I have an input file where every value is stored as a string.
It is inside a csv file with each entry inside double quotes.

Example file:

"column1","column2", "column3", "column4", "column5", "column6"
"AM", "07", "1", "SD", "SD", "CR"
"AM", "08", "1,2,3", "PR,SD,SD", "PR,SD,SD", "PR,SD,SD"
"AM", "01", "2", "SD", "SD", "SD"

There are only six columns. What options do I need to enter to pandas read_csv to read this correctly?

I currently am trying:

import pandas as pd
df = pd.read_csv(file, quotechar=""")

but this gives me the error message:
CParserError: Error tokenizing data. C error: Expected 6 fields in line 3, saw 14

Which obviously means that it is ignoring the ‘”‘ and parsing every comma as a field.
However, for line 3, columns 3 through 6 should be strings with commas in them. (“1,2,3”, “PR,SD,SD”, “PR,SD,SD”, “PR,SD,SD”)

How do I get pandas.read_csv to parse this correctly?


This will work. It falls back to the python parser (as you have non-regular separators, e.g. they are comma and sometimes space). If you only have commas it would use the c-parser and be much faster.

In [1]: import csv

In [2]: !cat test.csv
"column1","column2", "column3", "column4", "column5", "column6"
"AM", "07", "1", "SD", "SD", "CR"
"AM", "08", "1,2,3", "PR,SD,SD", "PR,SD,SD", "PR,SD,SD"
"AM", "01", "2", "SD", "SD", "SD"

In [3]: pd.read_csv('test.csv',sep=',\s+',quoting=csv.QUOTE_ALL)
pandas/io/parsers.py:637: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators; you can avoid this warning by specifying engine="python".
     "column1","column2" "column3"   "column4"   "column5"   "column6"
"AM"                "07"       "1"        "SD"        "SD"        "CR"
"AM"                "08"   "1,2,3"  "PR,SD,SD"  "PR,SD,SD"  "PR,SD,SD"
"AM"                "01"       "2"        "SD"        "SD"        "SD"