`rna_library`¶

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
`Motif`	Abstract base class that `Hairpin()`, `Helix()`, `Junction()` and `SingleStrand()` all inherit from.
`Helix`	Represents a helix or stack in an RNA structure. Inherits from `Motif()`.
`Hairpin`	Represents a hairpin loop in an RNA structure. Inherits from `Motif()`.
`Junction`	Represents a junction of any size in an RNA structure including bulges and multi-loops.
`SingleStrand`	Represents a single stranded region in an RNA structure. Does not include unpaired regions that are part of a `Junction()` or `Helix()`.
`SecStruct`	Represents a
`JunctionData`	Composite class that represents a collection of JunctionEntry objects in an experiment.
`JunctionEntry`	Represents a single junction entry from an RNA construct

Functions¶

`parse_to_motifs`(structure, sequence)	Method takes a structure sequence pair and returns a root `Motif()` with a complete associated graph.
`highest_id`(m, best = 0)	Figures out the highest id number in a given `Motif()` graph.
`build_react_df`(**kwargs)	Builds the reactivity dataframe from the supplied arguments. Here each row reprsents a construct.
`build_motif_df`(df)	Function that creates a motif dataframe from a reactivity dataframe. Here each row represents a Motif.
`normalize_hairpin`(df, seq, ss, **kwargs)	Normalizes a reactivity pattern to a normalization hairpin. Creates fully normalize values
`normalize_coeff_fit`(reactivity_df)
`build_barcodes`(secstruct, start = None, distance = 3)

Attributes¶

`__author__`
`__email__`
`__version__`
`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.__author__ = Chris Jurich¶

rna_library.__email__ = cjurich2@huskers.unl.edu¶

rna_library.__version__ = 0.1.0¶

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

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

rna_library.NTS = ['A', 'C', 'G', 'U']¶: A tuple() of all 4 canonical nucleotide types. Ordered for each conversion by the Nucleotide() class.

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

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

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

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

class rna_library.MotifType¶

Bases: enum.IntEnum

Enumerated type for all motif types

UNASSIGNED = 0¶

SINGLESTRAND = 1¶

HELIX = 2¶

HAIRPIN = 3¶

JUNCTION = 4¶

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

class rna_library.Motif(**kwargs)¶

Bases: abc.ABC

Abstract base class that Hairpin(), Helix(), Junction() and SingleStrand() all inherit from.

link_children(self, depth=0)¶

Method used to link a Motif() object to its children and vice versa. Should only be called once by the root Motif().

Parameters: depth (int) – depth of the current Motif() object. defaults to 0
Return type: None

str(self)¶

Creates a recursive string representation of the current Motif() object.

Return type: str()

__eq__(self, other)¶

Overloaded == operator for Motif(). Requires that type of motif, sequence and token are identical.

Parameters: other (Motif) – Another Motif() to be compared against.
Return type: bool

__str__(self)¶

String representation of just the motif at hand.

Returns: The str() representation of the Motif().
Return type: str()

is_helix(self)¶

If the motif is a helix or not. Overridden by child Helix() class.

Returns: If the motif is of type Helix()
Return type: bool()

is_singlestrand(self)¶

If the motif is a singlestrand or not. Overridden by child SingleStrand() class.

Returns: If the motif is of type SingleStrand()
Return type: bool()

is_hairpin(self)¶

If the motif is a hairpin or not. Overridden by child Hairpin() class.

Returns: If the motif is of type Hairpin()
Return type: bool

is_junction(self)¶

If the motif is a junction or not. Overridden by child Junction() class.

Returns: If the motif is of type Junction()
Return type: bool()

type(self)¶

Returns the MotifType() type for the given motif.

Returns: The MotifType() enum value for the given motif.
Return type: MotifType()

children(self)¶

Getter for the Motif()’s child motifs. Returned as a list for iteration. Only returns direct children or an empty list if the motif has not children.

Returns: A list() of Motif() if the current Motif() has any.
Return type: list[Motif]

add_child(self, other)¶

Appends a new Motif() to the internal list of children for the current Motif().

Warning

Should NOT be called directly. Other function calls must occur to ensure that the internal graph is accurate.

Param: Motif other: Another Motif() to be appended to the internal children list.
Parameters: other (Motif) –
Return type: None

set_children(self, other)¶

Sets the entire list of Motif() to the internal list of children for the current Motif().

Warning

Should NOT be called directly. Other function calls must occur to ensure that the internal graph is accurate.

Parameters: other (List[Motif]) – Another Motif() to be appended to the internal children list.
Return type: None

parent(self, other)¶

Sets the Motif()’s parent to the supplied Motif().

Parameters: other (Motif) – The new parent for the current Motif().
Returns: None
Return type: NoneType

parent(self)¶

Gets the parent Motif()’s for the current Motif().

Returns: the parent motif
Return type: Motif()

token(self, tk)¶

Sets the Motif()’s identifying token to an inputted string. Input is NOT validated.

Parameters: tk (str) – the new token for the Motif().
Returns: None
Return type: NoneType

token(self)¶

Gets the identifying token for the Motif().

Returns: token
Return type: str

structure(self, secstruct)¶

Sets the Motif()’s structure to an inputted string. Input is NOT validated.

Parameters: tk (str) – the new structure for the Motif().
Returns: None
Return type: NoneType

structure(self)¶

Gets the secondary structure for the Motif().

Returns: token
Return type: str

strands(self)¶

Returns a list of list of int()’ss where each sub list contains a contiguous set of nucleotides that “belong” to the Motif(). Output varies by motif type and the expected values are below:

Hairpin() => 1
Helix() => 2
SingleStrand() => 1
Junction() => number of branches in Junction()

Returns: strands
Return type: List[List[int]]

sequence(self)¶

Gets the sequence for the Motif(). Because the nucleotides owned by the Motif() may not be contiguous, breaks will be separated by an ampersand ‘&’.

Returns: sequence
Return type: str

sequence(self, seq)¶

Sets the sequence for the Motif() to the supplied string. Warning the input NOT validated.

Parameters: seq (str) – the new sequence for the Motif().

id(self)¶

Gets the id int value for the given Motif().

Returns: id
Return type: int

id(self, new_id)¶

Sets the id for the Motif(). Warning: It is NOT currently validated.

Parameters: new_id (int) – the new id for the Motif()
Returns: none
Return type: NoneType

depth(self)¶

The depth of the Motif(), which describes how deep it is in the internal graph.

Returns: depth
Return type: int

depth(self, value)¶

Sets the depth of the current Motif().

Parameters: value (int) – the new depth value for the current Motif().

abstract buffer(self)¶

Buffer refers to the size of the closest adjacent :motif:`Helix()`. Varies by type of motif as seen below:

Helix() => size of the helix itself
Hairpin() => size of its parent helix
SingleStrand() => -1, meaningless in this context
Junction() => a list() of the branching helices’ length with the parent helix going first the in the direction of increasing nucleotide index.

Returns: buffer
Return type: int

has_children(self)¶

Returns whether the Motif() has any children.

Returns: has_children
Return type: bool

has_parent(self)¶

Returns whether the Motif() has a parent.

Returns: has_parent
Return type: bool

abstract recursive_sequence(self)¶

Builds and returns the continguous sequence of the structure viewing the current Motif() as the root of the structure. The returned sequence will be part of the main sequence.

Returns: sequence
Return type: str

abstract recursive_structure(self)¶

Builds and returns the continguous structure of the structure viewing the current Motif() as the root of the structure. The returned structure will be part of the main structure.

Returns: structure
Return type: str

abstract has_non_canonical(self)¶

Checks if the Motif() has any non-canonical (i.e. non AU/UA, UG/GU or GC/CG) pairings.

Returns: has_nc
Return type: bool

same_pattern(self, sequence)¶

Checks if a template sequence is compatible with an inputted sequence. Specifically if the length and placement of ‘&’ are the same.

Parameters: sequence (str) – template string to compare against.
Returns: is_same
Return type: bool

start_pos(self)¶

Starting (or lowest) nucleotide index owned by the Motif().

Returns: start_pos
Return type: int

end_pos(self)¶

Ending (or highest) nucleotide index owned by the Motif().

Returns: end_pos
Return type: int

contains(self, pos)¶

Indicates if a nucleotide index is contained or belongs to the current Motif().

Parameters: pos (list[int]) – the querying index
Returns: is_contained
Return type: bool

sequences(self, seqs)¶

Used to set the internal list of barcode temp sequences.

Parameters: seqs (List[str]) – the new barcode sequences to be applied to the current Motif().
Return type: None

number_sequences(self)¶

Gives the number of barcode sequences that the Motif() currently has.

Returns: num_sequence
Return type: int

set_sequence(self, idx)¶

Sets the current sequence to the sequence of the existing index from the internal barcodes list. Note that the Motif.number_sequences() method should be queried prior so that the index call will be known to be valid.

Parameters: idx (int) – The index to be used.
Return type: None

abstract generate_sequences(self)¶: Builds out all possible barcode sequences that fit the known constraints.

is_barcode(self)¶

Returns whether the current Motif() serves as a barcode.

Returns: is_barcode
Return type: bool

class rna_library.Helix(**kwargs)¶

Bases: rna_library.structure.motif.Motif

Represents a helix or stack in an RNA structure. Inherits from Motif().

size(self)¶

Returns the size of the Helix() which is just the number of pairs in the stack.

Returns: size
Return type: int

size(self, val)¶

Sets the current size for the Helix().

Parameters: val (int) – the new size of the helix.

buffer(self)¶

Returns the buffer of the Helix() which is just the number of pairs in the stack.

Returns: buffer
Return type: int

pairs(self)¶

Returns the basepairs in the stack as a list of strings of length 2. Pairs are returned in order of lowest 3 prime starting index.

Returns: pairs
Return type: List[str]

is_helix(self)¶

Indicates that the Motif() is of type Helix().

Returns: is_helix
Return type: bool

recursive_structure(self)¶

Builds and returns the continguous sequence of the structure viewing the current Motif() as the root of the structure. The returned sequence will be part of the main sequence.

Returns: sequence
Return type: str

recursive_sequence(self)¶

Builds and returns the continguous structure of the structure viewing the current Motif() as the root of the structure. The returned structure will be part of the main structure.

Returns: structure
Return type: str

has_non_canonical(self)¶

Checks if any of the basepairs are non-canonical (i.e. non- AU/UA, GU/UG, GC/CG).

Returns: has_non_canonical
Return type: bool

generate_sequences(self)¶: Generates all possible sequences for the Helix() that are compatible with the constraints for the motif.

class rna_library.Hairpin(**kwargs)¶

Bases: rna_library.structure.motif.Motif

Represents a hairpin loop in an RNA structure. Inherits from Motif().

buffer(self)¶

For the Hairpin() type, this is simply the size of the closing helix meaning the number of closing pairs.

Returns: buffer
Return type: int

is_hairpin(self)¶

Indicates that the Motif() is of type Hairpin().

Returns: is_hairpin
Return type: bool

recursive_structure(self)¶

Returns the owned portion of the structure. In this coding of structure it is just the loop portion and does not include the closing pair.

Returns: recursive_structure
Return type: str

recursive_sequence(self)¶

Returns the owned portion of the sequence. In this coding of sequence it is just the loop portion and does not include the closing pair.

Returns: recursive_sequence
Return type: str

has_non_canonical(self)¶

Returns whether or not the closing pair is canonical (i.e. is AU/UA, CG/GC, GU/UG).

Returns: has_non_canonical
Return type: bool

generate_sequences(self)¶: Generates all possible sequences for the Hairpin() that are compatible with the constraints for the motif.

class rna_library.Junction(**kwargs)¶

Bases: rna_library.structure.motif.Motif

Represents a junction of any size in an RNA structure including bulges and multi-loops.

dms_active_idxs(self)¶

buffer(self)¶

For the Junction() type this is a list() of int()’s where the first is the size of the parent Helix() and then they are arranged in 3’ to 5’ order. Will have the same size as number of branches in the Jucntion().

Returns: buffers
Return type: List[int]

gaps(self)¶

Returns a list() of int()’s of gap sizes in 3’ to 5’ order. Will have the same size as number of branches in the Jucntion().

Returns: gaps
Return type: List[int]

is_junction(self)¶

Indicates that the Motif() is of type Junction().

Returns: is_hairpin
Return type: bool

recursive_structure(self)¶

Returns the owned portion of the structure. In this coding of structure it is the closing pairs as well as the child Helix()’s and their children.

Returns: recursive_structure
Return type: str

recursive_sequence(self)¶

Returns the owned portion of the sequence. In this coding of structure it is the closing pairs as well as the child Helix()’s and their children.

Returns: recursive_sequence
Return type: str

closing_pairs(self)¶

Returns a list() of str()’s that correspond to the closing pairs in the Junction() Motif.

Returns: closing_pairs
Return type: List[str]

has_non_canonical(self)¶

Returns whether or not any of the closing pairs are non-canonical (i.e. not AU/UA, CG/GC, GU/UG).

Returns: has_non_canonical
Return type: bool

number_branches(self)¶

Returns the number of branches in the current Junction().

Returns: number_branches
Return type: int

symmetric(self)¶

Indicates if the current Junction() is symmetric, that is the sizes of all of the gaps are the same.

Returns: is_symmetric
Return type: bool

generate_sequences(self)¶

Would generate all possible sequences for the Junction() that are compatible with the constraints for the motif. Not currently implemented.

Raises: TypeError

class rna_library.SingleStrand(**kwargs)¶

Bases: rna_library.structure.motif.Motif

Represents a single stranded region in an RNA structure. Does not include unpaired regions that are part of a Junction() or Helix().

buffer(self)¶

For the SingleStrand() type, this does not have any meaning and is always the value -1.

Returns: buffer
Return type: int

is_singlestrand(self)¶

Indicates that the Motif() is of type SingleStrand().

Returns: is_singlestrand
Return type: bool

recursive_structure(self)¶

Returns the owned portion of the structure. In this coding of structure it is just the nucleotides in the single strand plus its child if it exists.

Returns: recursive_structure
Return type: str

recursive_sequence(self)¶

Returns the owned portion of the sequence. In this coding of sequence it is just the nucleotides in the single strand plus its child if it exists.

Returns: recursive_sequence
Return type: str

has_non_canonical(self)¶

Because there are no pairs “owned” by SingleStrand()’s, it always returns False.

Returns: has_non_canonical
Return type: bool

generate_sequences(self)¶: Generates all possible sequences for the SingleStrand() that are compatible with the constraints for the motif.

class rna_library.SecStruct(secstruct, sequence)¶

Represents a

set_ids_(self, m)¶

Parameters: m (Motif) –

display(self)¶

property sequence(self)¶

property structure(self)¶

helix_replace_(self, id, secstruct, sequence)¶

motif_replace_(self, id, new_secstruct, new_sequence)¶

change_motif(self, id, new_secstruct, new_sequence)¶

get_sequence_structure(self)¶

_get_ids_internal(self, m, ids, mtype)¶

get_ids(self, motif_type)¶

get_motif(self, id)¶

Return type: Motif

get_substructure(self, id1, id2=None)¶

get(self, id)¶

__iter__(self)¶

itermotifs(self)¶

hairpins(self, **kwargs)¶

helix(self)¶

junctions(self)¶

singlestrands(self)¶

set_barcode(self, m_id, bc_seq)¶

__add__(self, other)¶

rna_library.parse_to_motifs(structure, sequence)¶

Method takes a structure sequence pair and returns a root Motif() with a complete associated graph.

Parameters

structure (str) – a valid dot-bracket structure
sequence (str) – the corresponding sequence composed of the alphabet [ACGUTNB]

Returns

motif

Return type

Motif

rna_library.highest_id(m, best=0)¶

Figures out the highest id number in a given Motif() graph.

Parameters

m (Motif) – motif to start the query on
best (int) – current highest or “best” motif id at that recursion level.

Returns

highest_id

Return type

int

class rna_library.JunctionData(**kwargs)¶

Composite class that represents a collection of JunctionEntry objects in an experiment.

get_active_data(self)¶

rebuild_data(self)¶

Method that rebuilds the internal data representation from the JunctionEntry objects.

Return type: NoneType

is_symmetrical(self)¶: Getter that tells if the current JunctionData object models a symmetrical junction. :rtype: bool

plot(self, plot_dir, overwrite=False)¶

Method that saves a plot of the JunctionData’s data points to the supplied directory.

Param: str plot_dir: The directory where the plot will be saved. Does not have to exist.
Return type: NoneType
Parameters: plot_dir (str) –

show(self)¶

Method that brings up a plot of the JunctionData’s data points

Return type: NoneType

bind(self, ax)¶

Method that binds the JunctionData points to a supplied matplotlib Axes object.

Param: matplotlib.axes.Axes ax: the Axes object which the plot will be bound to
Return type: NoneType
Parameters: ax (matplotlib.axes.Axes) –

measure_variance(self)¶

Return type: Dict[str, float]

class rna_library.JunctionEntry(**kwargs)¶

Represents a single junction entry from an RNA construct

validate_arguments_(self)¶: Helper method that validates arguments in the constructor.

key(self)¶

Getter that accesses the (sequence, structure) key for the JunctionEntry

Return type: Tuple[str,str]

is_symmetrical(self)¶

Getter that checks if the JunctionEntry is for a symmetrical unction.

Return type: bool

__getitem__(self, idx)¶

Parameters: idx (int) –
Return type: float

rna_library.build_react_df(**kwargs)¶

Builds the reactivity dataframe from the supplied arguments. Here each row reprsents a construct.: Note that all arguments are supplied as kwargs.

Params: str out_dir: base output directory where rna_library.process_histos was called :params: str start_seq: common start sequence for the RNA constructs
Params: str end_seq: common end sequence for the RNA constructs
Params: str fasta_file: path to the fast file for the construct
Params: str histos_file: path to histogram file from DREEM analysis :rtype: pd.DataFrame
Return type: pandas.DataFrame

rna_library.build_motif_df(df)¶

Function that creates a motif dataframe from a reactivity dataframe. Here each row represents a Motif.

Param: pd.DataFrame df: reactivity dataframe which is generated from build_react_df() :rtype: pd.DataFrame
Parameters: df (pandas.DataFrame) –
Return type: pandas.DataFrame

rna_library.normalize_hairpin(df, seq, ss, **kwargs)¶

Normalizes a reactivity pattern to a normalization hairpin. Creates fully normalize values for an entire pd.DataFrame

Param

pd.DataFrame df: reactivity_df created from rna_library.build_react_df

Param

str seq: reference hairpin sequence

Param

str ss: reference hairpin structure

Param

float factor: factor to set the hairpin values to, is a keyword argument

Param

str nts: string of nucleotide’s to be used for calc, is a keywrod argument

Parameters

df (pandas.DataFrame) –
seq (str) –
ss (str) –

Return type

List[List[float]]

rna_library.normalize_coeff_fit(reactivity_df)¶

rna_library.build_barcodes(secstruct, start=None, distance=3)¶

Parameters

secstruct (str) –
start (Union[str, None]) –
distance (int) –

rna_library¶

Subpackages¶

Package Contents¶

Classes¶

Functions¶

Attributes¶

`rna_library`¶