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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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Issues with fetch_ucsc.py #17

Closed harshameghadri closed 6 years ago

harshameghadri commented 6 years ago

I have been trying to use the inbuilt python script to get the reference genomes. This is the error I constantly get.

Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.5/bin/fetch_ucsc.py", line 9, in load_entry_point('CIRCexplorer2==2.3.2', 'console_scripts', 'fetch_ucsc.py')() File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/circ2/fetch_ucsc.py", line 89, in main fetch_file(sys.argv) File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/circ2/fetch_ucsc.py", line 32, in fetch_file outf.write(gzip.open('refFlat.txt.gz', 'rb').read()) TypeError: write() argument must be str, not bytes

Is there any way to get around this error?

I have downloaded the hg38 assembly; could I use this alternatively to create GTF flies?. If so How?

kepbod commented 6 years ago

Bug has been fixed. Please try the latest version.