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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(
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