infrared.rna Namespace Reference

Classes
class	BPComp
	Constrain complementarity of the base pair (i,j) More...
class	BPEnergy
	Function for Stack Energy model. More...
class	DifferentComplClassConstraint
	Parse RNA structure including pseudoknots. More...
class	GCCont
	Function for (basepair-wise) BasePair Energy model. More...
class	NotBPComp
	Function for (position-wise) GC content. More...
class	ParseError
class	SameComplClassConstraint
	Constrain nucleotides to be in different complementarity classes. More...
class	StackEnergy
	Constrain nucleotides to be in the same complementarity class. More...

Functions
	parse_array (structure, *opening="([{<", closing=")]}>")
	parse (structure, **kwargs)
	Parse RNA structure, returning list of base pairs.
	is_complementary (x, y)
	Check complementarity of nucleotides.
	invalid_bps (seq, struc)
	Get invalid base pairs.
	is_valid (seq, struc)
	Check whether sequence satisfies complementarity constraints due to structure.
	structure_to_basepair_dependencies (structure, edges=[])
	Convert structure to list of edges in basepair model.
	structure_to_stacking_dependencies (structure, edges=[])
	Convert structure to list of edges in stacking model.
	GC_content (seq)
	Compute GC content in a sequence.
	unique_edges (xs)
	Make edges unique (considering symmetry).
	read_inp (inpfh)
	Read multiple structures from file in inp format.
	nucleotide_to_value (x)
	Convert integer (variable value) to nucleotide.
	value_to_nucleotide (x)
	Convert integer (variable value) to nucleotide.
	values_to_seq (xs)
	Convert list of integers (variable values) to string (sequence) of nucleotides.
	ass_to_seq (ass)
	Convert assignment to sequence string.
	iupacvalues (symbol)
	set_bpenergy_table (params=def_params_bp)
	Set the bp energy table for Function BPEnergy.
	set_stacking_energy_table (params=def_params_stacking)
	Set the stacking energy table for Function StackEnergy.

Variables
dict	def_params_bp
	Default parameters for the base pair model (magic params from the Redprint paper)
dict	def_params_stacking
	Default parameters for the stacking model (magic params from the Redprint paper)

Detailed Description

Functionality for RNA-related Infrared applications.

import infrared.rna as rna

Function Documentation

ass_to_seq()

infrared.rna.ass_to_seq

(

ass

)

Convert assignment to sequence string.

Parameters

ass	assignment

GC_content()

infrared.rna.GC_content

(

seq

)

Compute GC content in a sequence.

Parameters

seq	sequence string

Returns

gc content (as ratio in [0,1])

invalid_bps()

infrared.rna.invalid_bps	(		seq,
			struc
	)

Get invalid base pairs.

Parameters

seq	sequence string
struc	structure as dot bracket string or base pair list

Returns

list of base pairs that violate the complementarity constraints

is_complementary()

infrared.rna.is_complementary	(		x,
			y
	)

Check complementarity of nucleotides.

Parameters

x	nucelotide
y	nucelotide

Returns

whether complementary (A-U,C-G, or G-U)

is_valid()

infrared.rna.is_valid	(		seq,
			struc
	)

Check whether sequence satisfies complementarity constraints due to structure.

Parameters

seq	sequence string
struc	structure as dot bracket string or base pair list

Returns

whether valid

iupacvalues()

infrared.rna.iupacvalues

(

symbol

)

nucleotide_to_value()

infrared.rna.nucleotide_to_value

(

x

)

Convert integer (variable value) to nucleotide.

Parameters

x	nucleotide or gap, A, C, G, U, T, -, or .

Note

encoding A=0, C=1, G=2, U/T=3, -/.=4

parse()

infrared.rna.parse	(		structure,
		**	kwargs
	)

Parse RNA structure, returning list of base pairs.

Parameters

structure

dot bracket string of RNA structure

Returns

list of base pairs (i,j)

See also

parse_array

parse_array()

infrared.rna.parse_array	(		structure,
		*	opening = "([{<",
			closing = ")]}>"
	)

read_inp()

infrared.rna.read_inp

(

inpfh

)

Read multiple structures from file in inp format.

inp format is a file format to specify instances for multi-target RNA design, e.g. used in the benchmarks of Modena and RNAblueprint

Parameters

inpfh

input file handle

Returns

list of the structures as dot bracket strings

set_bpenergy_table()

infrared.rna.set_bpenergy_table

(

params = def_params_bp

)

Set the bp energy table for Function BPEnergy.

Parameters

params

dictionary of parameters or a table of the parameters as expected by _bpenergy

set_stacking_energy_table()

infrared.rna.set_stacking_energy_table

(

params = def_params_stacking

)

Set the stacking energy table for Function StackEnergy.

Parameters

params

dictionary of parameters or a table of the parameters as expected by _stackenergy

structure_to_basepair_dependencies()

infrared.rna.structure_to_basepair_dependencies	(		structure,
			edges = []
	)

Convert structure to list of edges in basepair model.

Dependencies are appendes to edges

Parameters

structure	array representation of RNA structure
edges	edges list of edges [in,out]

Note

node indices are 0-based

structure_to_stacking_dependencies()

infrared.rna.structure_to_stacking_dependencies	(		structure,
			edges = []
	)

Convert structure to list of edges in stacking model.

Dependencies are appendes to edges

Parameters

structure	array representation of RNA structure
edges	list of edges [in,out]

See also

structure_to_basepair_dependencies

unique_edges()

infrared.rna.unique_edges

(

xs

)

Make edges unique (considering symmetry).

keeps only one of (x,y) and (y,x), namely (x,y) if x<y

Parameters

xs	list of edges

Returns

unique list of edges

value_to_nucleotide()

infrared.rna.value_to_nucleotide

(

x

)

Convert integer (variable value) to nucleotide.

Parameters

x

integer

Note

encoding A=0, C=1, G=2, U=3, -=4

values_to_seq()

infrared.rna.values_to_seq

(

xs

)

Convert list of integers (variable values) to string (sequence) of nucleotides.

Parameters

xs	list of integers

Variable Documentation

def_params_bp

dict infrared.rna.def_params_bp

Initial value:

=  {"GC_IN": -2.10208, "AU_IN": -0.52309, "GU_IN": -0.88474,
    "GC_TERM": -0.09070, "AU_TERM": 1.26630, "GU_TERM": 0.78566}

Default parameters for the base pair model (magic params from the Redprint paper)

def_params_stacking

dict infrared.rna.def_params_stacking

Initial value:

=  {"AUAU": -0.18826, "AUCG": -1.13291, "AUGC": -1.09787,
    "AUGU": -0.38606, "AUUA": -0.26510, "AUUG": -0.62086,
    "CGAU": -1.11752, "CGCG": -2.23740, "CGGC": -1.89434,
    "CGGU": -1.22942, "CGUA": -1.10548, "CGUG": -1.44085,
    "GUAU": -0.55066, "GUCG": -1.26209, "GUGC": -1.58478,
    "GUGU": -0.72185, "GUUA": -0.49625, "GUUG": -0.68876}

Default parameters for the stacking model (magic params from the Redprint paper)