Running python3.8.2 in Ubuntu

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")