Index

A

add_biopsy_number_column() (in module vardb.metadata_wrangling.oasis.demographics) aggregate() (in module scripts.vardb_aggregate) aggregate_effects() (vardb.connections.vardb_loader.Loader method) aggregate_somatic_cnvs() (vardb.connections.vardb_loader.Loader method) aggregate_somatic_snps_indel() (vardb.connections.vardb_loader.Loader method) aggregate_vcall() (vardb.connections.vardb_loader.Loader method) aligned_libcore_map (vardb.connections.bioapps_api.BioApps_API attribute) analysis_exists() (vardb.connections.vardb_connection.VarDB method) analysis_items() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method)

analysis_keys() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) analysis_record_exists() (vardb.connections.vardb_connection.VarDB method) analysis_values() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) analyze() (in module scripts.vardb_analyze) (in module scripts.vardb_update_db) (vardb.connections.vardb_loader.Loader method) annotate() (in module vardb.variant_data_files.vcf_tools) append_error_codes() (in module vardb.metadata_wrangling.oasis.error_code) append_patient_id_column() (in module vardb.metadata_wrangling.oasis.preprocess)

B

BioApps (class in vardb.connections.bioapps)

BioApps_API (class in vardb.connections.bioapps_api) BioappsException

C

check_vt() (in module vardb.variant_data_files.vcf_tools) clean_data() (in module vardb.metadata_wrangling.oasis.preprocess) close() (vardb.variant_data_files.variant_data_file.VariantDataFile method) collect_error_codes() (in module vardb.metadata_wrangling.oasis.error_code) collect_metadata() (vardb.metadata_wrangling.metadata_collector.ExpressionCollector method) (vardb.metadata_wrangling.metadata_collector.MetadataCollector method) (vardb.metadata_wrangling.metadata_collector.ReviewedSomaticCNVCollector method) (vardb.metadata_wrangling.metadata_collector.ReviewedSomaticLOHCollector method) Column (class in vardb.variant_file_loaders.sample_metadata) Columns (class in vardb.variant_data_files.variant_data_file) columns (vardb.variant_file_loaders.sample_metadata.SampleMetaData attribute) compare_death_dates_to_all_dates() (in module vardb.metadata_wrangling.oasis.preprocess)

compare_tumour_group_to_pog_tumour_groups() (in module vardb.metadata_wrangling.oasis.preprocess) complete() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) concatenate_error_codes() (in module vardb.metadata_wrangling.oasis.error_code) Config (class in vardb.metadata_wrangling.configuration) Connection (class in vardb.connections.connection) ConnectionException ControlFreeC (class in vardb.variant_data_files.cnv) ControlFreeCCollector (class in vardb.metadata_wrangling.metadata_collector) count() (vardb.connections.vardb_connection.VarDB method) count_non_null_treatment_type_for_treatment_groups() (in module vardb.metadata_wrangling.oasis.treatment) count_pog_informed_for_treatment_groups() (in module vardb.metadata_wrangling.oasis.treatment) create_external_table() (vardb.connections.vardb_loader.Loader method)

D

data_exists() (vardb.connections.vardb_connection.VarDB method) data_type (vardb.metadata_wrangling.metadata_collector.ControlFreeCCollector attribute) (vardb.metadata_wrangling.metadata_collector.ExpressionCollector attribute) (vardb.metadata_wrangling.metadata_collector.MetadataCollector attribute) (vardb.metadata_wrangling.metadata_collector.ReviewedSomaticCNVCollector attribute) (vardb.metadata_wrangling.metadata_collector.ReviewedSomaticLOHCollector attribute) (vardb.metadata_wrangling.metadata_collector.SomaticSmallVariantCollector attribute) (vardb.metadata_wrangling.metadata_collector.VCallCollector attribute) database (vardb.connections.bioapps_api.BioApps_API attribute) DataClass() (in module vardb.variant_data_files.data_classes) dataframe_to_tsv() (in module vardb.metadata_wrangling.oasis.output) default() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method)

delete() (vardb.connections.vardb_hdfs.HDFS method) delete_variant_file() (vardb.connections.vardb_hdfs.HDFS method) dict_query() (vardb.connections.vardb_connection.VarDB method) difference() (vardb.metadata_wrangling.metadata_collector.Metadata method) download_unannotated_snps_indels() (in module vardb.variant_file_loaders.loader) drop_comma_separated_drugs_column() (in module vardb.metadata_wrangling.oasis.drug_map) drop_duplicate_pogs_with_same_biopsy_dates() (in module vardb.metadata_wrangling.oasis.preprocess) drop_duplicate_rows() (in module vardb.metadata_wrangling.oasis.preprocess) drop_empty_pog_id_rows() (in module vardb.metadata_wrangling.oasis.preprocess) drop_external_table() (vardb.connections.vardb_loader.Loader method) drop_missing_pog_id_rows() (in module vardb.metadata_wrangling.oasis.preprocess) drop_table() (vardb.connections.vardb_loader.Loader method) dump_table() (vardb.connections.vardb_loader.Loader method)

E

eliminate_duplicates_and_sort_drug_list() (in module vardb.metadata_wrangling.oasis.drug_map) evaluate() (vardb.metadata_wrangling.configuration.Config method) ExpressionCollector (class in vardb.metadata_wrangling.metadata_collector) extract_biopsy_columns() (in module vardb.metadata_wrangling.oasis.demographics) extract_column_names_from_base_names() (in module vardb.metadata_wrangling.oasis.helpers)

extract_data() (in module vardb.metadata_wrangling.oasis.demographics) (in module vardb.metadata_wrangling.oasis.diagnosis) (in module vardb.metadata_wrangling.oasis.radiation) (in module vardb.metadata_wrangling.oasis.treatment) extract_date_columns() (in module vardb.metadata_wrangling.oasis.helpers)

F

factory() (vardb.metadata_wrangling.metadata_collector.MetadataCollector class method) filter_metadata() (vardb.metadata_wrangling.metadata_collector.TCFilter method)

filter_non_pediatric_ids() (in module vardb.metadata_wrangling.oasis.output) filter_somatic_snvs_indels() (vardb.connections.vardb_loader.Loader method)

G

generate_error_dataframe() (in module vardb.metadata_wrangling.oasis.error_code) get() (vardb.metadata_wrangling.configuration.Config method) get_analysis() (vardb.connections.vardb_connection.VarDB method) get_bam_cnvs() (in module vardb.metadata_wrangling.get_bam_cnvs) get_columns_from_pandas() (vardb.variant_data_files.variant_data_file.VariantDataFile method) get_data() (vardb.variant_data_files.variant_data_file.VariantDataFile method) get_data_ptr() (vardb.variant_data_files.variant_data_file.VariantDataFile method) get_demographics_data() (in module vardb.metadata_wrangling.oasis.demographics) get_diagnosis_data() (in module vardb.metadata_wrangling.oasis.diagnosis) get_drug_treatment_data() (in module vardb.metadata_wrangling.oasis.treatment) get_expression_data() (vardb.connections.bioapps.BioApps method) get_header() (vardb.variant_data_files.variant_data_file.VariantDataFile method) get_karen_info() (vardb.connections.karen.Karen method) get_latest_analysis() (vardb.connections.vardb_connection.VarDB method) get_LIMS_info() (vardb.connections.lims.LIMS method) get_login_from_file() (in module vardb.tools) get_longest_length_matched_token() (in module vardb.metadata_wrangling.oasis.drug_map) get_md5sum() (in module vardb.tools) (vardb.variant_data_files.variant_data_file.VariantDataFile method) (vardb.variant_data_files.vcf.VCall method)

get_merge_data() (vardb.connections.bioapps.BioApps method) get_most_recent_file() (in module scripts.vardb_update_db) get_patient_identifier() (in module vardb.metadata_wrangling.helpers) get_pog_controlfreec_library_name() (in module vardb.metadata_wrangling.helpers) get_pog_gene_model() (in module vardb.metadata_wrangling.helpers) get_pog_id() (in module vardb.metadata_wrangling.helpers) get_radiation_data() (in module vardb.metadata_wrangling.oasis.radiation) get_remote_path() (vardb.connections.vardb_hdfs.HDFS method) get_sample() (vardb.connections.vardb_connection.VarDB method) get_sample_info() (vardb.connections.bioapps_api.BioApps_API method) get_somatic_data() (vardb.connections.bioapps.BioApps method) get_tokens_matching_the_drug_map() (in module vardb.metadata_wrangling.oasis.drug_map) get_tumor_content() (vardb.connections.bioapps.BioApps method) get_tumour_content() (vardb.metadata_wrangling.metadata_collector.TCFilter method) get_unannotated_vcf() (vardb.connections.vardb_loader.Loader method) get_variant_calling_data() (vardb.connections.bioapps.BioApps method) GetBamCNVsException group_and_aggregate_error_codes() (in module vardb.metadata_wrangling.oasis.error_code)

H

HDFS (class in vardb.connections.vardb_hdfs) HdfsException HomozygousDeletion (class in vardb.variant_data_files.cnv)

HomozygousDeletion_v1 (class in vardb.variant_data_files.cnv) HomozygousDeletion_v2 (class in vardb.variant_data_files.cnv) HomozygousDeletion_v3 (class in vardb.variant_data_files.cnv)

I

identify_empty_pog_ids() (in module vardb.metadata_wrangling.oasis.preprocess) identify_missing_pog_ids() (in module vardb.metadata_wrangling.oasis.preprocess) initialize_logger() (in module vardb.tools) input_keys (vardb.variant_file_loaders.sample_metadata.SampleMetaData attribute)

insert_original_drug_string_column_before_error_column() (in module vardb.metadata_wrangling.oasis.drug_map) items() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) iteritems() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) iterkeys() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) itervalues() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method)

K

k (vardb.metadata_wrangling.metadata_collector.Metadata attribute) Karen (class in vardb.connections.karen)

key (vardb.variant_file_loaders.sample_metadata.SampleMetaData attribute) keys() (vardb.metadata_wrangling.configuration.Config method) (vardb.variant_file_loaders.sample_metadata.SampleMetaData method)

L

library_exists() (vardb.connections.vardb_connection.VarDB method) library_map (vardb.connections.bioapps_api.BioApps_API attribute) LIMS (class in vardb.connections.lims) LimsException line_count() (in module vardb.tools) (vardb.variant_data_files.variant_data_file.VariantDataFile method) load() (vardb.connections.vardb_loader.Loader method) load_annotations() (in module scripts.vardb_load_annotations) (in module scripts.vardb_update_db) load_dim_tables() (in module scripts.vardb_load_dim_tables) load_file() (in module vardb.variant_file_loaders.loader) load_files() (in module vardb.variant_file_loaders.loader)

load_functions (vardb.connections.vardb_loader.Loader attribute) load_table() (vardb.connections.vardb_loader.Loader method) load_temp_vcf_table() (vardb.connections.vardb_loader.Loader method) load_unannotated_snps_indels() (vardb.connections.vardb_loader.Loader method) load_variants() (in module scripts.vardb_load_variants) (in module scripts.vardb_update_db) load_vcall() (vardb.connections.vardb_loader.Loader method) load_vcf_annotations() (in module vardb.variant_file_loaders.loader) (vardb.connections.vardb_loader.Loader method) load_vcf_table() (vardb.connections.vardb_loader.Loader method) Loader (class in vardb.connections.vardb_loader) LoaderException locate_metadata_changes() (in module vardb.metadata_wrangling.locate_metadata_changes)

M

main() (in module scripts.vardb_aggregate) (in module scripts.vardb_analyze) (in module scripts.vardb_load_annotations) (in module scripts.vardb_load_dim_tables) (in module scripts.vardb_load_variants) (in module scripts.vardb_make_loader) (in module scripts.vardb_rollout_db) (in module scripts.vardb_update_db) (in module vardb.metadata_wrangling.oasis.oasis) (in module vardb.queries.CNV_overlap) (in module vardb.queries.experimental_records) (in module vardb.queries.experimental_records_external)

make_load_files() (in module scripts.vardb_update_db) make_loader() (in module scripts.vardb_make_loader) (in module vardb.metadata_wrangling.loader_maker) map_oasis_drug_to_ontology() (in module vardb.metadata_wrangling.oasis.drug_map) map_oasis_drugs_using_drug_map() (in module vardb.metadata_wrangling.oasis.drug_map) mark_non_production() (vardb.connections.vardb_loader.Loader method) Metadata (class in vardb.metadata_wrangling.metadata_collector) metadata (vardb.metadata_wrangling.metadata_collector.MetadataCollector attribute) MetadataCollector (class in vardb.metadata_wrangling.metadata_collector) MetadataCollectorException MutSeq_v1 (class in vardb.variant_data_files.vcf) MutSeq_v2 (class in vardb.variant_data_files.vcf)

N

normalize() (in module vardb.variant_data_files.vcf_tools)

normalize_indels() (vardb.variant_data_files.vcf.VCall method)

O

object_exists() (vardb.connections.vardb_connection.VarDB method) open() (vardb.variant_data_files.variant_data_file.VariantDataFile method)

output_to_tsv() (in module vardb.metadata_wrangling.oasis.output) (vardb.metadata_wrangling.metadata_collector.Metadata method)

P

pandas_query() (vardb.connections.karen.Karen method) (vardb.connections.vardb_connection.VarDB method)

parse_oasis_data() (in module vardb.metadata_wrangling.oasis.oasis) production_error_handling() (in module vardb.tools)

Q

query() (in module vardb.queries.CNV_overlap) (in module vardb.queries.experimental_records) (in module vardb.queries.experimental_records_external)

R

read_data() (in module vardb.metadata_wrangling.oasis.preprocess) remove_file() (in module vardb.variant_file_loaders.loader) rename_error_code_column_to_errors() (in module vardb.metadata_wrangling.oasis.error_code) replace_nan_with_empty_string() (in module vardb.metadata_wrangling.oasis.error_code) required() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) reshape_dataframe() (in module vardb.metadata_wrangling.oasis.helpers) reshape_diagnosis_data() (in module vardb.metadata_wrangling.oasis.diagnosis) reshape_radiation_data() (in module vardb.metadata_wrangling.oasis.radiation)

reshape_treatment_data() (in module vardb.metadata_wrangling.oasis.treatment) restore_table() (vardb.connections.vardb_loader.Loader method) ReviewedSomaticCNVCollector (class in vardb.metadata_wrangling.metadata_collector) ReviewedSomaticLOHCollector (class in vardb.metadata_wrangling.metadata_collector) rollout() (in module scripts.vardb_rollout_db) RSEM (class in vardb.variant_data_files.expression) run_aggregation() (in module scripts.vardb_update_db) run_germline_query() (in module scripts.vardb_update_db)

S

sample_exists() (vardb.connections.vardb_connection.VarDB method) sample_items() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) sample_keys() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) sample_record_exists() (vardb.connections.vardb_connection.VarDB method) sample_values() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) SampleMetaData (class in vardb.variant_file_loaders.sample_metadata) save_to_file() (vardb.connections.vardb_connection.VarDB method) scripts (module) scripts.load_weekly_variants_test_env (module) scripts.vardb_aggregate (module) scripts.vardb_analyze (module) scripts.vardb_load_annotations (module) scripts.vardb_load_dim_tables (module) scripts.vardb_load_variants (module) scripts.vardb_make_loader (module) scripts.vardb_rollout_db (module) scripts.vardb_update_db (module) scripts.vardb_update_db_env (module)

server_string (vardb.connections.bioapps_api.BioApps_API attribute) set() (vardb.metadata_wrangling.configuration.Config method) SomaticCna (class in vardb.variant_data_files.cnv) SomaticCnv (class in vardb.variant_data_files.cnv) SomaticLOH (class in vardb.variant_data_files.cnv) SomaticSmallVariantCollector (class in vardb.metadata_wrangling.metadata_collector) SomaticVAF (class in vardb.variant_data_files.cnv) source_map (vardb.connections.bioapps_api.BioApps_API attribute) split_and_strip_drug_names() (in module vardb.metadata_wrangling.oasis.drug_map) split_drug_names_on_special_characters() (in module vardb.metadata_wrangling.oasis.drug_map) split_gsc_pog_id_and_drop_it() (in module vardb.metadata_wrangling.oasis.preprocess) split_strip_and_join_column_data() (in module vardb.metadata_wrangling.oasis.preprocess) StreamToLogger (class in vardb.tools) StrelkaIndels (class in vardb.variant_data_files.vcf) StrelkaSnps (class in vardb.variant_data_files.vcf) strip_1_from_date() (in module vardb.metadata_wrangling.oasis.preprocess) strip_whitespace_and_consecutive_commas_from_column_data() (in module vardb.metadata_wrangling.oasis.preprocess) strip_whitespace_from_beginning_and_end() (in module vardb.metadata_wrangling.oasis.preprocess)

T

TCFilter (class in vardb.metadata_wrangling.metadata_collector) TcgaCnv (class in vardb.variant_data_files.cnv) TcgaGermlineMaskedCnv (class in vardb.variant_data_files.cnv) TCGASimpleSomatic (class in vardb.variant_data_files.maf) throw_exception() (in module vardb.metadata_wrangling.metadata_collector)

tokenize_drug_name() (in module vardb.metadata_wrangling.oasis.drug_map) TranscriptNormalized (class in vardb.variant_data_files.expression) truncate_table() (vardb.connections.vardb_loader.Loader method) truncate_unannotated_snps_indels() (vardb.connections.vardb_loader.Loader method) type() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method)

U

uniform_date_format() (in module vardb.metadata_wrangling.oasis.preprocess) update() (vardb.metadata_wrangling.configuration.Config method) update_analysis() (vardb.connections.vardb_loader.Loader method)

update_dim_tables() (in module scripts.vardb_update_db) update_sample() (vardb.connections.vardb_loader.Loader method) upload_dim_files() (vardb.connections.vardb_hdfs.HDFS method) upload_variant_file() (vardb.connections.vardb_hdfs.HDFS method)

V

valid_types (vardb.variant_data_files.variant_data_file.Columns attribute) validate() (vardb.metadata_wrangling.configuration.Config method) validate_best_response_should_not_be_null() (in module vardb.metadata_wrangling.oasis.treatment) validate_biopsy_date_less_than_or_equal_pog_report_date() (in module vardb.metadata_wrangling.oasis.demographics) validate_blood_collection_date_less_than_or_equal_pog_report_date() (in module vardb.metadata_wrangling.oasis.demographics) validate_consent_date_less_than_or_equal_pog_report_date() (in module vardb.metadata_wrangling.oasis.demographics) validate_data() (in module vardb.metadata_wrangling.oasis.demographics) (in module vardb.metadata_wrangling.oasis.diagnosis) (in module vardb.metadata_wrangling.oasis.preprocess) (in module vardb.metadata_wrangling.oasis.treatment) validate_death_date() (in module vardb.metadata_wrangling.oasis.preprocess) validate_demographics_post_pog_activity_categories() (in module vardb.metadata_wrangling.oasis.treatment) validate_demographics_with_treatment() (in module vardb.metadata_wrangling.oasis.treatment) validate_drug_treatment_for_bcca_treatment_type() (in module vardb.metadata_wrangling.oasis.treatment) validate_duplicate_pogs_with_same_biopsy_dates() (in module vardb.metadata_wrangling.oasis.preprocess) validate_duplicate_rows() (in module vardb.metadata_wrangling.oasis.preprocess) validate_empty_pog_ids() (in module vardb.metadata_wrangling.oasis.preprocess) validate_for_bcca_treatment_type_should_not_be_null() (in module vardb.metadata_wrangling.oasis.treatment) validate_for_post_pog_activities_bcca_province_compassionate_private() (in module vardb.metadata_wrangling.oasis.treatment) validate_mandatory_columns() (in module vardb.metadata_wrangling.oasis.demographics) (in module vardb.metadata_wrangling.oasis.diagnosis) (in module vardb.metadata_wrangling.oasis.treatment) validate_missing_pog_ids() (in module vardb.metadata_wrangling.oasis.preprocess) validate_pog_report_date_mandatory_columns() (in module vardb.metadata_wrangling.oasis.demographics) validate_post_pog_treatment_columns_for_null() (in module vardb.metadata_wrangling.oasis.demographics) validate_post_pog_treatment_columns_for_ys() (in module vardb.metadata_wrangling.oasis.demographics) validate_progression_documentation_is_not_null() (in module vardb.metadata_wrangling.oasis.treatment) validate_re_bx_date_for_not_null() (in module vardb.metadata_wrangling.oasis.demographics) validate_re_bx_date_greater_than_or_equal_biopsy_date() (in module vardb.metadata_wrangling.oasis.demographics) validate_treatment_data() (in module vardb.metadata_wrangling.oasis.treatment) validate_treatment_time_either_pre_or_post_pog_report() (in module vardb.metadata_wrangling.oasis.treatment) validate_treatment_time_for_pre_or_post_pog_report() (in module vardb.metadata_wrangling.oasis.treatment) validate_treatment_time_is_post_pog_report() (in module vardb.metadata_wrangling.oasis.treatment) validate_treatment_with_demographics() (in module vardb.metadata_wrangling.oasis.treatment) validate_tumour_groups() (in module vardb.metadata_wrangling.oasis.preprocess) values() (vardb.variant_file_loaders.sample_metadata.SampleMetaData method) VarDB (class in vardb.connections.vardb_connection) vardb (module) vardb.connections (module) vardb.connections.bioapps (module) vardb.connections.bioapps_api (module) vardb.connections.bioapps_sql (module) vardb.connections.connection (module) vardb.connections.karen (module) vardb.connections.lims (module)

vardb.connections.vardb_connection (module) vardb.connections.vardb_hdfs (module) vardb.connections.vardb_loader (module) vardb.metadata_wrangling (module) vardb.metadata_wrangling.configuration (module) vardb.metadata_wrangling.get_bam_cnvs (module) vardb.metadata_wrangling.helpers (module) vardb.metadata_wrangling.loader_maker (module) vardb.metadata_wrangling.locate_metadata_changes (module) vardb.metadata_wrangling.metadata_collector (module) vardb.metadata_wrangling.oasis (module) vardb.metadata_wrangling.oasis.demographics (module) vardb.metadata_wrangling.oasis.diagnosis (module) vardb.metadata_wrangling.oasis.drug_map (module) vardb.metadata_wrangling.oasis.error_code (module) vardb.metadata_wrangling.oasis.helpers (module) vardb.metadata_wrangling.oasis.oasis (module) vardb.metadata_wrangling.oasis.output (module) vardb.metadata_wrangling.oasis.preprocess (module) vardb.metadata_wrangling.oasis.radiation (module) vardb.metadata_wrangling.oasis.treatment (module) vardb.queries (module) vardb.queries.CNV_overlap (module) vardb.queries.experimental_records (module) vardb.queries.experimental_records_external (module) vardb.tools (module) vardb.variant_data_files (module) vardb.variant_data_files.cnv (module) vardb.variant_data_files.data_classes (module) vardb.variant_data_files.expression (module) vardb.variant_data_files.maf (module) vardb.variant_data_files.variant_data_file (module) vardb.variant_data_files.vcf (module) vardb.variant_data_files.vcf_tools (module) vardb.variant_file_loaders (module) vardb.variant_file_loaders.loader (module) vardb.variant_file_loaders.sample_metadata (module) VarDBException VariantDataFile (class in vardb.variant_data_files.variant_data_file) VariantDataFileException VCall (class in vardb.variant_data_files.vcf) VCallCollector (class in vardb.metadata_wrangling.metadata_collector) VCF (class in vardb.variant_data_files.vcf) VcfAnnotations (class in vardb.variant_data_files.vcf) VcfToolsException

W

write() (vardb.tools.StreamToLogger method)

write_output_to_tsv() (in module vardb.metadata_wrangling.oasis.output)