oscar_colony.colony_management.pyrat.standardise.standardise_pyrat_csv

oscar_colony.colony_management.pyrat.standardise.standardise_pyrat_csv(input_df)

Standardise a csv file exported from pyRAT.

Processing steps include: - standardising column names with a dynamic dict - adding columns for the number of mutations per line (n_mutations) and a summary of the mutation names (mutations) - Correcting or removing forbidden genotypes like +/-, Tg, ko/ko - adding summary columns for ‘genotype_offspring’, ‘genotype_father’ and ‘genotype_mother’ that match the order of ‘mutations’. - marking ungenotyped-offspring as NaN in the ‘genotype_offspring’ column - filling any missing genotypes with wildtype - removing columns that aren’t needed for further processing steps - checking data input validity and removing impossible input data

Parameters:

input_csv (pd.DataFrame | Path | str) – Csv file exported from pyRAT.

Returns:

Standardised dataframe, ready for further processing

Return type:

DataFrame