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fix compatibility issue with newline separator

Open ftschirpke opened this issue 2 years ago • 2 comments

In newer versions the python engine seems to have a problem with \n as separator or delimiter #14. Therefore, I propose another way of reading only the non-empty lines of the strandedness_check.txt files avoiding the following line

result = pd.read_csv(test_folder + '/' + 'strandedness_check.txt', sep="\r\n", header=None, engine='python')

(check_strandedness.py:213) and instead reading the file and filtering out the emtpy lines:

with open(test_folder + '/' + 'strandedness_check.txt', 'r') as f:
    result = list(filter(None, (line.rstrip() for line in f)))

ftschirpke avatar Aug 30 '22 11:08 ftschirpke

I had this same issue when using Python 3.10.9 . I solved it by creating a conda environment with Python 3.6.2 and it resolved. Great fix idea and great tool! Thank you!

Logan-Wallace avatar Aug 29 '23 23:08 Logan-Wallace

@ftschirpke, I applied your changes and it worked well. Thank you for your help!

ducphuc2000 avatar Jul 01 '24 03:07 ducphuc2000