GFFUtils import error

Question

[GLFrey]

Hello,

I'm trying to build a database of my GFF3 file using GFFutils, however whenever I run the first command: "import GFFutils" I get the traceback:

In [1]: import GFFutils
Traceback (most recent call last):
File "/Users/user/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2862, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-1-431d87a82436>", line 1, in <module>
import GFFutils
File "/Users/juliannezickovich/GFFutils/GFFutils.py", line 76
raise ValueError, "specifying both chrom and name not supported"
                ^
SyntaxError: invalid syntax

Could anyone shed any light on this error for me? At this point, I've not specified any files so I've not provided any chromosomes or names, so I don't understand the error at all.

Thank you

[h.mon]

How did you install GFFutils?

I have to apologize to you, on your previous question, I pointed to the repository of a really old GFFutils, and a fork, not the original. Current GFFutils versions are fount at:

https://github.com/daler/gffutils

[GLFrey]

Hello h.mon,

Ah, I followed the installation instructions from the link you kindly provided yesterday. I followed the instructions in your new link and there's no error message any longer. It should have occurred to me to check the version. Thank you for your help as always, I really appreciate it.

Answer 1

[GenoMax]

Should that actually be import gffutils instead of import GFFutils (case difference).

[GLFrey]

Hello genomax,

You are correct. The previous link I followed for the instructions specified "import GFFutils", however, the newer version that seems to be working, and does not produce the above error is indeed "import gffutils".