Index

_

__init__() (missense_kinase_toolkit.databases.cbioportal.cBioPortal method), [1] (missense_kinase_toolkit.databases.cbioportal.Mutations method), [1] (missense_kinase_toolkit.databases.hgnc.HGNC method), [1] (missense_kinase_toolkit.databases.klifs.KinaseInfo method), [1] (missense_kinase_toolkit.databases.klifs.KLIFS method), [1] (missense_kinase_toolkit.databases.pfam.Pfam method), [1] (missense_kinase_toolkit.databases.uniprot.UniProt method), [1]

_convert_fasta2seq() (missense_kinase_toolkit.databases.uniprot.UniProt static method) _extract_list_from_hgnc_response_docs() (missense_kinase_toolkit.databases.hgnc.HGNC static method) _generate_key_set_hgnc_response_docs() (missense_kinase_toolkit.databases.hgnc.HGNC static method) _set_api_key() (missense_kinase_toolkit.databases.cbioportal.cBioPortal method) (missense_kinase_toolkit.databases.cbioportal.Mutations method)

A

AA_MAPPING (in module missense_kinase_toolkit.databases.colors)

add_retry_to_session() (in module missense_kinase_toolkit.databases.requests_wrapper)

C

cBioPortal (class in missense_kinase_toolkit.databases.cbioportal) CBIOPORTAL_INSTANCE_VAR (in module missense_kinase_toolkit.databases.config) CBIOPORTAL_TOKEN_VAR (in module missense_kinase_toolkit.databases.config)

check_outdir_exists() (in module missense_kinase_toolkit.databases.io_utils) concatenate_csv_files_with_glob() (in module missense_kinase_toolkit.databases.io_utils) convert_str2list() (in module missense_kinase_toolkit.databases.io_utils)

D

DICT_COLORS (in module missense_kinase_toolkit.databases.colors)

F

find_pfam_domain() (in module missense_kinase_toolkit.databases.pfam)

G

get_all_mutations_by_study() (missense_kinase_toolkit.databases.cbioportal.Mutations method) get_cached_session() (in module missense_kinase_toolkit.databases.requests_wrapper) get_cbioportal() (missense_kinase_toolkit.databases.cbioportal.cBioPortal method) (missense_kinase_toolkit.databases.cbioportal.Mutations method) get_cbioportal_cohort_mutations() (missense_kinase_toolkit.databases.cbioportal.Mutations method) get_cbioportal_instance() (in module missense_kinase_toolkit.databases.config) get_instance() (missense_kinase_toolkit.databases.cbioportal.cBioPortal method) (missense_kinase_toolkit.databases.cbioportal.Mutations method) get_kinase_info() (missense_kinase_toolkit.databases.klifs.KinaseInfo method) get_kinase_name() (missense_kinase_toolkit.databases.klifs.KinaseInfo method)

get_klifs() (missense_kinase_toolkit.databases.klifs.KinaseInfo method) (missense_kinase_toolkit.databases.klifs.KLIFS method) get_mutations() (missense_kinase_toolkit.databases.cbioportal.Mutations method) get_output_dir() (in module missense_kinase_toolkit.databases.config) get_species() (missense_kinase_toolkit.databases.klifs.KinaseInfo method) get_study_id() (missense_kinase_toolkit.databases.cbioportal.Mutations method) get_uniprot_fasta() (missense_kinase_toolkit.databases.uniprot.UniProt method) get_url() (missense_kinase_toolkit.databases.cbioportal.cBioPortal method) (missense_kinase_toolkit.databases.cbioportal.Mutations method) (missense_kinase_toolkit.databases.klifs.KinaseInfo method) (missense_kinase_toolkit.databases.klifs.KLIFS method)

H

HGNC (class in missense_kinase_toolkit.databases.hgnc)

K

KinaseInfo (class in missense_kinase_toolkit.databases.klifs)

kinhub() (in module missense_kinase_toolkit.databases.scrapers) KLIFS (class in missense_kinase_toolkit.databases.klifs)

L

load_csv_to_dataframe() (in module missense_kinase_toolkit.databases.io_utils)

M

main() (in module missense_kinase_toolkit.databases.cli.extract_cbioportal) (in module missense_kinase_toolkit.databases.cli.extract_kinase_annotations) (in module missense_kinase_toolkit.databases.cli.transform_cbioportal) map_aa_to_single_letter_code() (in module missense_kinase_toolkit.databases.colors) map_single_letter_aa_to_color() (in module missense_kinase_toolkit.databases.colors) maybe_get_cbioportal_token() (in module missense_kinase_toolkit.databases.config) maybe_get_info_from_hgnc_fetch() (missense_kinase_toolkit.databases.hgnc.HGNC method) maybe_get_request_cache() (in module missense_kinase_toolkit.databases.config) maybe_get_symbol_from_hgnc_search() (missense_kinase_toolkit.databases.hgnc.HGNC method) missense_kinase_toolkit module missense_kinase_toolkit.databases module missense_kinase_toolkit.databases.cbioportal module missense_kinase_toolkit.databases.cli module missense_kinase_toolkit.databases.cli.extract_cbioportal module missense_kinase_toolkit.databases.cli.extract_kinase_annotations module missense_kinase_toolkit.databases.cli.transform_cbioportal module missense_kinase_toolkit.databases.colors module missense_kinase_toolkit.databases.config module missense_kinase_toolkit.databases.data_models module missense_kinase_toolkit.databases.hgnc module missense_kinase_toolkit.databases.io_utils module

missense_kinase_toolkit.databases.klifs module missense_kinase_toolkit.databases.pfam module missense_kinase_toolkit.databases.requests_wrapper module missense_kinase_toolkit.databases.scrapers module missense_kinase_toolkit.databases.uniprot module missense_kinase_toolkit.databases.utils_requests module module missense_kinase_toolkit missense_kinase_toolkit.databases missense_kinase_toolkit.databases.cbioportal missense_kinase_toolkit.databases.cli missense_kinase_toolkit.databases.cli.extract_cbioportal missense_kinase_toolkit.databases.cli.extract_kinase_annotations missense_kinase_toolkit.databases.cli.transform_cbioportal missense_kinase_toolkit.databases.colors missense_kinase_toolkit.databases.config missense_kinase_toolkit.databases.data_models missense_kinase_toolkit.databases.hgnc missense_kinase_toolkit.databases.io_utils missense_kinase_toolkit.databases.klifs missense_kinase_toolkit.databases.pfam missense_kinase_toolkit.databases.requests_wrapper missense_kinase_toolkit.databases.scrapers missense_kinase_toolkit.databases.uniprot missense_kinase_toolkit.databases.utils_requests Mutations (class in missense_kinase_toolkit.databases.cbioportal)

O

OUTPUT_DIR_VAR (in module missense_kinase_toolkit.databases.config) (in module missense_kinase_toolkit.databases.io_utils)

P

parse_iterabc2dataframe() (in module missense_kinase_toolkit.databases.io_utils) parsearg_utils() (in module missense_kinase_toolkit.databases.cli.extract_cbioportal) (in module missense_kinase_toolkit.databases.cli.extract_kinase_annotations) (in module missense_kinase_toolkit.databases.cli.transform_cbioportal)

Pfam (class in missense_kinase_toolkit.databases.pfam) POCKET_KLIFS_REGION_COLORS (in module missense_kinase_toolkit.databases.klifs) POCKET_KLIFS_REGIONS (in module missense_kinase_toolkit.databases.klifs) print_status_code_if_res_not_ok() (in module missense_kinase_toolkit.databases.utils_requests)

Q

query_cbioportal_api() (missense_kinase_toolkit.databases.cbioportal.cBioPortal method) (missense_kinase_toolkit.databases.cbioportal.Mutations method) query_kinase_info() (missense_kinase_toolkit.databases.klifs.KinaseInfo method)

query_klifs_api() (missense_kinase_toolkit.databases.klifs.KinaseInfo method) (missense_kinase_toolkit.databases.klifs.KLIFS method) query_pfam_api() (missense_kinase_toolkit.databases.pfam.Pfam method)

R

REQUESTS_CACHE_VAR (in module missense_kinase_toolkit.databases.config)

S

save_dataframe_to_csv() (in module missense_kinase_toolkit.databases.io_utils) set_cbioportal_instance() (in module missense_kinase_toolkit.databases.config)

set_cbioportal_token() (in module missense_kinase_toolkit.databases.config) set_output_dir() (in module missense_kinase_toolkit.databases.config) set_request_cache() (in module missense_kinase_toolkit.databases.config)

U

UniProt (class in missense_kinase_toolkit.databases.uniprot)