tests/alphagenome/test_scripts.py

• _load_script · function · L35-L41 — def _load_script(name: str)
• run_main · function · L60-L64 — def run_main(module, argv)
• rows_from_tsv · function · L67-L70 — def rows_from_tsv(text)
• ChromosomeTests · class · L85-L97 — class ChromosomeTests(unittest.TestCase)
• test_chr_prefix_is_added_once · method · L86-L89 — def test_chr_prefix_is_added_once(self)
• test_mitochondrion_spellings_collapse · method · L91-L93 — def test_mitochondrion_spellings_collapse(self)
• test_empty_is_rejected · method · L95-L97 — def test_empty_is_rejected(self)
• VariantParsingTests · class · L100-L129 — class VariantParsingTests(unittest.TestCase)
• test_default_gnomad_gtex_and_open_targets_spellings_agree · method · L101-L112 — def test_default_gnomad_gtex_and_open_targets_spellings_agree(self)
• test_bases_are_uppercased_and_indels_kept · method · L114-L118 — def test_bases_are_uppercased_and_indels_kept(self)
• test_rsid_and_garbage_are_rejected_with_guidance · method · L120-L124 — def test_rsid_and_garbage_are_rejected_with_guidance(self)
• test_string_form_round_trips · method · L126-L129 — def test_string_form_round_trips(self)
• IntervalParsingTests · class · L132-L147 — class IntervalParsingTests(unittest.TestCase)
• test_one_based_closed_becomes_zero_based_half_open · method · L133-L135 — def test_one_based_closed_becomes_zero_based_half_open(self)
• test_thousands_separators_and_missing_prefix · method · L137-L138 — def test_thousands_separators_and_missing_prefix(self)
• test_single_base_window_has_width_one · method · L140-L142 — def test_single_base_window_has_width_one(self)
• test_invalid_intervals_are_rejected · method · L144-L147 — def test_invalid_intervals_are_rejected(self)
• VariantFileTests · class · L150-L190 — class VariantFileTests(unittest.TestCase)
• test_tsv_with_vcf_style_columns · method · L151-L156 — def test_tsv_with_vcf_style_columns(self)
• test_csv_with_variant_column_reports_unparseable_rows · method · L158-L162 — def test_csv_with_variant_column_reports_unparseable_rows(self)
• test_vcf_splits_multiallelic_and_skips_symbolic · method · L164-L172 — def test_vcf_splits_multiallelic_and_skips_symbolic(self)
• test_missing_columns_are_an_error · method · L174-L180 — def test_missing_columns_are_an_error(self)
• test_missing_file_is_an_error · method · L182-L184 — def test_missing_file_is_an_error(self)
• test_collect_variants_merges_flags_and_file · method · L186-L190 — def test_collect_variants_merges_flags_and_file(self)
• ScoreArithmeticTests · class · L193-L218 — class ScoreArithmeticTests(unittest.TestCase)
• test_phred_scale_matches_the_report · method · L194-L198 — def test_phred_scale_matches_the_report(self)
• test_saturated_quantile_is_floored_not_infinite · method · L200-L203 — def test_saturated_quantile_is_floored_not_infinite(self)
• test_nan_propagates · method · L205-L207 — def test_nan_propagates(self)
• test_top_percent · method · L209-L211 — def test_top_percent(self)
• test_feature_display_names_cover_all_eighteen · method · L213-L218 — def test_feature_display_names_cover_all_eighteen(self)
• ExportTests · class · L221-L252 — class ExportTests(unittest.TestCase)
• test_tsv_to_stdout_orders_columns_by_first_appearance · method · L224-L231 — def test_tsv_to_stdout_orders_columns_by_first_appearance(self)
• test_json_to_file · method · L233-L239 — def test_json_to_file(self)
• test_format_follows_extension_then_flag · method · L241-L246 — def test_format_follows_extension_then_flag(self)
• test_unknown_format_and_parquet_without_path_are_rejected · method · L248-L252 — def test_unknown_format_and_parquet_without_path_are_rejected(self)
• ApiKeyTests · class · L255-L275 — class ApiKeyTests(unittest.TestCase)
• test_primary_then_fallback_spelling · method · L256-L260 — def test_primary_then_fallback_spelling(self)
• test_explicit_variable_name · method · L262-L264 — def test_explicit_variable_name(self)
• test_missing_key_exits_with_signup_url · method · L266-L269 — def test_missing_key_exits_with_signup_url(self)
• test_portal_url_encodes_the_allele_separator · method · L271-L275 — def test_portal_url_encodes_the_allele_separator(self)
• AtlasLinkTests · class · L283-L327 — class AtlasLinkTests(unittest.TestCase)
• test_variant_link_normalises_and_encodes · method · L284-L288 — def test_variant_link_normalises_and_encodes(self)
• test_locus_link_keeps_one_based_closed_coordinates · method · L290-L294 — def test_locus_link_keeps_one_based_closed_coordinates(self)
• test_gene_uses_entity_mode_and_motifs_take_zoom · method · L296-L301 — def test_gene_uses_entity_mode_and_motifs_take_zoom(self)
• test_tf_filter_pulls_in_rna_seq_and_dnase · method · L303-L309 — def test_tf_filter_pulls_in_rna_seq_and_dnase(self)
• test_modalities_are_validated · method · L311-L316 — def test_modalities_are_validated(self)
• test_cli_prints_url_or_markdown_and_rejects_rsids · method · L318-L327 — def test_cli_prints_url_or_markdown_and_rejects_rsids(self)
• SequenceLengthTests · class · L335-L349 — class SequenceLengthTests(unittest.TestCase)
• test_names_and_integers · method · L336-L341 — def test_names_and_integers(self)
• test_lengths_match_the_sdk_constants · method · L344-L349 — def test_lengths_match_the_sdk_constants(self)
• ScorerSelectionTests · class · L353-L379 — class ScorerSelectionTests(unittest.TestCase)
• test_default_excludes_active_scorers · method · L354-L358 — def test_default_excludes_active_scorers(self)
• test_mouse_drops_polyadenylation · method · L360-L365 — def test_mouse_drops_polyadenylation(self)
• test_named_selection_and_unknown_names · method · L367-L372 — def test_named_selection_and_unknown_names(self)
• test_list_scorers_needs_no_network · method · L374-L379 — def test_list_scorers_needs_no_network(self)
• _variant · function · L389-L390 — def _variant(text)
• _avi_adata · function · L392-L398 — def _avi_adata(variants, raws, cdfs)
• _fi_adata · function · L400-L407 — def _fi_adata(variants, top_index)
• _rna_adata · function · L420-L429 — def _rna_adata(variant)
• FakeAtlasClient · class · L431-L471 — class FakeAtlasClient
• init · method · L434-L435 — def init(self)
• query_variant · method · L437-L448 — def query_variant(self, variant, requested_scorers, **filters)
• query_interval · method · L450-L465 — def query_interval(self, interval, requested_scorers, progress_bar=True, **filters)
• scorer_metadata · method · L467-L471 — def scorer_metadata(self)
• AtlasConversionTests · class · L475-L522 — class AtlasConversionTests(unittest.TestCase)
• test_summarize_avi_computes_phred_and_top_feature · method · L476-L488 — def test_summarize_avi_computes_phred_and_top_feature(self)
• test_summarize_avi_without_attributions_or_quantiles · method · L490-L497 — def test_summarize_avi_without_attributions_or_quantiles(self)
• test_tidy_atlas_scores_is_one_row_per_gene_track · method · L499-L508 — def test_tidy_atlas_scores_is_one_row_per_gene_track(self)
• test_max_abs_track_and_metadata_rows · method · L510-L522 — def test_max_abs_track_and_metadata_rows(self)
• AtlasQueryCliTests · class · L526-L631 — class AtlasQueryCliTests(unittest.TestCase)
• setUp · method · L527-L533 — def setUp(self)
• test_avi_for_variants_writes_one_row_each_and_keeps_failures · method · L535-L551 — def test_avi_for_variants_writes_one_row_each_and_keeps_failures(self)
• test_avi_from_vcf_warns_about_indels_and_filters_by_phred · method · L553-L563 — def test_avi_from_vcf_warns_about_indels_and_filters_by_phred(self)
• test_avi_with_tracks_adds_the_strongest_track · method · L565-L572 — def test_avi_with_tracks_adds_the_strongest_track(self)
• test_avi_interval_scans_three_variants_per_base_and_sorts · method · L574-L582 — def test_avi_interval_scans_three_variants_per_base_and_sorts(self)
• test_avi_interval_refuses_wide_windows_and_large_stdout · method · L584-L593 — def test_avi_interval_refuses_wide_windows_and_large_stdout(self)
• test_avi_without_inputs_exits · method · L595-L597 — def test_avi_without_inputs_exits(self)
• test_scores_forwards_filters_and_flattens · method · L599-L614 — def test_scores_forwards_filters_and_flattens(self)
• test_scores_min_abs_quantile_keeps_tails · method · L616-L623 — def test_scores_min_abs_quantile_keeps_tails(self)
• test_scorers_and_tracks_subcommands · method · L625-L631 — def test_scorers_and_tracks_subcommands(self)