genebe package

Submodules

genebe.client module

exception genebe.client.TooManyRequestsError: Bases: Exception

exception genebe.client.WrongServerResponseError: Bases: Exception

genebe.client.annotate_variants_list(variants: List[str], genome: str = 'hg38', use_ensembl: bool = True, use_refseq: bool = True, flatten_consequences: bool = True, batch_size: int = 500, username: str = None, api_key: str = None, use_netrc: bool = True, endpoint_url: str = 'https://api.genebe.net/cloud/api-public/v1/variants', progress_bar: bool = True, omit_acmg: bool = False, omit_csq: bool = False, omit_basic: bool = False, omit_advanced: bool = False, omit_normalization: bool = False, annotator: str = 'snpeff') → List[Dict[str, object]]

Annotates a list of genetic variants.

Args:

variants (List[str]): A list of genetic variants to be annotated.: Format: chr-pos-ref-alt. Look at examples below.
use_ensembl (bool, optional): Whether to use Ensembl for annotation.: Defaults to True.
use_refseq (bool, optional): Whether to use RefSeq for annotation.: Defaults to True.
genome (str, optional): The genome version for annotation (e.g., ‘hg38’).: Defaults to ‘hg38’.
flatten_consequences (bool, optional): If set to False, return consequences as a list of objects.: If set to True, only the most important consequence is returned in a flat form. Defaults to True.
batch_size (int, optional): The size of each batch for processing variants.: Defaults to 100. Must be smaller or equal 1000.
username (str, optional): The username for authentication.: Defaults to None.
api_key (str, optional): The API key for authentication.: Defaults to None.
use_netrc (bool, optional): Whether to use credentials from the user’s: .netrc file for authentication. Defaults to True.
endpoint_url (str, optional): The API endpoint for variant annotation.: Defaults to ‘https://api.genebe.net/cloud/api-public/v1/variants’.
progress_bar (bool, optional): Show progress bar.: Defaults to True.

omit_acmg (bool, optional): Don’t add ACMG scores in the output. Defaults to False. omit_csq (bool, optional): Don’t add consequences in the output. Defaults to False. omit_basic (bool, optional): Don’t add basic annotations (GnomAD frequencies etc) in the output. Defaults to False. omit_advanced (bool, optional): Don’t add advanced annotations (ClinVar etc) in the output. Defaults to False. omit_normalization (bool, optional): Don’t normalize variants. Use only if you are sure they are normalized already. Defaults to False. annotator (str, optional): Which VEP implementation to use.

Defaults to snpeff.

Returns:

List[Dict[str, object]]: A list of dictionaries containing annotation information for each variant. The dictionary structure may vary. Check the current documentation on https://genebe.net/about/api

Example:

>>> variants = ["7-69599651-A-G", "6-160585140-T-G"]
>>> annotations = annotate_variants_list(variants, use_ensembl=True,
...                                      use_refseq=False, genome='hg38',
...                                      batch_size=500, username="user123@example.com",
...                                      api_key="apikey456", use_netrc=False,
...                                      endpoint_url='https://api.genebe.net/cloud/api-public/v1/variants')
>>> print(annotations)
[{'chr': '7', 'pos':69599651 (...) }]

Note:

The number of the elements in returned list is always equal to the number of queries.

genebe.client.annotate_variants_list_to_dataframe(variants: List[str], use_ensembl: bool = True, use_refseq: bool = True, genome: str = 'hg38', batch_size: int = 100, flatten_consequences: bool = True, username: str = None, api_key: str = None, use_netrc: bool = True, endpoint_url: str = 'https://api.genebe.net/cloud/api-public/v1/variants') → DataFrame

genebe.client.parse_hgvs(hgvs: List[str], batch_size: int = 500, username: str = None, api_key: str = None, use_netrc: bool = True, endpoint_url: str = 'https://api.genebe.net/cloud/api-public/v1/hgvs') → List[str]

Parses a list of genetic variants encoded in HGVS.

Args:

hgvs (List[str]): A list of genetic variants in hgvs format.: Supports .n:, .c:, .g: and .m:. Look at examples below.
batch_size (int, optional): The size of each batch for processing variants.: Defaults to 500. Must be smaller or equal 1000.
username (str, optional): The username for authentication.: Defaults to None.
api_key (str, optional): The API key for authentication.: Defaults to None.
use_netrc (bool, optional): Whether to use credentials from the user’s: .netrc file for authentication. Defaults to True.
endpoint_url (str, optional): The API endpoint for parsing hgvs.: Defaults to ‘https://api.genebe.net/cloud/api-public/v1/hgvs’.

Returns:

List[str]: A list of dictionaries containing annotation information for each variant. Check the current documentation on https://genebe.net/about/api

Example:

>>> hgvs_variants = ["'NM_000277.2:c.1A>G"]
>>> variants = parse_hgvs(hgvs_variants)
>>> print(variants)
['12-102917129-AT-AC', '12-102852850-GA-G']

Note:

The number of the elements in returned list is always equal to the number of queries.

If some position cannot be parsed, an empty string is returned.

genebe.client.whoami(username: str = None, api_key: str = None, use_netrc: bool = True, endpoint_url: str = 'https://api.genebe.net/cloud/api-public/v1/whoami') → List[str]

Information about me: usage statistics, limits etc.

Args:

username (str, optional): The username for authentication.: Defaults to None.
api_key (str, optional): The API key for authentication.: Defaults to None.
use_netrc (bool, optional): Whether to use credentials from the user’s: .netrc file for authentication. Defaults to True.
endpoint_url (str, optional): The API endpoint to use.: Defaults to ‘https://api.genebe.net/cloud/api-public/v1/whoami’.

Returns:

An object. Check the current documentation on https://genebe.net/about/api

genebe.entrypoint module

genebe.entrypoint.account_command(args)

genebe.entrypoint.main()

genebe.gbid module

exception genebe.gbid.InvalidPositionException(message): Bases: Exception

class genebe.gbid.PositionEncoder

Bases: object

CHR_NOT_SUPPORTED = -1

ERROR_WRONG_CHR_POSITION = -2

encode(chromosome: str, position: int)

encode_1_based_without_throw(chromosome, position)

class genebe.gbid.VariantIdEncoder

Bases: object

BASES = ['A', 'C', 'G', 'T']

MASK_CHANGE_HASH_VALUE = 536870911

MASK_C_HASH = 536870912

MASK_DEL = 33292288

MASK_HASH = 9223372036854775808

MASK_INS = 262143

MASK_INS_LEN = 503316480

MASK_NULL = 4611686018427387904

MASK_POS = 4611686017353646080

MAX_DEL_LENGTH = 127

MAX_INS_LENGTH = 9

RADIX = 36

change_hash(del_length, alt)

encode1based(chromosome, position, ref, alt)

encode_bases(alt)

hash(chromosome, position, del_length, alt)

positionEncoder = <genebe.gbid.PositionEncoder object>

set_value(input, mask, value)

genebe.json_simple_annotator module

genebe.json_simple_annotator.annotate_json(input_json_path: str, output_json_path: str, genome: str = 'hg38', use_ensembl: bool = True, use_refseq: bool = True, flatten_consequences: bool = True, batch_size: int = 500, username: str | None = None, api_key: str | None = None, use_netrc: bool = True, endpoint_url: str = 'https://api.genebe.net/cloud/api-public/v1/variants', omit_acmg: bool = False, omit_csq: bool = False, omit_basic: bool = False, omit_advanced: bool = False, omit_normalization: bool = False, progress: bool = False)

Annotates a JSON file using the annotate_variants_list function.

Args:

input_json_path (str): Path to the input json lines file. output_json_path (str): Path to the output annotated json lines file. genome (str, optional): The genome version for annotation (e.g., ‘hg38’).

Defaults to ‘hg38’.

use_ensembl (bool, optional): Whether to use Ensembl for annotation.: Defaults to True.
use_refseq (bool, optional): Whether to use RefSeq for annotation.: Defaults to True.
flatten_consequences (bool, optional): If set to False, return consequences as a list of objects.: If set to True, only the most important consequence is returned in a flat form. Defaults to True.
batch_size (int, optional): The size of each batch for processing variants.: Defaults to 100. Must be smaller or equal 1000.
username (str, optional): The username for authentication.: Defaults to None.
api_key (str, optional): The API key for authentication.: Defaults to None.
use_netrc (bool, optional): Whether to use credentials from the user’s: .netrc file for authentication. Defaults to True.
endpoint_url (str, optional): The API endpoint for variant annotation.: Defaults to ‘https://api.genebe.net/cloud/api-public/v1/variants’.

omit_acmg (bool, optional): Don’t add ACMG scores in the output. Defaults to False. omit_csq (bool, optional): Don’t add consequences in the output. Defaults to False. omit_basic (bool, optional): Don’t add basic annotations (GnomAD frequencies etc) in the output. Defaults to False. omit_advanced (bool, optional): Don’t add advanced annotations (ClinVar etc) in the output. Defaults to False. omit_normalization (bool, optional): Don’t normalize variants. Use only if you are sure they are normalized already. Defaults to False. progress (bool, optional): Show progress bar

genebe.vcf_simple_annotator module

genebe.vcf_simple_annotator.annotate_vcf(input_vcf_path: str, output_vcf_path: str, genome: str = 'hg38', use_ensembl: bool = True, use_refseq: bool = True, flatten_consequences: bool = True, batch_size: int = 500, username: str | None = None, api_key: str | None = None, use_netrc: bool = True, endpoint_url: str = 'https://api.genebe.net/cloud/api-public/v1/variants', omit_acmg: bool = False, omit_csq: bool = False, omit_basic: bool = False, omit_advanced: bool = False, omit_normalization: bool = False, progress: bool = False)

Annotates a VCF file using the annotate_variants_list function.

Args:

input_vcf_path (str): Path to the input VCF file. output_vcf_path (str): Path to the output annotated VCF file. genome (str, optional): The genome version for annotation (e.g., ‘hg38’).

Defaults to ‘hg38’.

use_ensembl (bool, optional): Whether to use Ensembl for annotation.: Defaults to True.
use_refseq (bool, optional): Whether to use RefSeq for annotation.: Defaults to True.
flatten_consequences (bool, optional): If set to False, return consequences as a list of objects.: If set to True, only the most important consequence is returned in a flat form. Defaults to True.
batch_size (int, optional): The size of each batch for processing variants.: Defaults to 100. Must be smaller or equal 1000.
username (str, optional): The username for authentication.: Defaults to None.
api_key (str, optional): The API key for authentication.: Defaults to None.
use_netrc (bool, optional): Whether to use credentials from the user’s: .netrc file for authentication. Defaults to True.
endpoint_url (str, optional): The API endpoint for variant annotation.: Defaults to ‘https://api.genebe.net/cloud/api-public/v1/variants’.

omit_acmg (bool, optional): Don’t add ACMG scores in the output. Defaults to False. omit_csq (bool, optional): Don’t add consequences in the output. Defaults to False. omit_basic (bool, optional): Don’t add basic annotations (GnomAD frequencies etc) in the output. Defaults to False. omit_advanced (bool, optional): Don’t add advanced annotations (ClinVar etc) in the output. Defaults to False. omit_normalization (bool, optional): Don’t normalize variants. Use only if you are sure they are normalized already. Defaults to False. progress (bool, optional): Show progress bar

genebe package

Submodules

genebe.client module

genebe.entrypoint module

genebe.gbid module

genebe.json_simple_annotator module

genebe.vcf_simple_annotator module

genebe.version module

Module contents