tests/genomic-coordinates/test_scripts.py

• _load_script · function · L29-L38 — def _load_script(name: str)
• run_main · function · L48-L53 — def run_main(module, argv)
• rows_from_tsv · function · L56-L59 — def rows_from_tsv(text)
• ConventionTests · class · L67-L97 — class ConventionTests(unittest.TestCase)
• test_round_trip_through_canonical_is_identity · method · L68-L73 — def test_round_trip_through_canonical_is_identity(self)
• test_only_the_start_moves_between_conventions · method · L75-L79 — def test_only_the_start_moves_between_conventions(self)
• test_length_is_convention_independent · method · L81-L85 — def test_length_is_convention_independent(self)
• test_samtools_region_spans_both_endpoints · method · L87-L93 — def test_samtools_region_spans_both_endpoints(self): # The samtools manual: chr3:1000-2000 is a 1001 bp region.
• test_unknown_format_is_rejected · method · L95-L97 — def test_unknown_format_is_rejected(self)
• RegionStringTests · class · L100-L136 — class RegionStringTests(unittest.TestCase)
• test_thousands_separators_are_accepted · method · L101-L106 — def test_thousands_separators_are_accepted(self)
• test_ensembl_double_dot_and_strand · method · L108-L111 — def test_ensembl_double_dot_and_strand(self)
• test_start_without_end_is_refused · method · L113-L117 — def test_start_without_end_is_refused(self): # In samtools, chr2:1000000 runs to the end of the contig -- not one base.
• test_bare_contig_is_refused · method · L119-L121 — def test_bare_contig_is_refused(self)
• test_braced_hla_contig_round_trips · method · L123-L129 — def test_braced_hla_contig_round_trips(self)
• test_unbraced_colon_bearing_name_is_refused · method · L131-L136 — def test_unbraced_colon_bearing_name_is_refused(self)
• ConvertCoordsCliTests · class · L139-L194 — class ConvertCoordsCliTests(unittest.TestCase)
• test_bed_to_gff · method · L140-L146 — def test_bed_to_gff(self)
• test_ucsc_region_to_bed · method · L148-L156 — def test_ucsc_region_to_bed(self)
• test_zero_length_bed_feature_is_unrepresentable_in_gff · method · L158-L163 — def test_zero_length_bed_feature_is_unrepresentable_in_gff(self)
• test_zero_length_survives_a_half_open_target · method · L165-L169 — def test_zero_length_survives_a_half_open_target(self)
• test_inverted_interval_is_invalid · method · L171-L175 — def test_inverted_interval_is_invalid(self)
• test_list_covers_every_convention · method · L177-L181 — def test_list_covers_every_convention(self)
• test_json_output_is_parseable · method · L183-L186 — def test_json_output_is_parseable(self)
• test_reads_a_bed_file · method · L188-L194 — def test_reads_a_bed_file(self)
• ReferenceTests · class · L205-L246 — class ReferenceTests(unittest.TestCase)
• test_fetch_is_zero_based_half_open · method · L206-L211 — def test_fetch_is_zero_based_half_open(self)
• test_chr_prefix_is_resolved_both_ways · method · L213-L215 — def test_chr_prefix_is_resolved_both_ways(self)
• test_past_the_end_is_an_error_naming_the_assembly · method · L217-L221 — def test_past_the_end_is_an_error_naming_the_assembly(self)
• test_missing_contig_names_the_likely_cause · method · L223-L227 — def test_missing_contig_names_the_likely_cause(self)
• test_indexed_and_unindexed_readers_agree · method · L229-L246 — def test_indexed_and_unindexed_readers_agree(self)
• NormalisationTests · class · L249-L329 — class NormalisationTests(unittest.TestCase)
• setUp · method · L252-L253 — def setUp(self)
• normalise · method · L255-L258 — def normalise(self, pos, ref, alt, **kwargs)
• test_deletion_left_aligns_through_the_repeat · method · L260-L264 — def test_deletion_left_aligns_through_the_repeat(self)
• test_every_spelling_of_one_deletion_agrees · method · L266-L272 — def test_every_spelling_of_one_deletion_agrees(self)
• test_insertion_left_aligns · method · L274-L277 — def test_insertion_left_aligns(self)
• test_untrimmed_snv_becomes_parsimonious · method · L279-L283 — def test_untrimmed_snv_becomes_parsimonious(self)
• test_normalised_snv_is_untouched · method · L285-L288 — def test_normalised_snv_is_untouched(self)
• test_normalisation_is_idempotent · method · L290-L296 — def test_normalisation_is_idempotent(self)
• test_cannot_shift_past_the_contig_start · method · L298-L301 — def test_cannot_shift_past_the_contig_start(self)
• test_window_limits_the_shift_and_says_so · method · L303-L306 — def test_window_limits_the_shift_and_says_so(self)
• test_ref_mismatch_is_reported_not_normalised · method · L308-L312 — def test_ref_mismatch_is_reported_not_normalised(self)
• test_symbolic_allele_passes_through · method · L314-L318 — def test_symbolic_allele_passes_through(self)
• test_spanning_deletion_allele_passes_through · method · L320-L321 — def test_spanning_deletion_allele_passes_through(self)
• test_ref_equal_to_alt_is_rejected · method · L323-L325 — def test_ref_equal_to_alt_is_rejected(self)
• test_zero_position_is_rejected · method · L327-L329 — def test_zero_position_is_rejected(self)
• NormaliseCliTests · class · L332-L380 — class NormaliseCliTests(unittest.TestCase)
• test_compare_declares_identity · method · L333-L340 — def test_compare_declares_identity(self)
• test_compare_declares_difference · method · L342-L348 — def test_compare_declares_difference(self)
• test_mismatch_sets_a_failing_exit_code · method · L350-L355 — def test_mismatch_sets_a_failing_exit_code(self)
• test_split_expands_multiallelic_alt · method · L357-L363 — def test_split_expands_multiallelic_alt(self)
• test_reads_a_vcf · method · L365-L373 — def test_reads_a_vcf(self)
• test_missing_reference_is_a_usage_error · method · L375-L380 — def test_missing_reference_is_a_usage_error(self)
• BuildTableTests · class · L388-L406 — class BuildTableTests(unittest.TestCase)
• test_every_build_lists_the_same_chromosomes · method · L389-L392 — def test_every_build_lists_the_same_chromosomes(self)
• test_builds_are_mutually_distinguishable · method · L394-L400 — def test_builds_are_mutually_distinguishable(self)
• test_grch37_and_grch38_differ_on_chr1 · method · L402-L406 — def test_grch37_and_grch38_differ_on_chr1(self)
• IdentifyTests · class · L409-L487 — class IdentifyTests(unittest.TestCase)
• test_hg19_is_identified_by_its_mitochondrion · method · L410-L418 — def test_hg19_is_identified_by_its_mitochondrion(self)
• test_grch37_is_identified_by_its_mitochondrion · method · L420-L426 — def test_grch37_is_identified_by_its_mitochondrion(self)
• test_grch38_is_identified · method · L428-L432 — def test_grch38_is_identified(self)
• test_grch37_and_hg19_are_reported_as_incompatible · method · L434-L441 — def test_grch37_and_hg19_are_reported_as_incompatible(self)
• test_matching_files_are_compatible · method · L443-L449 — def test_matching_files_are_compatible(self)
• test_vcf_header_lengths_are_read · method · L451-L457 — def test_vcf_header_lengths_are_read(self)
• test_grch38_vcf_against_hg19_genome_fails · method · L459-L465 — def test_grch38_vcf_against_hg19_genome_fails(self)
• test_bed_max_coordinate_is_not_treated_as_a_contig_length · method · L467-L475 — def test_bed_max_coordinate_is_not_treated_as_a_contig_length(self)
• test_bed_past_the_contig_end_is_caught · method · L477-L483 — def test_bed_past_the_contig_end_is_caught(self)
• test_unknown_extension_is_refused · method · L485-L487 — def test_unknown_extension_is_refused(self)
• AuditBedTests · class · L495-L521 — class AuditBedTests(unittest.TestCase)
• test_clean_bed_has_no_findings · method · L496-L499 — def test_clean_bed_has_no_findings(self)
• test_one_based_data_in_a_bed_is_flagged · method · L501-L504 — def test_one_based_data_in_a_bed_is_flagged(self)
• test_bed12_absolute_block_starts_are_fatal · method · L506-L509 — def test_bed12_absolute_block_starts_are_fatal(self)
• test_valid_bed12_passes · method · L511-L514 — def test_valid_bed12_passes(self)
• test_space_separated_bed_is_named_as_such · method · L516-L521 — def test_space_separated_bed_is_named_as_such(self)
• AuditGffTests · class · L524-L539 — class AuditGffTests(unittest.TestCase)
• test_zero_start_proves_zero_based_data · method · L525-L530 — def test_zero_start_proves_zero_based_data(self)
• test_end_before_start_is_fatal_regardless_of_strand · method · L532-L534 — def test_end_before_start_is_fatal_regardless_of_strand(self)
• test_clean_gtf_passes · method · L536-L539 — def test_clean_gtf_passes(self)
• AuditVcfTests · class · L542-L565 — class AuditVcfTests(unittest.TestCase)
• test_vep_dash_allele_is_fatal · method · L543-L549 — def test_vep_dash_allele_is_fatal(self)
• test_untrimmed_alleles_are_warned_about · method · L551-L554 — def test_untrimmed_alleles_are_warned_about(self)
• test_contig_order_not_coordinate_order_drives_the_sort_check · method · L556-L561 — def test_contig_order_not_coordinate_order_drives_the_sort_check(self)
• test_interleaved_contigs_are_caught · method · L563-L565 — def test_interleaved_contigs_are_caught(self)
• AuditCliTests · class · L568-L597 — class AuditCliTests(unittest.TestCase)
• test_format_can_be_forced · method · L569-L573 — def test_format_can_be_forced(self)
• test_unknown_extension_is_refused · method · L575-L577 — def test_unknown_extension_is_refused(self)
• test_missing_file_is_a_usage_error · method · L579-L582 — def test_missing_file_is_a_usage_error(self)
• test_examples_are_capped · method · L584-L590 — def test_examples_are_capped(self)
• test_suppressed_findings_still_count_towards_the_exit_code · method · L592-L597 — def test_suppressed_findings_still_count_towards_the_exit_code(self)
• SkillStructureTests · class · L605-L652 — class SkillStructureTests(unittest.TestCase)
• test_frontmatter_name_matches_the_directory · method · L606-L608 — def test_frontmatter_name_matches_the_directory(self)
• test_version_is_a_quoted_string · method · L610-L612 — def test_version_is_a_quoted_string(self)
• test_skill_md_is_within_the_line_budget · method · L614-L616 — def test_skill_md_is_within_the_line_budget(self)
• test_no_tests_ship_inside_the_skill · method · L618-L620 — def test_no_tests_ship_inside_the_skill(self)
• test_local_markdown_links_resolve · method · L622-L630 — def test_local_markdown_links_resolve(self)
• test_every_referenced_file_exists · method · L632-L636 — def test_every_referenced_file_exists(self)
• test_every_script_is_mentioned_in_the_skill · method · L638-L644 — def test_every_script_is_mentioned_in_the_skill(self)
• test_scripts_import_nothing_outside_the_standard_library · method · L646-L652 — def test_scripts_import_nothing_outside_the_standard_library(self)