Index

A

access_civic_by_coordinate() (in module querynator.query_api.civic_api) add_cgi_metadata() (in module querynator.query_api.cgi_api) add_civic_metadata() (in module querynator.query_api.civic_api)

add_tiers_and_scores_to_df() (in module querynator.report_scripts.sort_variants) add_variant_name_report() (in module querynator.report_scripts.create_report) append_to_dict() (in module querynator.query_api.civic_api) assign_comb_evidence_labels() (in module querynator.report_scripts.create_report)

C

Cancer() (in module querynator.__main__) check_if_nan() (in module querynator.report_scripts.create_report) check_nan_in_pair() (in module querynator.report_scripts.sort_variants) check_vcf_input() (in module querynator.query_api.civic_api) combine_cgi() (in module querynator.report_scripts.combine_cgi) combine_cgi_civic() (in module querynator.report_scripts.combine_cgi_civic) combine_civic() (in module querynator.report_scripts.combine_civic) concat_dicts() (in module querynator.query_api.civic_api) convert() (querynator.__main__.EnumType method)

create_barplot() (in module querynator.report_scripts.create_report) create_civic_results() (in module querynator.query_api.civic_api) create_evidence_table() (in module querynator.report_scripts.create_report) create_html_link() (in module querynator.report_scripts.create_report) create_link_col() (in module querynator.report_scripts.create_report) create_report() (in module querynator.__main__) create_report_htmls() (in module querynator.report_scripts.create_report) create_therapy_table() (in module querynator.report_scripts.create_report) create_tier_table() (in module querynator.report_scripts.create_report) create_upsetplots() (in module querynator.report_scripts.create_report)

D

delete_job_cgi() (in module querynator.query_api.cgi_api)

download_cgi() (in module querynator.query_api.cgi_api)

E

encode_upsetplot() (in module querynator.report_scripts.create_report) EnumType (class in querynator.__main__)

extract_coords() (in module querynator.report_scripts.combine_cgi) extract_num() (in module querynator.report_scripts.sort_variants)

F

filter_vcf_by_vep() (in module querynator.__main__)

G

generate_allele_freq_score() (in module querynator.report_scripts.sort_variants) generate_consequence_score() (in module querynator.report_scripts.sort_variants) generate_evidence_score() (in module querynator.report_scripts.sort_variants) generate_pathogenicity_score_score() (in module querynator.report_scripts.sort_variants) get_all_alterations() (in module querynator.report_scripts.combine_cgi) get_allele_freq_tiering() (in module querynator.report_scripts.sort_variants) get_assertion_information_from_variant() (in module querynator.query_api.civic_api) get_cgi_consequence_score() (in module querynator.report_scripts.sort_variants) get_civic_consequence_score() (in module querynator.report_scripts.sort_variants) get_consequence_score() (in module querynator.report_scripts.sort_variants) get_coordinates_from_vcf() (in module querynator.query_api.civic_api) get_disease_names_CIViC() (in module querynator.report_scripts.create_report) get_evidence_description() (in module querynator.report_scripts.create_report) get_evidence_information_from_variant() (in module querynator.query_api.civic_api)

get_gene_information_from_variant() (in module querynator.query_api.civic_api) get_highest_evidence() (in module querynator.report_scripts.combine_cgi) get_KB_count() (in module querynator.report_scripts.create_report) get_largest_af() (in module querynator.report_scripts.sort_variants) get_largest_path_score() (in module querynator.report_scripts.sort_variants) get_min() (in module querynator.report_scripts.sort_variants) get_molecular_profile_information_from_variant() (in module querynator.query_api.civic_api) get_positional_information_from_coord_obj() (in module querynator.query_api.civic_api) get_querynator_id() (in module querynator.query_api.civic_api) get_reference_build() (in module querynator.report_scripts.create_report) get_sources() (in module querynator.report_scripts.create_report) get_therapy_information_CGI() (in module querynator.report_scripts.create_report) get_therapy_names() (in module querynator.report_scripts.create_report) get_unique_querynator_dir() (in module querynator.__main__) get_variant_information_from_variant() (in module querynator.query_api.civic_api)

H

hg_assembly() (in module querynator.query_api.cgi_api)

L

link_biomarkers() (in module querynator.report_scripts.combine_cgi)

M

make_enum() (in module querynator.__main__) merge_alterations_vep() (in module querynator.report_scripts.combine_cgi) merge_civic_cgi() (in module querynator.report_scripts.combine_cgi_civic) merge_civic_vep() (in module querynator.report_scripts.combine_civic) module querynator.__main__ querynator.query_api.cgi_api querynator.query_api.civic_api querynator.report_scripts.combine_cgi querynator.report_scripts.combine_cgi_civic querynator.report_scripts.combine_civic querynator.report_scripts.create_report querynator.report_scripts.sort_variants

Q

query_api_cgi() (in module querynator.__main__) query_api_civic() (in module querynator.__main__) query_cgi() (in module querynator.query_api.cgi_api) query_civic() (in module querynator.query_api.civic_api) querynator.__main__ module querynator.query_api.cgi_api module querynator.query_api.civic_api module

querynator.report_scripts.combine_cgi module querynator.report_scripts.combine_cgi_civic module querynator.report_scripts.combine_civic module querynator.report_scripts.create_report module querynator.report_scripts.sort_variants module

R

read_civic_results() (in module querynator.report_scripts.combine_civic) read_filtered_vcf() (in module querynator.report_scripts.combine_cgi) (in module querynator.report_scripts.combine_civic)

read_modify_alterations() (in module querynator.report_scripts.combine_cgi) remove_dups() (in module querynator.report_scripts.create_report) remove_prefix() (in module querynator.report_scripts.combine_cgi) retrieve_info_from_row() (in module querynator.report_scripts.create_report)

S

save_plot() (in module querynator.report_scripts.create_report) scoring_variants() (in module querynator.report_scripts.sort_variants) smoothen_dict() (in module querynator.query_api.civic_api) sort_coord_list() (in module querynator.query_api.civic_api) sort_rules() (in module querynator.query_api.civic_api)

split_cols() (in module querynator.report_scripts.create_report) status_done() (in module querynator.query_api.cgi_api) submit_query_cgi() (in module querynator.query_api.cgi_api) subset_alterations() (in module querynator.report_scripts.combine_cgi) subset_variants_into_tiers() (in module querynator.report_scripts.sort_variants)

V

vcf_file() (in module querynator.query_api.civic_api)

W

write_individual_report() (in module querynator.report_scripts.create_report)

write_overall_report() (in module querynator.report_scripts.create_report) write_vcf() (in module querynator.__main__)