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bioinfo-biols / CIRIquant

circular RNA quantification tools
https://sourceforge.net/projects/ciri/files/CIRIquant
MIT License
27 stars 17 forks source link

Issue running prepDE.py #32

Open G-Molano-LA opened 3 years ago

G-Molano-LA commented 3 years ago

Hi, I was trying to to execute the script prepDE.py and I get the following error:

Traceback (most recent call last): File "utils/prepDE.py", line 266, in <module> transcript_len+=int(v[4])-int(v[3])+1 #because end coordinates are inclusive in GTF ValueError: invalid literal for int() with base 10: '14374r\x16("&/\xcf\xbe\xa9\xb16A\xf9\x04\x14\x1f\x89~\x13\xa5\x83\xff\xf9\xa6l\xa0\xeb\x97\xdb\x7f\x16\xe2|\x80]\xedr?\x0b\xd5\x7f\xb0\xac\x93\x0b5O\x13Q\xceR\x11\x0e\x89\xba}\xbf\x83aC\x8edW\x15\xe4\xfa}\xf3]'

Do you have any idea why this error is occurring and what I may do to address it?

Kevinzjy commented 3 years ago

Hi @G-Molano-LA , which version of StringTie and prepDE.py are you using?

The latest version of StringTie has already included prepDE.py along with other binary files, so maybe you could try running the prepDE.py from StringTie rather than that from the CIRIquant directory.

G-Molano-LA commented 3 years ago

I'm using the 2.1.7 version of StringTie. I've tried to running prepDE.py from StringTie but it raises the same error

Kevinzjy commented 3 years ago

What's your command line running prepDE.py? Could you post the content of the input sample list as well?