CODEWITHSUNDEEP
pythoncsvpandasgziptar
Geet
Geet

Reputation: 2575

How can I read tar.gz file using pandas read_csv with gzip compression option?

I have a very simple csv, with the following data, compressed inside the tar.gz file. I need to read that in dataframe using pandas.read_csv. 

   A  B
0  1  4
1  2  5
2  3  6

import pandas as pd
pd.read_csv("sample.tar.gz",compression='gzip')

However, I am getting error:

CParserError: Error tokenizing data. C error: Expected 1 fields in line 440, saw 2

Following are the set of read_csv commands and the different errors I get with them:

pd.read_csv("sample.tar.gz",compression='gzip',  engine='python')
Error: line contains NULL byte

pd.read_csv("sample.tar.gz",compression='gzip', header=0)
CParserError: Error tokenizing data. C error: Expected 1 fields in line 440, saw 2

pd.read_csv("sample.tar.gz",compression='gzip', header=0, sep=" ")
CParserError: Error tokenizing data. C error: Expected 2 fields in line 94, saw 14    

pd.read_csv("sample.tar.gz",compression='gzip', header=0, sep=" ", engine='python')
Error: line contains NULL byte

What's going wrong here? How can I fix this?

Upvotes: 54

Views: 116873

Answers (2)

teichert
teichert

Reputation: 4713

You can use the tarfile module to read a particular file from the tar.gz archive (as discussed in this resolved issue). If there is only one file in the archive, then you can do this:

import tarfile
import pandas as pd
with tarfile.open("sample.tar.gz", "r:*") as tar:
    csv_path = tar.getnames()[0]
    df = pd.read_csv(tar.extractfile(csv_path), header=0, sep=" ")

The read mode r:* handles the gz extension (or other kinds of compression) appropriately. If there are multiple files in the zipped tar file, then you could do something like csv_path = list(n for n in tar.getnames() if n.endswith('.csv'))[-1] line to get the last csv file in the archived folder.

Upvotes: 15

Marlon Abeykoon
Marlon Abeykoon

Reputation: 12465

df = pd.read_csv('sample.tar.gz', compression='gzip', header=0, sep=' ', quotechar='"', error_bad_lines=False)

Note: error_bad_lines=False will ignore the offending rows.

Upvotes: 88

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