how_are_we_stranded_here
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fix compatibility issue with newline separator
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)))
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!
@ftschirpke, I applied your changes and it worked well. Thank you for your help!