I have a df that looks like this. it is a multi-index df resulting from a group-by
grouped = df.groupby(['chromosome', 'start_pos', 'end_pos',
'observed']).agg(lambda x: x.tolist())
reference zygosity
chromosome start_pos end_pos observed
chr1 69428 69428 G [T, T] [hom, hom]
69511 69511 G [A, A] [hom, hom]
762273 762273 A [G, G, G] [hom, het, hom]
762589 762589 C [G] [hom]
762592 762592 G [C] [het]
For each row i want to count the number of het and hom in the zygosity. and make a new column called ‘count_hom’ and ‘count_het’
I have tried using for loop it is slow and not very reliable with changing data. Is there a way to do this using something like df.zygosity.len().sum() but only for het or only for hom
>Solution :
Use Series.apply with List count:
grouped['count_hom'] = grouped['zygosity'].apply(lambda x: x.count('hom'))
grouped['count_het'] = grouped['zygosity'].apply(lambda x: x.count('het'))