Question

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?

Answer 1

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.

Answer 2

您可以使用tarfile module从tar.gz存档中读取特定文件（如this resolved issue中所述）。如果存档中只有一个文件，则可以执行以下操作：

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=" ")

读取模式r:*适当地处理gz扩展名（或其他类型的压缩）。如果压缩的tar文件中包含多个文件，则可以执行类似csv_path = list(n for n in tar.getnames() if n.endswith('.csv'))[-1]行的操作来获取存档文件夹中的最后一个csv文件。

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

2 个答案: