How to read/print the ( _io.TextIOWrapper) data?

Question

With the following code I want to > open a file > read the contents and strip the non-required lines > then write the data to the file and also read the file for downstream analyses.

with open("chr2_head25.gtf", 'r') as f,\
    open('test_output.txt', 'w+') as f2:
    for lines in f:
        if not lines.startswith('#'):
            f2.write(lines)
    f2.close()

Now, I want to read the f2 data and do further processing in pandas or other modules but I am running into a problem while reading the data(f2).

data = f2 # doesn't work
print(data) #gives
<_io.TextIOWrapper name='test_output.txt' mode='w+' encoding='UTF-8'>

data = io.StringIO(f2)  # doesn't work
# Error message
Traceback (most recent call last):
  File "/home/everestial007/PycharmProjects/stitcher/pHASE-Stitcher-Markov/markov_final_test/phase_to_vcf.py", line 64, in <module>
data = io.StringIO(f2)
TypeError: initial_value must be str or None, not _io.TextIOWrapper

Can you please be specific. I tried doing `f2.read()` on the second line of the code while `open(...) as f2.read()`, but it didn't work. — everestial007, Apr 16 '17 at 14:38

score 43 · Accepted Answer · answered Apr 16 '17 at 14:41

43

The file is already closed (when the previous with block finishes), so you cannot do anything more to the file. To reopen the file, create another with statement and use the read attribute to read the file.

with open('test_output.txt', 'r') as f2:
    data = f2.read()
    print(data)

answered Apr 16 '17 at 14:41

Taku

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I tried not putting `f2.close()` at the end of that for loop, but it didn't work either. I already know what you have suggested. I just didn't wanted to read the file again and again. Was wondering if that codes is missing something. – everestial007 Apr 16 '17 at 14:43
8

@everestial007: The `f2.close()` is redundant because the preceding `with` does it automatically. – martineau Apr 16 '17 at 14:45
How can I convert `f2` to an `str` object ? – Leevo Aug 10 '19 at 09:14
@Leevo `data` is the str object of the file’s content. – Taku Aug 22 '19 at 10:02
@abccd how this answer is using io.TextIOWrapper ? – Ivailo Bardarov Jul 09 '21 at 12:16
Well the person asking forgot to read from the file handler. So he was trying to read using the wrong object. – nlhnt Nov 22 '21 at 11:29

How to read/print the ( _io.TextIOWrapper) data?

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