RNAmediator.Tweaks.RNAmediator.set_run_settings_dict

RNAmediator.Tweaks.RNAmediator.set_run_settings_dict(sequence, constraint: str, conslength: int, genes: str, constraintype: str = 'hard') → Dict[str, SequenceSettings]

Use command line parameters to build the run settings dictionary.

Parameters:

• sequence (str) – The file location of the sequence

• constraint (str) – The file location of constrain file

• conslength (int) – Length of the constraint, only used if constrain is sliding

• genes – The file location of the genomic coordinates bed file

• constraintype (str, optional) – Type of constraint to apply, can be [‘hard’(Default), ‘soft’, ‘mutate’]

Returns:

a dictionary using the fasta sequence id as key and stores corresponding settings in an SequenceSettings object

Return type:

Dict[str, SequenceSettings]