`rna_library.core.folding`¶

Holds utility functions for folding RNA sequences.

Module Contents¶

`folding_params`()	See the default folding parameters being used with Vienna.
`fold_cache`(sequence, params = _DEFAULT_PARAMS)	Uses RNAfold to predict the mfe for a structure using a global cache of results to save time.
`save_cache`()	Saves fold results to the cache and updats the _LAST_SIZE value to _CURRENT_SIZE.

`_CACHE_FILE`	Value where the cached fold results will be stored. Set to {_CACHE_FILE} in current system.
`_DEFAULT_PARAMS`	Default folding parameters for Vienna’s RNAfold. Default values are {_DEFAULT_PARAMS}
`_CACHE`	Cache that holds folding results.
`_CURRENT_SIZE`	The current size of the cache.
`_LAST_SIZE`	The size of the cache the last time it was saved.
`_CACHE`	Cache that holds folding results.
`FoldResult`	namedtuple that holds sequence, structure, ensembled defect and folding parameters for an RNAfold prediction.

rna_library.core.folding._CACHE_FILE¶: Value where the cached fold results will be stored. Set to {_CACHE_FILE} in current system.

rna_library.core.folding._DEFAULT_PARAMS = ['-p', '--noLP', '-d2']¶: Default folding parameters for Vienna’s RNAfold. Default values are {_DEFAULT_PARAMS}

rna_library.core.folding._LAST_SIZE¶: The size of the cache the last time it was saved.

rna_library.core.folding.FoldResult¶: namedtuple that holds sequence, structure, ensembled defect and folding parameters for an RNAfold prediction.

rna_library.core.folding.folding_params()¶

See the default folding parameters being used with Vienna. :rtype: Tuple[str]

rna_library.core.folding.fold_cache(sequence, params=_DEFAULT_PARAMS)¶

Uses RNAfold to predict the mfe for a structure using a global cache of results to save time.

Param

str sequence: RNA sequence ot be folded.

Param

Tuple[str] params: default folding params for RNAfold, defaults to (‘-p’,’–noLP’,’-d2’) :rtype: FoldResult

Parameters

Return type

FoldResult

rna_library.core.folding.save_cache()¶

Saves fold results to the cache and updats the _LAST_SIZE value to _CURRENT_SIZE.