RNAmediator.Tweaks.RNAmediator.SequenceSettings

class RNAmediator.Tweaks.RNAmediator.SequenceSettings(sequence_record: Bio.SeqIO.SeqRecord, gene: str = 'nogene', chrom: str = 'nochrom', strand: str = '+', constraintype: str = 'hard', constrainlist: Iterable[Tuple[Constraint]] = None, genomic_coords: Constraint = None)

Constraint(PL)fold settings for a sequence object.

Attributes

genestr, optional

name of the gene of interest (default is nogene)

chrom: str, optional

chromosome of the gene (default is nochrom)

strand: str, optional

strand of the gene (default is +)

constraintype: str, optional

Type of constraint to apply, can be [‘hard’(Default), ‘soft’, ‘mutate’]

constrainlist: Iterable[Tuple[Constraint]], optional

List of constraint objects. (default is None)

genomic_coords: Constraint, optional optional

genomic coordinates of the sequence record (default is None)

__init__(sequence_record: Bio.SeqIO.SeqRecord, gene: str = 'nogene', chrom: str = 'nochrom', strand: str = '+', constraintype: str = 'hard', constrainlist: Iterable[Tuple[Constraint]] = None, genomic_coords: Constraint = None)

Methods

__init__(sequence_record[, gene, chrom, ...])
add_constraints(constraints)	adds a constraint to the list of constraints
set_constraintype(ctype)	sets constraint type

Attributes

constrainlist	getter method for constraintlist attribute
constraintype	getter method for constraintype attribute

add_constraints(constraints: Tuple[Constraint])

adds a constraint to the list of constraints

property constrainlist

getter method for constraintlist attribute

property constraintype

getter method for constraintype attribute

set_constraintype(ctype: str)

sets constraint type