTATTT GCAATCCAGGTCAGTTTC Gb 301 311 292 310 187
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ACTTTTCCTAGTACGAAA TGCCACCCCAGTATGTCC bG 307 443 299 442 191
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GCCACCCCAGTATGTCCT TTTTCCTAGTACGAAAGG Gb 307 445 299 444 191
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CGGAGCAATCCAGGTCAG GCCACCCCAGTATGTCCT bG 303 443 295 442 191
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CCGGAGCAATCCAGGTCA GCCACCCCAGTATGTCCT bG 303 443 295 442 191
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CTTTTCCTAGTACGAAAG TGCCACCCCAGTATGTCC bG 307 448 299 447 191
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AGACCGGAGCAATCCAGG GCCACCCCAGTATGTCCT bG 303 445 295 444 191
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ACTTTTCCTAGTACGAAA CCACCCCAGTATGTCCTT bG 309 478 300 476 191
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CCACCCCAGTATGTCCTT CTTTTCCTAGTACGAAAG Gb 309 482 300 480 191
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GCCACCCCAGTATGTCCT GTCAGTTTCTATCTGTAA Gb 301 390 293 390 189
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AGACCGGAGCAATCCAGG CCCAGTATGTCCTTATTT bG 300 310 291 309 186
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CAGACCGGAGCAATCCAG CCCAGTATGTCCTTATTT bG 300 310 291 309 186
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CCCAGTATGTCCTTATTT GAGCAATCCAGGTCAGTT Gb 300 310 291 309 186
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ACCGGAGCAATCCAGGTC CCCAGTATGTCCTTATTT bG 300 311 291 310 186
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CCCAGTATGTCCTTATTT GACCGGAGCAATCCAGGT Gb 300 311 291 310 186
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CCCAGTATGTCCTTATTT TCAGACCGGAGCAATCCA Gb 300 311 291 310 186
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CCCAGTATGTCCTTATTT TTCAGACCGGAGCAATCC Gb 300 311 291 310 186
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CCCAGTATGTCCTTATTT GTTCAGACCGGAGCAATC Gb 300 311 291 310 186
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CTTTTCCTAGTACGAAAG GCCACCCCAGTATGTCCT bG 306 443 298 442 190
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ACTTTTCCTAGTACGAAA GCCACCCCAGTATGTCCT bG 306 443 298 442 190
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AGACCGGAGCAATCCAGG TGCCACCCCAGTATGTCC bG 302 453 294 451 190
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CCACCCCAGTATGTCCTT TCAGACCGGAGCAATCCA Gb 304 485 295 483 190
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AGGTCAGTTTCTATCTGT CCCAGTATGTCCTTATTT bG 299 309 290 308 185
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CAGGTCAGTTTCTATCTG CCCAGTATGTCCTTATTT bG 299 309 290 308 185
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CCCAGTATGTCCTTATTT GGTCAGTTTCTATCTGTA Gb 299 309 290 308 185
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ATCCAGGTCAGTTTCTAT CCCAGTATGTCCTTATTT bG 299 311 290 310 185
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CCAGGTCAGTTTCTATCT CCCAGTATGTCCTTATTT bG 299 311 290 310 185
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CCCAGTATGTCCTTATTT GGAGCAATCCAGGTCAGT Gb 299 311 290 310 185
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CCCAGTATGTCCTTATTT TCCAGGTCAGTTTCTATC Gb 299 311 290 310 185
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CAATCCAGGTCAGTTTCT CCCAGTATGTCCTTATTT bG 299 311 290 310 185
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AATCCAGGTCAGTTTCTA CCCAGTATGTCCTTATTT bG 299 311 290 310 185
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TGCCACCCCAGTATGTCC TTTCCTAGTACGAAAGGA Gb 305 449 297 447 189
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CAGACCGGAGCAATCCAG GCCACCCCAGTATGTCCT bG 301 446 293 445 189
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CCACCCCAGTATGTCCTT TTTCCTAGTACGAAAGGA Gb 307 479 298 477 189
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CCACCCCAGTATGTCCTT TACGAAAGGATCGGAAAA Gb 307 453 298 452 188
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CCCAGTATGTCCTTATTT CCGGAGCAATCCAGGTCA Gb 298 309 289 308 184
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CCCAGTATGTCCTTATTT CGGAGCAATCCAGGTCAG Gb 298 309 289 308 184
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GCCACCCCAGTATGTCCT TTTCCTAGTACGAAAGGA Gb 304 440 296 439 188
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GCAATTTACCATGCTCTG TTTTCCTAGTACGAAAGG Gb 308 505 299 501 189
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ACTTTTCCTAGTACGAAA GCAATTTACCATGCTCTG bG 307 478 298 474 188
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CAGACCGGAGCAATCCAG TGCCACCCCAGTATGTCC bG 300 454 292 452 188
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CCTAGTACGAAAGGATCG TGCCACCCCAGTATGTCC bG 303 427 295 425 187
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CCACCCCAGTATGTCCTT TTCAGACCGGAGCAATCC Gb 302 485 293 483 188
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TACGAAAGGATCGGAAAA TGCCACCCCAGTATGTCC bG 304 430 296 430 187
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GCCACCCCAGTATGTCCT TACGAAAGGATCGGAAAA Gb 304 430 296 430 187
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CCACCCCAGTATGTCCTT CCTAGTACGAAAGGATCG Gb 305 459 296 457 187
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CTTTTCCTAGTACGAAAG GCAATTTACCATGCTCTG bG 307 498 298 494 188
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CGCAATTTACCATGCTCT TTTTCCTAGTACGAAAGG Gb 306 463 297 459 187
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GCAATTTACCATGCTCTG TTTCCTAGTACGAAAGGA Gb 307 506 298 502 188
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GCAATTTACCATGCTCTG GGTCAGTTTCTATCTGTA Gb 301 433 292 429 186
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GCCACCCCAGTATGTCCT TCAGACCGGAGCAATCCA Gb 299 446 291 445 187
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CCTAGTACGAAAGGATCG GCCACCCCAGTATGTCCT bG 302 419 294 418 186
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CCCAGTATGTCCTTATTT GTCAGTTTCTATCTGTAA Gb 295 264 286 263 181
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ACTTTTCCTAGTACGAAA CGCAATTTACCATGCTCT bG 305 449 296 445 186
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TCGCAATTTACCATGCTC TTTTCCTAGTACGAAAGG Gb 305 456 296 452 186
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TTCGCAATTTACCATGCT TTTTCCTAGTACGAAAGG Gb 305 456 296 452 186
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AGTTCAGACCGGAGCAAT CCCAGTATGTCCTTATTT bG 296 310 287 309 182
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CGCAATTTACCATGCTCT CTTTTCCTAGTACGAAAG Gb 305 460 296 456 186
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CGCAATTTACCATGCTCT TTTCCTAGTACGAAAGGA Gb 305 463 296 459 186
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CCTAGTACGAAAGGATCG GCAATTTACCATGCTCTG bG 305 472 296 468 186
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TCAGACCGGAGCAATCCA TGCCACCCCAGTATGTCC bG 298 454 290 452 186
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ACTTTTCCTAGTACGAAA TCGCAATTTACCATGCTC bG 304 447 295 443 185
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ACTTTTCCTAGTACGAAA TTCGCAATTTACCATGCT bG 304 447 295 443 185
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CTTTTCCTAGTACGAAAG TCGCAATTTACCATGCTC bG 304 453 295 449 185
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CTTTTCCTAGTACGAAAG TTCGCAATTTACCATGCT bG 304 453 295 449 185
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CCACCCCAGTATGTCCTT GTTCAGACCGGAGCAATC Gb 300 485 291 483 186
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TCGCAATTTACCATGCTC TTTCCTAGTACGAAAGGA Gb 304 456 295 452 185
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TTTCGCAATTTACCATGC TTTTCCTAGTACGAAAGG Gb 304 456 295 452 185
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TTCGCAATTTACCATGCT TTTCCTAGTACGAAAGGA Gb 304 456 295 452 185
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GCAATTTACCATGCTCTG TACGAAAGGATCGGAAAA Gb 304 427 295 425 184
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CCTAGTACGAAAGGATCG CGCAATTTACCATGCTCT bG 303 433 294 429 184
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AGGTCAGTTTCTATCTGT GCAATTTACCATGCTCTG bG 299 431 290 427 184
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GCCACCCCAGTATGTCCT TTCAGACCGGAGCAATCC Gb 297 446 289 445 185
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ACTTTTCCTAGTACGAAA TTTCGCAATTTACCATGC bG 303 447 294 443 184
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GCAATTTACCATGCTCTG GTCAGTTTCTATCTGTAA Gb 295 375 286 373 182
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CTTTTCCTAGTACGAAAG TTTCGCAATTTACCATGC bG 303 453 294 449 184
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TTTCCTAGTACGAAAGGA TTTCGCAATTTACCATGC bG 303 456 294 452 184
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CCCAGTATGTCCTTATTT TTTTCCTAGTACGAAAGG Gb 300 311 291 310 180
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CCCAGTATGTCCTTATTT GAGTTCAGACCGGAGCAA Gb 294 310 285 309 180
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CCTAGTACGAAAGGATCG TCGCAATTTACCATGCTC bG 302 430 293 426 183
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CCTAGTACGAAAGGATCG TTCGCAATTTACCATGCT bG 302 430 293 426 183
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CGCAATTTACCATGCTCT TACGAAAGGATCGGAAAA Gb 302 420 293 418 182
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ACTTTTCCTAGTACGAAA CCCAGTATGTCCTTATTT bG 299 311 290 310 179
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CCCAGTATGTCCTTATTT CTTTTCCTAGTACGAAAG Gb 299 311 290 310 179
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CGCAATTTACCATGCTCT GGTCAGTTTCTATCTGTA Gb 297 426 288 422 182
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CCTAGTACGAAAGGATCG TTTCGCAATTTACCATGC bG 301 430 292 426 182
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CAGGTCAGTTTCTATCTG GCAATTTACCATGCTCTG bG 297 431 288 427 182
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TACGAAAGGATCGGAAAA TTCGCAATTTACCATGCT bG 301 418 292 416 181
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TACGAAAGGATCGGAAAA TCGCAATTTACCATGCTC bG 301 418 292 416 181
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GGCCTTTCGCAATTTACC TTTTCCTAGTACGAAAGG Gb 302 510 293 506 183
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ACTTTTCCTAGTACGAAA GGCCTTTCGCAATTTACC bG 301 479 292 475 182
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TACGAAAGGATCGGAAAA TTTCGCAATTTACCATGC bG 300 418 291 416 180
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CCCAGTATGTCCTTATTT TTTCCTAGTACGAAAGGA Gb 297 310 288 309 177
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CTTTTCCTAGTACGAAAG GGCCTTTCGCAATTTACC bG 301 500 292 496 182
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AGGTCAGTTTCTATCTGT CGCAATTTACCATGCTCT bG 295 428 286 424 180
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GGCCTTTCGCAATTTACC TTTCCTAGTACGAAAGGA Gb 301 511 292 507 182
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GCCTTTCGCAATTTACCA TTTTCCTAGTACGAAAGG Gb 299 440 290 436 180
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CTTTCGCAATTTACCATG TTTTCCTAGTACGAAAGG Gb 298 412 289 408 179
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CCCAGTATGTCCTTATTT CCTAGTACGAAAGGATCG Gb 296 305 287 304 176
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CCCAGTATGTCCTTATTT TACGAAAGGATCGGAAAA Gb 297 307 288 306 176
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GGTCAGTTTCTATCTGTA TCGCAATTTACCATGCTC bG 294 425 285 421 179
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ACTTTTCCTAGTACGAAA GCCTTTCGCAATTTACCA bG 298 436 289 432 179
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CTTTTCCTAGTACGAAAG GCCTTTCGCAATTTACCA bG 298 438 289 434 179
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GCCTTTCGCAATTTACCA TTTCCTAGTACGAAAGGA Gb 298 440 289 436 179
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CCTAGTACGAAAGGATCG GGCCTTTCGCAATTTACC bG 299 484 290 480 180
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ACTTTTCCTAGTACGAAA CTTTCGCAATTTACCATG bG 297 411 288 407 178
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CTTTCGCAATTTACCATG CTTTTCCTAGTACGAAAG Gb 297 411 288 407 178
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CTTTCGCAATTTACCATG TTTCCTAGTACGAAAGGA Gb 297 412 288 408 178
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GGCCTTTCGCAATTTACC TACGAAAGGATCGGAAAA Gb 298 425 289 423 178
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AGTTCAGACCGGAGCAAT CCACCCCAGTATGTCCTT bG 293 484 284 482 179
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CCTAGTACGAAAGGATCG GCCTTTCGCAATTTACCA bG 296 416 287 412 177
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CCTAGTACGAAAGGATCG CTTTCGCAATTTACCATG bG 295 390 286 386 176
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CCAGGTCAGTTTCTATCT GCAATTTACCATGCTCTG bG 294 513 285 509 179
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CCTTTCGCAATTTACCAT TTTTCCTAGTACGAAAGG Gb 295 411 286 407 176
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GCAATTTACCATGCTCTG TTCCTAGTACGAAAGGAT Gb 293 423 284 419 176
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CTTTCGCAATTTACCATG TACGAAAGGATCGGAAAA Gb 295 398 286 396 175
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ACTTTTCCTAGTACGAAA CCTTTCGCAATTTACCAT bG 294 409 285 405 175
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CCTTTCGCAATTTACCAT CTTTTCCTAGTACGAAAG Gb 294 409 285 405 175
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CCTTTCGCAATTTACCAT TTTCCTAGTACGAAAGGA Gb 294 410 285 406 175
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GCCTTTCGCAATTTACCA TACGAAAGGATCGGAAAA Gb 295 413 286 411 175
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