read_table read all data to one column

Question

I got a file like this:

TCGA1 0 QWE
TCGA2 1 QWE
TCGA2 -2 RAF
TCGA3 2 KLS

and tried to read it into a dataframe using pandas.

Answer 1

You have to add sep='s\+' for separator arbitrary whitespace in read_table.

It does not work as you expected, because default separator is ,, so all data are in one column.

import pandas as pd
import io

temp=u"""TCGA1 0 QWE
TCGA2 1 QWE
TCGA2 -2 RAF
TCGA3 2 KLS"""
#after testing replace io.StringIO(temp) to filename
df = pd.read_table(io.StringIO(temp), sep="\s+", header=None)
print df
       0  1    2
0  TCGA1  0  QWE
1  TCGA2  1  QWE
2  TCGA2 -2  RAF
3  TCGA3  2  KLS

Another solution with parameter delim_whitespace=True:

import pandas as pd
import io

temp=u"""TCGA1 0 QWE
TCGA2 1 QWE
TCGA2 -2 RAF
TCGA3 2 KLS"""
#after testing replace io.StringIO(temp) to filename
df = pd.read_table(io.StringIO(temp), delim_whitespace=True, header=None)
print df
       0  1    2
0  TCGA1  0  QWE
1  TCGA2  1  QWE
2  TCGA2 -2  RAF
3  TCGA3  2  KLS