double quoted elements in csv cant read with pandas
Question:
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?
Thanks.
Answers:
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'.
ParserWarning)
Out[3]:
"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"
This worked for me: (I used Python 3.9)
dataset = pd.read_csv('test.csv', sep=',', skipinitialspace=True)
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?
Thanks.
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'.
ParserWarning)
Out[3]:
"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"
This worked for me: (I used Python 3.9)
dataset = pd.read_csv('test.csv', sep=',', skipinitialspace=True)