rna_library.core.enums

Enumerated types for base pairs, nucleotides and motifs. Assist with ensuring type correctness and lowers overhead vs string-based implementations.

Module Contents

Classes

BasePair	Enumerated type for canoncial and wobble basepairs.
Nucleotide	Enumerated type for all nucleotide types.
MotifType	Enumerated type for all motif types

Attributes

ALLOWED_PAIRS	A set() containing all 6 canonical and wobble basepairings.
BPS	A tuple() of allowed canonical and wobble basepairings.
LEGAL_BPS	A set() of all 4 allowed nucleotide types.
NTS	A tuple() of all 4 canonical nucleotide types. Ordered
BP_VALS	A list() that contains the integer values for all of the
BASEPAIR_MAPPER	A dict() object that maps a canonical basepair to its
NT_VALS	A list() that contains the integer values for all of the
NUCLEOTIDE_MAPPER	A dict() object that maps a canoncial nucleotide to its
TYPE_MAPPER	A :class: dict() object that maps a :class: MotifType to its value

rna_library.core.enums.ALLOWED_PAIRS

A set() containing all 6 canonical and wobble basepairings.

rna_library.core.enums.BPS = ['GU', 'UG', 'AU', 'UA', 'GC', 'CG']

A tuple() of allowed canonical and wobble basepairings. Ordered for easy conversion by the BasePair() class.

rna_library.core.enums.LEGAL_BPS

A set() of all 4 allowed nucleotide types.

rna_library.core.enums.NTS = ['A', 'C', 'G', 'U']

A tuple() of all 4 canonical nucleotide types. Ordered for each conversion by the Nucleotide() class.

class rna_library.core.enums.BasePair

Bases: enum.IntEnum

Enumerated type for canoncial and wobble basepairs.

GU = 0

UG = 1

AU = 2

UA = 3

GC = 4

CG = 5

is_GU(self)

Returns

If the instance is a UG or GU pair.

Return type

bool()

is_AU(self)

Returns

If the instance is a UA or AU pair.

Return type

bool()

is_GC(self)

Returns

If the instance is a CG or GC pair.

Return type

bool()

is_canoncial(self)

Returns

If the instance is a canonical Watson-Crick basepair.

Return type

bool()

to_str(self)

Returns

The BasePair() instance in text form.

Return type

str()

rna_library.core.enums.BP_VALS

A list() that contains the integer values for all of the BasePair() enumerations.

rna_library.core.enums.BASEPAIR_MAPPER

A dict() object that maps a canonical basepair to its BasePair() value.

class rna_library.core.enums.Nucleotide

Bases: enum.IntEnum

Enumerated type for all nucleotide types.

A = [0]

C = [1]

G = [2]

U = 3

to_str(self)

Returns

The Nucleotide() instance in text form.

Return type

str()

rna_library.core.enums.NT_VALS

A list() that contains the integer values for all of the Nucleotide() enumerations.

rna_library.core.enums.NUCLEOTIDE_MAPPER

A dict() object that maps a canoncial nucleotide to its Nucleotide() value.

class rna_library.core.enums.MotifType

Bases: enum.IntEnum

Enumerated type for all motif types

UNASSIGNED = 0

SINGLESTRAND = 1

HELIX = 2

HAIRPIN = 3

JUNCTION = 4

rna_library.core.enums.TYPE_MAPPER

A :class: dict() object that maps a :class: MotifType to its value as a str().