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Running on Zero
Running on Zero
EmmaScharfmann HF Staff
Claude Opus 5
Report the sites the cutoff rejected, instead of nothing
c357a0a | """ | |
| Tests for the deterministic half of the pipeline. | |
| The model outputs cannot be asserted on, but the glue can -- and the glue is | |
| where a silent error does the most damage. An off-by-one in the TIS coordinate | |
| shifts every reading frame and still produces a plausible-looking protein, so | |
| these cases exist mainly to pin that down. | |
| """ | |
| import orf | |
| import pipeline | |
| class TestTranslate: | |
| def test_basic(self): | |
| assert orf.translate("ATGGCCTAA") == "MA" | |
| def test_stops_at_stop(self): | |
| assert orf.translate("ATGGCCTAAATGGGG") == "MA" | |
| def test_can_read_through(self): | |
| assert orf.translate("ATGTAAATG", stop_at_stop=False) == "M*M" | |
| def test_rna_input(self): | |
| assert orf.translate("AUGGCCUAA") == "MA" | |
| def test_n_becomes_x(self): | |
| assert orf.translate("ATGNNNGCC") == "MXA" | |
| def test_trailing_partial_codon_ignored(self): | |
| assert orf.translate("ATGGCCA") == "MA" | |
| class TestExtractORF: | |
| def test_finds_in_frame_stop(self): | |
| o = orf.extract_orf("AAATGGCCTAAGGG", 2) | |
| assert o.start_codon == "ATG" | |
| assert o.protein == "MA" | |
| assert o.stop_pos == 8 | |
| assert o.has_stop | |
| def test_skips_out_of_frame_stop(self): | |
| # ATG CTA AGC TAA -- there is a TAA at index 4 which is out of frame | |
| # and must be ignored in favour of the in-frame one at index 9. | |
| o = orf.extract_orf("ATGCTAAGCTAA", 0) | |
| assert o.has_stop | |
| assert o.stop_pos == 9 | |
| assert o.protein == "MLS" | |
| def test_runs_off_end(self): | |
| o = orf.extract_orf("ATGGCCGCC", 0) | |
| assert not o.has_stop | |
| assert o.stop_pos is None | |
| assert o.protein == "MAA" | |
| def test_microprotein_threshold(self): | |
| short = orf.extract_orf("ATG" + "GCC" * 50 + "TAA", 0) | |
| assert short.aa_len == 51 | |
| assert short.is_microprotein | |
| long = orf.extract_orf("ATG" + "GCC" * 120 + "TAA", 0) | |
| assert not long.is_microprotein | |
| class TestCoordinateConversion: | |
| """TIS Transformer reports TIS_pos 1-based; everything here is 0-based.""" | |
| def test_one_based_to_zero_based(self): | |
| assert orf.tis_pos_to_zero_based(1) == 0 | |
| assert orf.tis_pos_to_zero_based(60) == 59 | |
| def test_round_trip_against_real_values(self): | |
| # Observed: INS TIS_pos 60 is the annotated CDS start at 0-based 59. | |
| assert orf.tis_pos_to_zero_based(60) == 59 # INS | |
| assert orf.tis_pos_to_zero_based(379) == 378 # TYK2 | |
| assert orf.tis_pos_to_zero_based(85) == 84 # ACTB | |
| class TestClassifyORF: | |
| # A transcript with CDS at [100, 400). | |
| CDS_START, CDS_END = 100, 400 | |
| def _at(self, pos, stop=None): | |
| o = orf.extract_orf("ATG" + "GCC" * 10 + "TAA", 0) | |
| o.tis_pos = pos | |
| o.stop_pos = stop if stop is not None else pos + 30 | |
| return o | |
| def test_canonical(self): | |
| assert orf.classify_orf(self._at(100), self.CDS_START, self.CDS_END) == "CDS" | |
| def test_uorf_entirely_upstream(self): | |
| assert orf.classify_orf(self._at(10, 40), self.CDS_START, self.CDS_END) == "uORF" | |
| def test_n_extension_is_in_frame_upstream(self): | |
| # 100 - 91 = 9, divisible by 3, and it overlaps the CDS. | |
| assert orf.classify_orf(self._at(91, 200), self.CDS_START, self.CDS_END) == "N-ext" | |
| def test_uoorf_is_out_of_frame_upstream_overlap(self): | |
| assert orf.classify_orf(self._at(92, 200), self.CDS_START, self.CDS_END) == "uoORF" | |
| def test_n_truncation_in_frame_inside_cds(self): | |
| assert orf.classify_orf(self._at(163), self.CDS_START, self.CDS_END) == "N-trunc" | |
| def test_internal_orf_out_of_frame(self): | |
| assert orf.classify_orf(self._at(164), self.CDS_START, self.CDS_END) == "intORF" | |
| def test_downstream_orf(self): | |
| assert orf.classify_orf(self._at(450), self.CDS_START, self.CDS_END) == "dORF" | |
| def test_unannotated_is_ncorf(self): | |
| assert orf.classify_orf(self._at(50), None, None) == "ncORF" | |
| class TestTilePeptides: | |
| def test_lengths(self): | |
| peps = orf.tile_peptides("ACDEFGHIKLMNP", lengths=(9,)) | |
| assert all(len(p) == 9 for p in peps) | |
| assert "ACDEFGHIK" in peps | |
| def test_too_short_yields_nothing(self): | |
| assert orf.tile_peptides("ACDEF", lengths=(9,)) == [] | |
| def test_initiator_met_removal(self): | |
| # Without Met removal the 8mer starting at position 1 is unreachable. | |
| peps = orf.tile_peptides("MACDEFGHI", lengths=(8,), drop_initiator_met=True) | |
| assert "ACDEFGHI" in peps | |
| assert "MACDEFGH" in peps | |
| def test_drops_peptides_with_x(self): | |
| peps = orf.tile_peptides("ACDXFGHIKLMN", lengths=(9,)) | |
| assert all("X" not in p for p in peps) | |
| class TestHeaderAnnotation: | |
| def test_parses_real_header(self): | |
| header = ( | |
| "INS_ENST00000381330.5 Homo sapiens insulin (INS), MANE Select, " | |
| "cDNA len=465nt 5UTR=59nt CDS=333nt 3UTR=73nt | Ensembl GRCh38" | |
| ) | |
| start, end = orf.parse_cds_annotation(header) | |
| assert start == 59 | |
| assert end == 59 + 333 | |
| def test_missing_tags_returns_none(self): | |
| assert orf.parse_cds_annotation("just a name") == (None, None) | |
| class TestFastaParsing: | |
| def test_name_is_first_token(self): | |
| recs, headers = pipeline.parse_fasta_with_headers( | |
| ">INS_ENST1 some description here 5UTR=10nt CDS=30nt\nATGGCC\n" | |
| ) | |
| assert recs[0][0] == "INS_ENST1" | |
| assert "5UTR=10nt" in headers["INS_ENST1"] | |
| def test_bare_sequence_gets_a_header(self): | |
| recs, _ = pipeline.parse_fasta_with_headers("ATGGCCTAA") | |
| assert recs == [("query", "ATGGCCTAA")] | |
| def test_rna_normalised(self): | |
| recs, _ = pipeline.parse_fasta_with_headers(">x\nAUGGCC") | |
| assert recs[0][1] == "ATGGCC" | |
| def test_rejects_protein_sequence(self): | |
| try: | |
| pipeline.parse_fasta_with_headers(">x\nMAEEGFKL") | |
| assert False, "should have rejected amino acids" | |
| except ValueError as e: | |
| assert "unexpected characters" in str(e) | |
| class TestNovelty: | |
| def test_self_peptide_flagged_not_novel(self): | |
| import pandas as pd | |
| canonical = {"tx": "MAEEGFKLDYVPT"} | |
| df = pd.DataFrame({"peptide": ["EEGFKLDY", "QQQWWWYY"]}) | |
| out = pipeline.flag_peptide_novelty(df, canonical) | |
| assert out.loc[0, "novel"] is False or not out.loc[0, "novel"] | |
| assert out.loc[1, "novel"] | |
| def test_no_false_join_across_proteins(self): | |
| """A peptide spanning two concatenated proteins must not count as self.""" | |
| import pandas as pd | |
| canonical = {"a": "MAEEG", "b": "FKLDY"} | |
| df = pd.DataFrame({"peptide": ["AEEGFKLD"]}) | |
| out = pipeline.flag_peptide_novelty(df, canonical) | |
| assert out.loc[0, "novel"] | |
| class TestCutoffSplit: | |
| """Stage 1 runs at the floor, so the cutoff is applied here instead.""" | |
| def _table(): | |
| import pandas as pd | |
| return pd.DataFrame({ | |
| pipeline.TIS_SCORE_COL: [0.9, 0.03, 0.0037, 0.0008], | |
| "orf_type": ["CDS", "uORF", "N-trunc", "dORF"], | |
| }) | |
| def test_cutoff_is_inclusive(self): | |
| above, below = pipeline.split_at_cutoff(self._table(), 0.03) | |
| assert list(above["orf_type"]) == ["CDS", "uORF"] | |
| def test_rejected_sites_come_back_ranked(self): | |
| _, below = pipeline.split_at_cutoff(self._table(), 0.03) | |
| assert list(below["orf_type"]) == ["N-trunc", "dORF"] | |
| def test_empty_input_gives_two_empty_frames(self): | |
| import pandas as pd | |
| above, below = pipeline.split_at_cutoff(pd.DataFrame(), 0.03) | |
| assert above.empty and below.empty | |