mutcleaner.cleaners.antitoxin_pard3_custom_cleaners#

Functions

`infer_wt_sequence`(dataset, mutation_col[, ...])	infer wild type seuquence from mutation_sequence and mutation information
`simplify_mutations`(dataset[, ...])	Simplify mutation strings by removing no-change tokens like L47L.

mutcleaner.cleaners.antitoxin_pard3_custom_cleaners.infer_wt_sequence(dataset, mutation_col, sequence_col='mut_seq', wt_column='wt_seq')[source]#

infer wild type seuquence from mutation_sequence and mutation information

Return type:: DataFrame
Returns:: the dataset contatins added wild-type sequence

mutcleaner.cleaners.antitoxin_pard3_custom_cleaners.simplify_mutations(dataset, mutation_column='mut_info', mutation_sep=':')[source]#

Simplify mutation strings by removing no-change tokens like L47L. Keeps unknown tokens unchanged (does not filter rows).

Return type:: DataFrame

Examples

>>> import pandas as pd
>>> df = pd.DataFrame({
>>> 'name':["protein1", "protein1", "protein1"]
>>> 'mut_info':["L47L:D51D:I52I","L47A:D51D:I52A","L47_:D51D:I52I"]
>>> })
>>> df = simplify_mutations(df)
>>> df[mut_info]
    pd.Series("WT","L47A,I52A","L47_") # only simplify the mutations but not fliter