I want to put the output of this print(d) function into a pandas dataframe

December 8, 2021

I am working with the bioservices package in python and I want to take the output of this function and put it into a dataframe using pandas

from bioservices import UniProt
u = UniProt(verbose=False)
d = u.search("yourlist:M20211203F248CABF64506F29A91F8037F07B67D133A278O", frmt="tab", limit=5,
             columns="id, entry name")
print(d)

this is the result I am getting, almost like a neat little table

The problem however is I cannot work with the data in this form and I want to put it into a dataframe using pandas

trying this code below does not work and it only returns the error "ValueError: DataFrame constructor not properly called"

import pandas as pd
df = pd.DataFrame(columns= ['Entry','Entry name'],
              data=d)
print(df)

>Solution :

Use pd.read_csv, after encapsulating your output in a StringIO (to present a file-like interface):

import io
import pandas as pd

data = 'Entry\tEntry name\na\t1\nb\t2'
io_data = io.StringIO(data)

df = pd.read_csv(io_data, sep='\t')
print(df)

The output is a dataframe:

  Entry  Entry name
0     a           1
1     b           2

Sample data:

from bioservices import UniProt
import io

u = UniProt(verbose=False)
d = u.search("yourlist:M20211203F248CABF64506F29A91F8037F07B67D133A278O", frmt="tab", limit=5,
             columns="id, entry name")
#print(d)

df = pd.read_csv(io.StringIO(d), sep='\t')
print(df)
    Entry   Entry name
0  Q8TAS1  UHMK1_HUMAN
1  P35916  VGFR3_HUMAN
2  Q96SB4  SRPK1_HUMAN
3  Q6P3W7  SCYL2_HUMAN
4  Q9UKI8   TLK1_HUMAN