`rna_library.core`¶

Core module containing basic data types for RNA analysis.

Submodules¶

Package Contents¶

Classes¶

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

Functions¶

`valid_db`(structure)	Checks if a structure is a valid dot-bracket structure containing only ‘(‘, ‘.’ or ‘)’ characters.
`connectivity_list`(structure)	Generates a connectivity list or pairmap from a dot-bracket secondary structure.
`is_circular`(start, connections)	Checks if a starting point in a pairmap is in a circular portion.
`load_fasta`(fname)	Reads in sequences from a .fasta file and return a dictionary with construct names as keys
`is_symmetrical`(token)	Checks if a sequence or secondary structure is well-formed and symmetrical.
`safe_mkdir`(dirname)	Creates a directory if it does not already exist.
`safe_rm`(fname)	Removes a file only if the file already exists.
`dsci`(sequence, target, dms)	Calculates the DSCI score as developed by the Rouskin Group at MIT. The generated score
`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.
`folding_params`()	See the default folding parameters being used with Vienna.

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
`FoldResult`	namedtuple that holds sequence, structure, ensembled defect and folding parameters for an RNAfold prediction.

rna_library.core.ALLOWED_PAIRS¶: A set() containing all 6 canonical and wobble basepairings.

rna_library.core.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.LEGAL_BPS¶: A set() of all 4 allowed nucleotide types.

rna_library.core.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.BasePair¶

Bases: enum.IntEnum

Inheritance diagram of rna_library.core.BasePair

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

rna_library.core.BASEPAIR_MAPPER¶: A dict() object that maps a canonical basepair to its BasePair() value.

class rna_library.core.Nucleotide¶

Bases: enum.IntEnum

Inheritance diagram of rna_library.core.Nucleotide

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

rna_library.core.NUCLEOTIDE_MAPPER¶: A dict() object that maps a canoncial nucleotide to its Nucleotide() value.

class rna_library.core.MotifType¶

Bases: enum.IntEnum

Inheritance diagram of rna_library.core.MotifType

Enumerated type for all motif types

UNASSIGNED = 0¶

SINGLESTRAND = 1¶

HELIX = 2¶

HAIRPIN = 3¶

JUNCTION = 4¶

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

exception rna_library.core.InvalidDotBracket¶

Bases: Exception

Inheritance diagram of rna_library.core.InvalidDotBracket

Exception for a mal-formed dot-bracket secondary structure.

exception rna_library.core.MissingDependency¶

Bases: Exception

Inheritance diagram of rna_library.core.MissingDependency

Exception for when a dependency is missing in the system

exception rna_library.core.InvalidArgument¶

Bases: Exception

Inheritance diagram of rna_library.core.InvalidArgument

Exception for a bad argument being supplied.

rna_library.core.valid_db(structure)¶

Checks if a structure is a valid dot-bracket structure containing only ‘(‘, ‘.’ or ‘)’ characters. :param: str structure: dot bracket structure :rtype: bool

Parameters: structure (str) –
Return type: bool

rna_library.core.connectivity_list(structure)¶

Generates a connectivity list or pairmap from a dot-bracket secondary structure. The list has a value of -1 for unpaired positions else has the index of a positions complement.

Parameters: structure (str) – a dot-bracket structure
Return type: list[int]
Raises: TypeError – if the number of left parentheses exceeds the number of right parentheses

rna_library.core.is_circular(start, connections)¶

Checks if a starting point in a pairmap is in a circular portion. This can include the closing pairs of both hairpins and junctions.

Parameters

start (int) – staring index in the pairmap
connections (list[int]) – pairmap generated from util.connectivity_list()

Return type

bool

rna_library.core.load_fasta(fname)¶

Reads in sequences from a .fasta file and return a dictionary with construct names as keys and RNA sequences as values.

Param: str fname: name of the .fasta file to load
Return type: dict
Parameters: fname (str) –

rna_library.core.is_symmetrical(token)¶

Checks if a sequence or secondary structure is well-formed and symmetrical.

Param: str token: sequence or secondary structure to test
Return type: bool
Parameters: token (str) –

rna_library.core.safe_mkdir(dirname)¶

Creates a directory if it does not already exist. :param: str dirname: name of the directory to create :rtype: NoneType

Parameters: dirname (str) –
Return type: None

rna_library.core.safe_rm(fname)¶

Removes a file only if the file already exists. :param: str fname: name of file to be removed :rtype: NoneType

Parameters: fname (str) –
Return type: None

rna_library.core.dsci(sequence, target, dms)¶

Calculates the DSCI score as developed by the Rouskin Group at MIT. The generated score is on the range of [0,1] and 0.95 is a common quality cutoff.

Param

str sequence: the RNA sequence to be analyzed

Param

str target: the target secondary structure

Param

List[float] dms: the DMS reactivities for the construct

Return type

Tuple[float]

Parameters

sequence (str) –
target (str) –
dms (List[float]) –

rna_library.core.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

sequence (str) –
params (Tuple[str]) –

Return type

FoldResult

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

rna_library.core.save_cache()¶

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

Return type: None

rna_library.core.folding_params()¶

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

Return type: Tuple[str]

rna_library.core¶

Submodules¶

Package Contents¶

Classes¶

Functions¶

Attributes¶

`rna_library.core`¶