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 1 Answer
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) 
