aegis_sim.utilities.analysis.genome 

 1def get_sorted_allele_frequencies(interval_genotypes):
 2    total_frequency = interval_genotypes.sum(0)
 3    return interval_genotypes.T.assign(total=total_frequency).sort_values(by="total", ascending=False).T.iloc[:-1]
 4
 5
 6def get_derived_allele_freq(interval_genotypes):
 7    reference = interval_genotypes.round()
 8    derived_allele_freq = (
 9        interval_genotypes.iloc[1:].reset_index(drop=True) - reference.iloc[:-1].reset_index(drop=True)
10    ).abs()
11    return derived_allele_freq
12
13
14def get_mean_allele_freq(interval_genotypes):
15    mean_allele_freq = interval_genotypes.mean(0)
16    return mean_allele_freq
17
18
19def get_quantile_allele_freq(interval_genotypes, quantile):
20    quantile_allele_freq = interval_genotypes.quantile(quantile)
21    return quantile_allele_freq
def get_sorted_allele_frequencies(interval_genotypes): 
2def get_sorted_allele_frequencies(interval_genotypes):
3    total_frequency = interval_genotypes.sum(0)
4    return interval_genotypes.T.assign(total=total_frequency).sort_values(by="total", ascending=False).T.iloc[:-1]
def get_derived_allele_freq(interval_genotypes): 
 7def get_derived_allele_freq(interval_genotypes):
 8    reference = interval_genotypes.round()
 9    derived_allele_freq = (
10        interval_genotypes.iloc[1:].reset_index(drop=True) - reference.iloc[:-1].reset_index(drop=True)
11    ).abs()
12    return derived_allele_freq
def get_mean_allele_freq(interval_genotypes): 
15def get_mean_allele_freq(interval_genotypes):
16    mean_allele_freq = interval_genotypes.mean(0)
17    return mean_allele_freq
def get_quantile_allele_freq(interval_genotypes, quantile): 
20def get_quantile_allele_freq(interval_genotypes, quantile):
21    quantile_allele_freq = interval_genotypes.quantile(quantile)
22    return quantile_allele_freq