biotransformers#

Subpackages#

Submodules#

Package Contents#

Classes#

BioTransformers

General class to choose an ESM or ProtBert backend

Functions#

logger(module_name: str) → logging.Logger

Configure the logger with formatter and handlers.

Attributes#

VERSION

log

__version__

class biotransformers.BioTransformers(backend: str = 'esm1_t6_43M_UR50S', num_gpus: int = 0)#

Bases: biotransformers.wrappers.transformers_wrappers.TransformersWrapper

General class to choose an ESM or ProtBert backend Abstract method are implemented in transformers

static list_backend() → None#

Get all possible backend for the model

biotransformers.logger(module_name: str) → logging.Logger#

Configure the logger with formatter and handlers.

The log level depends on the environment variable BIO_LOG_LEVEL.

  • 0: NOTSET, will be set to DEBUG

  • 1: DEBUG

  • 2: INFO (default)

  • 3: WARNING

  • 4: ERROR

  • 5: CRITICAL

https://docs.python.org/3/library/logging.html#levels

Parameters

module_name (str) – module name

Returns

instantiate logger object

Return type

[Logger]

biotransformers.VERSION = 0.1.17#
biotransformers.log#
biotransformers.__version__#