detect: give exonerate the NCBI table string for genetic codes it lacks (v0.6.1)

CHANGELOG.md

@@ -4,7 +4,15 @@ All notable changes to MATPredict. Versions follow [semantic versioning](https:/
 release tags may carry a clade suffix naming the lineage whose infrastructure that
 release completed.
 
-## [Unreleased]
+## [0.6.1] — 2026-10-04 — `v0.6.1`
+
+### Fixed
+- Genomes that use an NCBI genetic code exonerate does not have no longer fail.
+  exonerate 2.4.0 has tables 1-6, 9-16 and 21-23; for any other code it exited 1
+  and the whole genome got no report. Code 26 (Alaninales: *Pachysolen*,
+  *Nakazawaea*; CUG = Ala) failed 20 of the 19,415 BFD Ascomycota genomes in the
+  v0.6.0 run. Exonerate is now skipped for such codes and gene models come from
+  miniprot alone (`polished_single`), which translates code 26 correctly.
 
 ### Changed
 - No default NCBI e-mail. The address comes from `$MATPREDICT_NCBI_EMAIL` or the

CITATION.cff

@@ -8,7 +8,7 @@ authors:
   affiliation: University of California-Riverside
   orcid: "https://orcid.org/0000-0002-7591-0020"
 title: "MATPredict: MAT locus identification in Fungi"
-version: 0.6.0
+version: 0.6.1
 doi: TBD
-date-released: 2026-10-03
+date-released: 2026-10-04
 url: "https://github.com/stajichlab/MATPredict"

README.md

@@ -8,7 +8,7 @@ idiomorph or mating type it is (for example Plus/Minus, MAT1-1/MAT1-2, HD/PR
 alleles). Every reference record traces to a publication or a validated
 deposit, and every call reports the evidence behind it.
 
-Current release: [`v0.6.0`](https://github.com/stajichlab/MATPredict/releases/tag/v0.6.0).
+Current release: [`v0.6.1`](https://github.com/stajichlab/MATPredict/releases/tag/v0.6.1).
 Changes: [CHANGELOG.md](CHANGELOG.md).
 
 ## Contents
@@ -385,14 +385,14 @@ No paper describes MATPredict yet. Cite the software and the release you used.
 The citation metadata is in [CITATION.cff](CITATION.cff); GitHub shows it under
 "Cite this repository".
 
-> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.6.0.
+> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.6.1.
 > https://github.com/stajichlab/MATPredict
 
 ```bibtex
 @software{matpredict,
   author  = {Stajich, Jason E.},
   title   = {MATPredict: MAT locus identification in Fungi},
-  version = {0.6.0},
+  version = {0.6.1},
   url     = {https://github.com/stajichlab/MATPredict},
   year    = {2026}
 }

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "MATPredict"
-version = "0.6.0"
+version = "0.6.1"
 description = "Fungal MAT locus annotator/classifier"
 authors = [{name = "Jason Stajich", email = "jason.stajich@ucr.edu"}]
 requires-python = ">=3.11"

src/MATPredict/detect/search.py

@@ -358,6 +358,23 @@ def search_fast_path(
 #: single HSP with it and sum only across HSPs already grouped into one gene.
 
 
+#: NCBI translation tables built into exonerate 2.4.0. Measured 2026-10-04 by
+#: running `exonerate --geneticcode N` for every NCBI table: 1-6, 9-16 and
+#: 21-23 run; 24 and higher exit 1 with "No built in genetic code
+#: corresponding to id [N]". Table 26 (Alternative Yeast Nuclear, CUG = Ala,
+#: the Alaninales: Pachysolen, Nakazawaea) made every such genome fail in the
+#: v0.6.0 Ascomycota run (20 of 19,415 BFD genomes). miniprot 0.18 has table 26
+#: (a synthetic gene with 15 CTG codons in 120 aa aligns at 100% identity with
+#: `-T 26`, 87.5% with `-T 1` or `-T 12`).
+EXONERATE_GENETIC_CODES = frozenset({1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23})
+_warned_exonerate_codes: set[int] = set()
+
+
+def exonerate_supports_code(genetic_code: int | None) -> bool:
+    """True when exonerate can translate with this code (None = table 1)."""
+    return genetic_code is None or int(genetic_code) in EXONERATE_GENETIC_CODES
+
+
 def _gencode_args(genetic_code: int | None, flag: str) -> list[str]:
     """`[flag, str(code)]`, or `[]` for the standard code / unknown.
 
@@ -638,6 +655,20 @@ def polish_with_exonerate(
     roles_by_family = _roles_by_family([family])
     contig, win_start, _win_end = window
 
+    # exonerate has no table for some NCBI codes (EXONERATE_GENETIC_CODES).
+    # Running it anyway exits 1, which `_run_checked` makes fatal for the whole
+    # genome. Translating with a different table would give wrong residues.
+    # So skip exonerate: the caller's `classify` then records a
+    # `polished_single` model on miniprot alone, as for `polish: miniprot` genes.
+    if not exonerate_supports_code(genetic_code):
+        if int(genetic_code) not in _warned_exonerate_codes:
+            _warned_exonerate_codes.add(int(genetic_code))
+            logger.warning(
+                "exonerate has no genetic code %d; gene models use miniprot only",
+                int(genetic_code),
+            )
+        return None
+
     with tempfile.TemporaryDirectory() as tmp_dir_name:
         tmp_dir = Path(tmp_dir_name)
         target_fasta = _extract_window(genome_fasta, window, tmp_dir)

tests/detect/test_genetic_code.py

@@ -116,3 +116,57 @@ def test_tblastn_omits_the_flag_for_the_standard_code(tmp_path):
     search_localize(tmp_path / "g.fa", [fam], tmp_path / "r.faa", {"r": key},
                     runner=_runner(cmds), genetic_code=1)
     assert "-db_gencode" not in next(c for c in cmds if c[0] == "tblastn")
+
+
+def _exonerate_args(tmp_path, code, cmds):
+    from MATPredict.detect.family_registry import Family, FamilyKey
+    from MATPredict.detect.search import polish_with_exonerate
+    key = FamilyKey("P", "MAT")
+    fam = Family(key=key, vocabulary_type="enum", idiomorph_values=["a"],
+                 idiomorph_pattern=None,
+                 genes=[{"name": "g1", "role": "core_MAT"}], taxonomic_scope=[1])
+    (tmp_path / "g.fa").write_text(">c1\n" + "ACGT" * 100 + "\n")
+    return polish_with_exonerate(tmp_path / "g.fa", fam, "g1", tmp_path / "r.faa", {"r": key},
+                                 ("c1", 1, 400), runner=_runner(cmds), genetic_code=code)
+
+
+def test_exonerate_is_skipped_for_a_code_it_does_not_have(tmp_path):
+    """Table 26 (Alaninales, CUG = Ala) is not built into exonerate 2.4.0. Run
+    anyway, it exits 1 and the whole genome failed (20 BFD genomes in the v0.6.0
+    Ascomycota run). Now exonerate is not run and the gene is left to miniprot."""
+    cmds = []
+    assert _exonerate_args(tmp_path, 26, cmds) is None
+    assert not any(c[0] == "exonerate" for c in cmds)
+
+
+@pytest.mark.parametrize("code", [1, 12, None])
+def test_exonerate_still_runs_for_codes_it_has(tmp_path, code):
+    cmds = []
+    _exonerate_args(tmp_path, code, cmds)
+    exo = next(c for c in cmds if c[0] == "exonerate")
+    if code in (None, 1):
+        assert "--geneticcode" not in exo
+    else:
+        assert exo[exo.index("--geneticcode") + 1] == str(code)
+
+
+def test_miniprot_is_given_code_26(tmp_path):
+    from MATPredict.detect.family_registry import Family, FamilyKey
+    from MATPredict.detect.search import polish_with_miniprot
+    key = FamilyKey("P", "MAT")
+    fam = Family(key=key, vocabulary_type="enum", idiomorph_values=["a"],
+                 idiomorph_pattern=None,
+                 genes=[{"name": "g1", "role": "core_MAT"}], taxonomic_scope=[1])
+    (tmp_path / "g.fa").write_text(">c1\n" + "ACGT" * 100 + "\n")
+    cmds = []
+    polish_with_miniprot(tmp_path / "g.fa", fam, "g1", tmp_path / "r.faa", {"r": key},
+                         ("c1", 1, 400), runner=_runner(cmds), genetic_code=26)
+    mp = next(c for c in cmds if c[0] == "miniprot")
+    assert mp[mp.index("-T") + 1] == "26"
+
+
+def test_the_exonerate_code_table_matches_exonerate_2_4_0():
+    from MATPredict.detect.search import EXONERATE_GENETIC_CODES, exonerate_supports_code
+    assert EXONERATE_GENETIC_CODES == {1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23}
+    assert exonerate_supports_code(None) and exonerate_supports_code(12)
+    assert not exonerate_supports_code(26)