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YangLab / CLEAR

direct comparison of circular and linear RNA expression
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CLEAR: python2 or python3? #21

Open nliorni opened 2 years ago

nliorni commented 2 years ago

Greetings,

I tried to use the CLEAR pipeline under a python3 environment, and it worked well until the TopHat, where I got:

TopHat2 is not compable to python3. You can change to a python2 environment or change tophat shebang "#!/usr/bin/env python" to "#!/usr/bin/env python2"

Therefore, I created a python2 environment as suggested. This time I couldn't even got to the TopHat step, getting an error as soon as I launched CLEAR:

File "/opt/miniconda3/envs/TopHat/lib/python2.7/site-packages/pybedtools/contrib/long_range_interaction.py", line 357 print("%d (%.1f%%)\r" % (c, c / float(n) * 100), end="") What can I do to solve the issue. Thanks in advance

nl

wangmengbo commented 1 year ago

Greetings,

I tried to use the CLEAR pipeline under a python3 environment, and it worked well until the TopHat, where I got:

TopHat2 is not compable to python3. You can change to a python2 environment or change tophat shebang "#!/usr/bin/env python" to "#!/usr/bin/env python2"

Therefore, I created a python2 environment as suggested. This time I couldn't even got to the TopHat step, getting an error as soon as I launched CLEAR:

File "/opt/miniconda3/envs/TopHat/lib/python2.7/site-packages/pybedtools/contrib/long_range_interaction.py", line 357 print("%d (%.1f%%)\r" % (c, c / float(n) * 100), end="") What can I do to solve the issue. Thanks in advance

nl

I met the same exact error although I was running circ_quant directly. It seems not working with at least pybedtools v0.9.0.

nliorni commented 1 year ago

I dropped :\

Si-Nan commented 1 year ago

dependencies: