A lot of questions have been already asked about this topic on SO. (and many others). Among the numerous answers, none of them was really helpful to me so far. If I missed the useful one, please let me know.
I simply would like to read a CSV file with pandas into a dataframe. Sounds like a simple task.
My file Test.csv
1,2,3,4,5
1,2,3,4,5,6
,,3,4,5
1,2,3,4,5,6,7
,2,,4
My code:
import pandas as pd
df = pd.read_csv('Test.csv',header=None)
My error:
pandas.errors.ParserError: Error tokenizing data. C error: Expected 5 fields in line 2, saw 6
My guess about the issue is that Pandas looks to the first line and expects the same number of tokens in the following rows. If this is not the case it will stop with an error.
In the numerous answers, the suggestions for using options are, e.g.:
error_bad_lines=False
or header=None
or skiprows=3
and more non-helpful suggestions.
However, I don't want to ignore any lines or skip. And I don't know in advance how many columns and rows the datafile has.
So it basically boils down to how to find the maximum number of columns in the datafile. Is this the way to go? I hoped that there was an easy way to simply read a CSV file which does not have the maximum column number in the first line. Thank you for any hints. I'm using Python 3.6.3, Pandas 0.24.1 on Win7.
Thank you @ALollz for the "very fresh" link (lucky coincidence) and @Rich Andrews for pointing out that my example actually is not "strictly correct" CSV data.
So, the way it works for me for the time being is adapted from @ALollz' compact solution (https://stackoverflow.com/a/55129746/7295599)
### reading an "incorrect" CSV to dataframe having a variable number of columns/tokens
import pandas as pd
df = pd.read_csv('Test.csv', header=None, sep='\n')
df = df[0].str.split(',', expand=True)
# ... do some modifications with df
### end of code
df
contains empty string ''
for the missing entries at the beginning and the middle, and None
for the missing tokens at the end.
0 1 2 3 4 5 6
0 1 2 3 4 5 None None
1 1 2 3 4 5 6 None
2 3 4 5 None None
3 1 2 3 4 5 6 7
4 2 4 None None None
If you write this again to a file via:
df.to_csv("Test.tab",sep="\t",header=False,index=False)
1 2 3 4 5
1 2 3 4 5 6
3 4 5
1 2 3 4 5 6 7
2 4
None
will be converted to empty string ''
and everything is fine.
The next level would be to account for data strings in quotes which contain the separator, but that's another topic.
1,2,3,4,5
,,3,"Hello, World!",5,6
1,2,3,4,5,6,7