RNAmediator.Tweaks.RNAtweaks.FoldOutput

class RNAmediator.Tweaks.RNAtweaks.FoldOutput(condition: str = 'unconstrained', anno: str = None, gibbs: float = None, constraint: str = None, bpp: float = None, bppm: numpy.array = None, nrg: float = None, ddg: float = None, dnrg: float = None)

Output wrapper for ouput files of RNAfold

Inherits from collections.defaultdict

__init__(condition: str = 'unconstrained', anno: str = None, gibbs: float = None, constraint: str = None, bpp: float = None, bppm: numpy.array = None, nrg: float = None, ddg: float = None, dnrg: float = None)

Output wrapper for RNAfold

Parameters:

• condition (str, optional) – Condition used for folding, by default ‘raw’

• text (str, optional) – string representation of an RNAfold output file

• gibbs (float, optional) – Gibbs Free Energy, by default None

• constraint (str, optional) – Constraint applied for folding, by default None

• bpp (float, optional) – Base-Pairing Probability, by default None

• bppm (np.array, optional) – BasePairProbability matrix, by default None

• nrg (float, optional) – Folding Pseudo-Energy, by default None

• ddg (float, optional) – Delta-delta-Gibbs to unconstrained, by default None

• dnrg (float, optional) – Delta-Folding Pseudo-Energy, by default None

Methods

__init__([condition, anno, gibbs, ...])	Output wrapper for RNAfold
annotate(anno)	Annotate FoldOutput
clear()
copy()
from_RNAfold_file(file_path[, condition, ...])	creates FoldOutput from a file
from_rnamediator_fold_compound(fc[, ...])	creates FoldOutput from original rnamediator fold compound
fromkeys([value])	Create a new dictionary with keys from iterable and values set to value.
get(key[, default])	Return the value for key if key is in the dictionary, else default.
get_text([h])	return formatted string output
items()
keys()
merge(*args)
parse_anno()	returns annotation from FoldOutput
pop(k[,d])	If the key is not found, return the default if given; otherwise, raise a KeyError.
popitem()	Remove and return a (key, value) pair as a 2-tuple.
setdefault(key[, default])	Insert key with a value of default if key is not in the dictionary.
update([E, ]**F)	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
values()

Attributes

default_factory

Factory for default value called by __missing__().

annotate(anno)

Annotate FoldOutput

Parameters:

anno (str) – Annotation to set

classmethod from_RNAfold_file(file_path: str, condition: str = 'unconstrained', constraint: str = None)

creates FoldOutput from a file

Parameters

conditionstr, optional

which folding condition, e.g. raw, constraint, constraint-paired

constraintstr, optional

which constraint was applied when folding

Returns

from_rnamediator_fold_compound(fc, condition: str = 'unconstrained', constr: str = None, start: int = None, end: int = None)

creates FoldOutput from original rnamediator fold compound

Parameters

fc: fold_compound object

ViennaRNA fold_compound object

condition: str

Condition for folding

constr: str

Constraint string

start: int

Start of folding window

end: int

End of folding window

Returns

get_text(h=True)

return formatted string output

Parameters:

h (bool) – Prints header if True

Returns:

Contents of FoldOutput as formatted string

Return type:

formatted_string

parse_anno()

returns annotation from FoldOutput

Returns:

Returns goi, chrom, start, end, strand

Return type:

list([str, str, str, str, str])