`rna_library.structure.motif`¶

Motif classes that serve as the driver for this library’s functionality.

Module Contents¶

Classes¶

Motif

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

Functions¶

highest_id(m, best = 0)

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

class rna_library.structure.motif.Motif(**kwargs)¶

Bases: abc.ABC

Inheritance diagram of rna_library.structure.motif.Motif

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

rna_library.structure.motif.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

rna_library.structure.motif¶

Module Contents¶

Classes¶

Functions¶

`rna_library.structure.motif`¶