pandas: records with lists to separate rows

Question

I have a Python Pandas DataFrame like this (UCSC schema for NCBI RefSeq):

chrom   exonStart     exonEnds      name
chr1    100,200,300   110,210,310   gen1
c         


        

Answer 1

This is one way using numpy and intertools.chain.

The idea is to first split your comma separated fields into lists. Then construct a results dataframe, repeating or chaining values were necessary.

import numpy as np
from itertools import chain

df['exonStart'] = df['exonStart'].str.split(',')
df['exonEnds'] = df['exonEnds'].str.split(',')

lens = list(map(len, df['exonStart']))

res = pd.DataFrame({'chrom': np.repeat(df['chrom'], lens),
                    'exonStart': list(chain.from_iterable(df['exonStart'])),
                    'exonEnds': list(chain.from_iterable(df['exonEnds'])),
                    'name': np.repeat(df['name'], lens)})

print(res)

#   chrom exonEnds exonStart  name
# 0  chr1      110       100  gen1
# 0  chr1      210       200  gen1
# 0  chr1      310       300  gen1
# 1  chr1      600       500  gen2
# 1  chr1      800       700  gen2
# 2  chr2       55        50  gen3
# 2  chr2       65        60  gen3
# 2  chr2       75        70  gen3
# 2  chr2       85        80  gen3

Note you may wish to convert your numeric columns to int at the end of this process.