RNAmediator.Tweaks.RNAmediator.add_rnamediator_constraint

RNAmediator.Tweaks.RNAmediator.add_rnamediator_constraint(run_settings: Dict[str, SequenceSettings], constraints: str, record: Bio.SeqIO.SeqRecord, goi: str = 'nogene', chrom: str = 'nochrom', sequence_strand: str = '+', constraintype: str = 'hard')

Adds constraints in string format to the goi in the run settings dict. Creates sequence settings if missing

Parameters:

• run_settings (Dict[str, SequenceSettings]) – run settings dictionary using fasta ids as keys and Sequence Settings as values

• constraints (str) – constraint in string format start-end|strand

• record (SeqIO.SeqRecord) – Sequence record of the sequence to which the constraint should be added

• goi – gene name assumed from fasta sequence header

• chrom – chromosome of the sequence

• sequence_strand – strand of the sequence

• 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]