Question: GFFUtils import error
1
gravatar for GLFrey
12 months ago by
GLFrey20
Montana
GLFrey20 wrote:

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

gffutils • 523 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by GLFrey20

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

ADD REPLYlink written 12 months ago by h.mon26k

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.

ADD REPLYlink written 12 months ago by GLFrey20
0
gravatar for genomax
12 months ago by
genomax70k
United States
genomax70k wrote:

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

ADD COMMENTlink written 12 months ago by genomax70k

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".

ADD REPLYlink written 12 months ago by GLFrey20
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