I am trying to run python3.8.2 with Ubuntu20.04.
I successfully installed python3.8.2 and velocyto, then via velocyto --help command I checked that the package has been successfully installed.
[email protected]:/usr/local/lib/python3.8$ velocyto --help
However since I want to use velocyto within python3.8 (not in Ubuntu terminal), I executed python3.8 via:
[email protected]:/usr/local/lib/python3.8$ python3.8 Python 3.8.2 (default, Apr 1 2021, 18:47:06) [GCC 9.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>>
and I successfully import velocyto without any error via:
import velocyto as vcy
But when I run velocyto --help, I bumped into NameError.
velocyto --help
Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'velocyto' is not defined
How can I normally run velocyto within python3.8 (from Ubuntu)?
I appreciate your help in advance.
Answer
You imported it as vcy, not velocyto. However, if you do vcy --help, you’re going to get another NameError saying that help is not defined, because velocyto --help is a shell command, not a Python command.
You can simply go ahead and start using it. For example, the tutorial says you can try this:
vlm = vcy.VelocytoLoom("YourData.loom")