tests/waypoint-bio/test_scripts.py

• run_script · function · L42-L52 — def run_script(name: str, *arguments: str) -> subprocess.CompletedProcess[str]
• LineageNormalisationTests · class · L65-L97 — class LineageNormalisationTests(unittest.TestCase)
• test_pipe_separator_becomes_semicolon · method · L69-L73 — def test_pipe_separator_becomes_semicolon(self) -> None
• test_domain_prefix_is_rewritten_to_kingdom · method · L76-L81 — def test_domain_prefix_is_rewritten_to_kingdom(self) -> None: # SILVA/Greengenes2 write d__; the tokenizer would skip it entirely.
• test_strain_and_empty_segments_are_dropped · method · L84-L88 — def test_strain_and_empty_segments_are_dropped(self) -> None
• test_deepest_rank · method · L91-L97 — def test_deepest_rank(self) -> None
• MetaphlanConversionTests · class · L100-L127 — class MetaphlanConversionTests(unittest.TestCase)
• test_species_rows_only_and_renormalised · method · L102-L119 — def test_species_rows_only_and_renormalised(self) -> None
• test_genus_rank_selection · method · L122-L127 — def test_genus_rank_selection(self) -> None
• KrakenConversionTests · class · L130-L163 — class KrakenConversionTests(unittest.TestCase)
• test_lineage_rebuilt_from_indentation · method · L132-L141 — def test_lineage_rebuilt_from_indentation(self) -> None
• test_subranks_and_unclassified_excluded · method · L144-L151 — def test_subranks_and_unclassified_excluded(self) -> None
• test_counts_normalise_to_relative_abundance · method · L154-L163 — def test_counts_normalise_to_relative_abundance(self) -> None
• QiimeConversionTests · class · L166-L185 — class QiimeConversionTests(unittest.TestCase)
• test_biom_banner_taxonomy_column_and_unassigned · method · L168-L185 — def test_biom_banner_taxonomy_column_and_unassigned(self) -> None
• WaypointFormatTests · class · L188-L217 — class WaypointFormatTests(unittest.TestCase)
• test_duplicate_lineages_are_summed · method · L190-L201 — def test_duplicate_lineages_are_summed(self) -> None
• test_zero_total_sample_is_rejected · method · L204-L209 — def test_zero_total_sample_is_rejected(self) -> None
• test_min_abundance_filter · method · L212-L217 — def test_min_abundance_filter(self) -> None
• ConverterCliTests · class · L220-L269 — class ConverterCliTests(unittest.TestCase)
• test_metaphlan_end_to_end_with_metadata · method · L222-L238 — def test_metaphlan_end_to_end_with_metadata(self) -> None
• test_kraken_end_to_end_parquet · method · L241-L259 — def test_kraken_end_to_end_parquet(self) -> None
• test_missing_input_is_an_error · method · L261-L269 — def test_missing_input_is_an_error(self) -> None
• StubTokenizer · class · L272-L294 — class StubTokenizer
• init · method · L277-L280 — def init(self, known: set[str]) -> None
• get_vocab · method · L282-L283 — def get_vocab(self) -> dict[str, int]
• convert_tokens_to_ids · method · L285-L294 — def convert_tokens_to_ids(self, token: str) -> int
• VocabCoverageTests · class · L297-L331 — class VocabCoverageTests(unittest.TestCase)
• test_coverage_weights_by_abundance · method · L299-L313 — def test_coverage_weights_by_abundance(self) -> None
• test_sample_with_no_known_taxa · method · L316-L323 — def test_sample_with_no_known_taxa(self) -> None
• test_non_waypoint_file_is_rejected · method · L326-L331 — def test_non_waypoint_file_is_rejected(self) -> None