← Về thư mục
tests/pathway-enrichment/test_scripts.py
- SymbolCleaningTests · class · L35-L76 — class SymbolCleaningTests(unittest.TestCase)
- test_human_symbols_are_upper_cased · method · L36-L40 — def test_human_symbols_are_upper_cased(self) -> None
- test_mouse_symbols_are_title_cased · method · L42-L48 — def test_mouse_symbols_are_title_cased(self) -> None: # Mouse libraries key on Trp53, not TRP53 -- getting this wrong returns # an empty enrichment with no error.
- test_an_unknown_organism_leaves_case_alone · method · L50-L53 — def test_an_unknown_organism_leaves_case_alone(self) -> None
- test_blank_and_placeholder_entries_are_dropped · method · L55-L61 — def test_blank_and_placeholder_entries_are_dropped(self) -> None
- test_duplicates_are_removed_after_normalisation · method · L63-L67 — def test_duplicates_are_removed_after_normalisation(self) -> None: # "tp53" and "TP53" are the same gene once case is normalised.
- test_input_order_is_preserved · method · L69-L73 — def test_input_order_is_preserved(self) -> None
- test_surrounding_whitespace_is_stripped · method · L75-L76 — def test_surrounding_whitespace_is_stripped(self) -> None
- GeneListReadingTests · class · L79-L100 — class GeneListReadingTests(unittest.TestCase)
- setUp · method · L80-L83 — def setUp(self) -> None
- test_a_plain_text_list_is_read_one_gene_per_line · method · L85-L90 — def test_a_plain_text_list_is_read_one_gene_per_line(self) -> None
- test_a_csv_uses_its_first_column · method · L92-L95 — def test_a_csv_uses_its_first_column(self) -> None
- test_a_tsv_is_split_on_tabs_not_commas · method · L97-L100 — def test_a_tsv_is_split_on_tabs_not_commas(self) -> None
- RankingTests · class · L103-L170 — class RankingTests(unittest.TestCase)
- setUp · method · L104-L107 — def setUp(self) -> None
- _deseq2 · method · L109-L112 — def _deseq2(self, text: str) -> Path
- test_the_wald_statistic_is_preferred_when_present · method · L114-L123 — def test_the_wald_statistic_is_preferred_when_present(self) -> None
- test_the_fallback_metric_keeps_the_direction_of_the_fold_change · method · L125-L137 — def test_the_fallback_metric_keeps_the_direction_of_the_fold_change(self) -> None: # sign(log2FC) * -log10(p): a strongly down-regulated gene must land at # the bottom of the ranking, not the top.
- test_a_zero_pvalue_is_clipped_rather_than_becoming_infinite · method · L139-L143 — def test_a_zero_pvalue_is_clipped_rather_than_becoming_infinite(self) -> None
- test_a_table_with_neither_metric_exits_naming_its_columns · method · L145-L149 — def test_a_table_with_neither_metric_exits_naming_its_columns(self) -> None
- test_column_names_are_matched_case_insensitively · method · L151-L154 — def test_column_names_are_matched_case_insensitively(self) -> None
- test_rows_with_missing_statistics_are_dropped · method · L156-L159 — def test_rows_with_missing_statistics_are_dropped(self) -> None
- test_duplicate_symbols_keep_their_first_occurrence · method · L161-L165 — def test_duplicate_symbols_keep_their_first_occurrence(self) -> None
- test_the_ranking_is_returned_in_descending_order · method · L167-L170 — def test_the_ranking_is_returned_in_descending_order(self) -> None
- RankedFileTests · class · L173-L210 — class RankedFileTests(unittest.TestCase)
- setUp · method · L174-L177 — def setUp(self) -> None
- _rnk · method · L179-L182 — def _rnk(self, text: str) -> Path
- test_a_headerless_two_column_file_is_read_directly · method · L184-L187 — def test_a_headerless_two_column_file_is_read_directly(self) -> None
- test_a_header_row_is_detected_and_dropped · method · L189-L193 — def test_a_header_row_is_detected_and_dropped(self) -> None
- test_a_single_column_file_is_refused · method · L195-L198 — def test_a_single_column_file_is_refused(self) -> None
- test_symbols_are_normalised_for_the_organism · method · L200-L202 — def test_symbols_are_normalised_for_the_organism(self) -> None
- test_rows_with_unparseable_scores_are_dropped · method · L204-L206 — def test_rows_with_unparseable_scores_are_dropped(self) -> None
- test_the_result_is_sorted_descending · method · L208-L210 — def test_the_result_is_sorted_descending(self) -> None
- LibraryTests · class · L213-L228 — class LibraryTests(unittest.TestCase)
- test_the_default_libraries_are_named_and_versioned · method · L214-L222 — def test_the_default_libraries_are_named_and_versioned(self) -> None: # Enrichr library names carry a year; an unversioned name silently # resolves to whatever is current and makes results irreproducible.
- test_the_default_set_is_free_of_duplicates · method · L224-L228 — def test_the_default_set_is_free_of_duplicates(self) -> None