RNAmediator.Tweaks.RNAmediator.preprocess

RNAmediator.Tweaks.RNAmediator.preprocess(sequence: str, constraint: str, conslength: int, constype: str, outdir: str, genes: str)

builds the run settings dict and creates the output directory

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

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

• outdir (str) – Location of the Output directory. If it is an empty string os.cwd() is used

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

Returns:

a dictionary using the fasta sequence id as key and stores corresponding settings in an SequenceSettings object and the absolute path to the output directory

Return type:

Tuple[Dict[str, SequenceSettings], str]