Module Import alias Import alias Import alias Import alias identifier Import alias Import alias identifier ImportFrom alias alias ImportFrom alias alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias Import alias ClassDef bases NameLoad body FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Call NameLoad Str Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Str Str decorator_list FunctionDef arguments args NameParam defaults body With Call NameLoad AttributeLoad NameLoad attr Str Str Str TupleStore NameStore NameStore NameStore NameStore body Expr Call AttributeLoad Call AttributeLoad NameLoad attr attr Expr Call AttributeLoad Call AttributeLoad NameLoad attr attr Expr Call AttributeLoad Call AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Str With Call NameLoad AttributeLoad NameLoad attr Str Str TupleStore NameStore NameStore NameStore body Assign NameStore Call AttributeLoad Call AttributeLoad Call AttributeLoad NameLoad attr CompareEq AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str attr attr Assign NameStore Call AttributeLoad Call AttributeLoad Call AttributeLoad NameLoad attr CompareEq AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str attr attr Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore Call NameLoad ListLoad Str Str Str Str Str Str Str Str Str Str Str Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str Num Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str Call NameLoad NameLoad With Call NameLoad Str Str NameStore body Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr ListComp NameLoad comprehension NameStore NameLoad Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr BinOpAdd SubscriptLoad NameLoad Index Str Str Call NameLoad NameLoad With Call NameLoad Str NameStore body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListComp NameLoad comprehension NameStore NameLoad Expr Call NameLoad NameLoad NameLoad Assign NameStore ListLoad Lambda arguments args NameParam defaults SubscriptLoad AttributeLoad NameLoad attr Index Str Lambda arguments args NameParam defaults SubscriptLoad AttributeLoad NameLoad attr Index Str Lambda arguments args NameParam defaults SubscriptLoad AttributeLoad NameLoad attr Index Str Lambda arguments args NameParam defaults SubscriptLoad AttributeLoad NameLoad attr Index Str Lambda arguments args NameParam defaults SubscriptLoad AttributeLoad NameLoad attr Index Str Assign NameStore ListLoad Lambda arguments args NameParam defaults Call NameLoad SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults Call NameLoad SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults Call NameLoad SubscriptLoad NameLoad Index Str Expr Call NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr Call NameLoad ListComp SubscriptLoad NameLoad Index Str comprehension NameStore NameLoad FunctionDef arguments args NameParam defaults body FunctionDef arguments args NameParam defaults body FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad AttributeLoad NameLoad attr Lambda arguments args NameParam defaults CompareEq AttributeLoad NameLoad attr NameLoad Return Call NameLoad AttributeLoad NameLoad attr NameLoad decorator_list Return NameLoad decorator_list Assign NameStore ListLoad Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Lambda arguments args NameParam defaults Call NameLoad Call Call NameLoad Str NameLoad Assign NameStore ListLoad Lambda arguments args NameParam defaults SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults IfExp SubscriptLoad NameLoad Index Str Call NameLoad SubscriptLoad NameLoad Index Str NameLoad Lambda arguments args NameParam defaults Call NameLoad SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults Call NameLoad SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults Call NameLoad SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults SubscriptLoad NameLoad Index Str Lambda arguments args NameParam defaults Call NameLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareEq SubscriptLoad NameLoad Index Str NameLoad Expr Call NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad decorator_list Expr Call NameLoad Str Expr Call NameLoad Str decorator_list decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults ListLoad ListLoad body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad AttributeLoad NameLoad attr Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Return Call NameLoad BinOpAdd NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str Assign NameStore ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Return Call NameLoad BinOpAdd NameLoad NameLoad decorator_list Assign NameStore Call NameLoad ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Assign NameStore Call NameLoad ListComp Call NameLoad NameLoad comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list
N/A N/A ast N/A mock N/A nose N/A nose.tools asserts N/A json N/A vcf pyvcf cycledash app db common.helpers tables find workers.genotype_extractor _extract test_projects_api create_project_with_name test_bams_api create_bam_with_name test_runs_api create_run_with_uri N/A helpers TestGenotypeExtractorWorker N/A object N/A setUp N/A N/A self N/A N/A N/A N/A self project N/A create_project_with_name my project N/A N/A self run N/A create_run_with_uri N/A N/A self project N/A id /tests/data/snv.vcf N/A tearDown N/A N/A self N/A N/A N/A N/A tables N/A db engine projects vcfs genotypes N/A con projects runs genotypes N/A N/A N/A N/A N/A N/A genotypes delete execute N/A N/A N/A N/A N/A runs delete execute N/A N/A N/A N/A N/A projects delete execute N/A tearDownClass N/A N/A cls N/A N/A N/A N/A N/A helpers delete_all_records db N/A classmethod test_extraction N/A N/A self N/A N/A N/A N/A _extract N/A N/A self run N/A id N/A N/A tables N/A db engine vcfs genotypes N/A con vcfs genotypes N/A N/A vcf N/A N/A N/A N/A N/A N/A vcfs select N/A N/A N/A vcfs c id N/A N/A self run N/A id execute fetchone N/A variants N/A N/A N/A N/A N/A N/A genotypes select N/A N/A N/A genotypes c vcf_id N/A N/A self run N/A id execute fetchall N/A variants N/A N/A dict v N/A v variants N/A expected_extant_columns N/A set N/A sample:GT sample:RD sample:FREQ info:SSC sample:DP sample:DP4 info:DP info:SS info:GPV sample:AD info:SPV N/A extant_columns N/A set N/A N/A ast literal_eval N/A vcf N/A extant_columns N/A N/A N/A asserts eq_ extant_columns expected_extant_columns N/A N/A N/A asserts eq_ N/A vcf N/A genotype_count 20 N/A N/A N/A asserts eq_ N/A vcf N/A genotype_count N/A len variants N/A N/A open tests/data/snv.vcf r vcffile N/A N/A vcflines N/A N/A vcffile readlines N/A expected_vcf_header N/A N/A join N/A l N/A l vcflines N/A N/A l startswith # N/A N/A N/A asserts eq_ N/A N/A vcf N/A vcf_header N/A unicode expected_vcf_header N/A N/A open tests/data/snv.vcf vcffile N/A N/A vcfreader N/A N/A pyvcf Reader vcffile N/A expected_pyvcf_variants N/A r N/A r vcfreader N/A N/A assert_keys_in_variants expected_pyvcf_variants variants N/A pyvcf_getters N/A N/A N/A N/A v N/A N/A N/A v INFO N/A DP N/A N/A N/A v N/A N/A N/A v INFO N/A SS N/A N/A N/A v N/A N/A N/A v INFO N/A SSC N/A N/A N/A v N/A N/A N/A v INFO N/A GPV N/A N/A N/A v N/A N/A N/A v INFO N/A SPV N/A db_variant_getters N/A N/A N/A N/A v N/A N/A int N/A v N/A info:DP N/A N/A N/A v N/A N/A v N/A info:SS N/A N/A N/A v N/A N/A v N/A info:SSC N/A N/A N/A v N/A N/A float N/A v N/A info:GPV N/A N/A N/A v N/A N/A float N/A v N/A info:SPV N/A N/A assert_keys_in_variants expected_pyvcf_variants variants expected_getters pyvcf_getters actual_getters db_variant_getters N/A N/A N/A asserts eq_ N/A set N/A vcfreader samples N/A set N/A N/A v N/A sample_name N/A v variants ensure_samples_equivalent N/A N/A sample_name N/A N/A get_sample_data N/A N/A attr N/A N/A get_from_variant N/A N/A variant N/A N/A N/A sample N/A find N/A variant samples N/A N/A N/A x N/A N/A N/A x sample sample_name N/A N/A getattr N/A sample data attr N/A N/A get_from_variant N/A N/A pyvcf_getters N/A N/A get_sample_data GT N/A get_sample_data GQ N/A get_sample_data DP N/A get_sample_data RD N/A get_sample_data AD N/A get_sample_data FREQ N/A N/A N/A v N/A N/A tuple N/A N/A get_sample_data DP4 v N/A db_variant_getters N/A N/A N/A N/A v N/A N/A v N/A sample:GT N/A N/A N/A v N/A N/A N/A v N/A sample:GQ N/A int N/A v N/A sample:GQ None N/A N/A N/A v N/A N/A int N/A v N/A sample:DP N/A N/A N/A v N/A N/A int N/A v N/A sample:RD N/A N/A N/A v N/A N/A int N/A v N/A sample:AD N/A N/A N/A v N/A N/A v N/A sample:FREQ N/A N/A N/A v N/A N/A tuple N/A N/A ast literal_eval N/A v N/A sample:DP4 N/A actual_db_variants N/A v N/A v variants N/A N/A v N/A sample_name sample_name N/A N/A assert_keys_in_variants expected_pyvcf_variants actual_db_variants expected_getters pyvcf_getters actual_getters db_variant_getters N/A N/A N/A ensure_samples_equivalent NORMAL N/A N/A ensure_samples_equivalent TUMOR N/A N/A assert_keys_in_variants N/A N/A expected_variants actual_variants expected_getters actual_getters N/A N/A N/A N/A N/A Asserts that the variants in expected and actual match each other on
    chromosome, position, reference, alternates, and the result of applying the
    functions in expected_getters and actual_getters to expected_variants
    and actual_variants, respectively.
     extract_expected_keys N/A N/A v N/A N/A N/A base N/A N/A v CHROM N/A v POS N/A v REF N/A N/A join N/A map str N/A v ALT N/A extra N/A N/A k v N/A k expected_getters N/A N/A tuple N/A base extra N/A extract_actual_keys N/A N/A v N/A N/A N/A base N/A N/A v N/A contig N/A v N/A position N/A v N/A reference N/A v N/A alternates N/A extra N/A N/A k v N/A k actual_getters N/A N/A tuple N/A base extra N/A N/A expected_variants N/A set N/A N/A extract_expected_keys v N/A v expected_variants N/A actual_variants N/A set N/A N/A extract_actual_keys v N/A v actual_variants N/A N/A N/A asserts eq_ expected_variants actual_variants N/A