[Tutor] Pass arguments from bash script to embedded python script

[David L Neil]

On 22/10/19 2:45 AM, Stephen P. Molnar wrote:
> First of all, let me emphasize that this is not a homework assignment.
> 
> I have a large number of data files form a Quantum Chemistry program 
> which all have the same format.
> 
> I have written a short python script to extract the data required for 
> another program.
...

> and I have a bash script in which I have embedded the python script:
...

> The ligand.list for the bash file have the format:
>>
>>> fname = ['C-VX3.log', '15-7.log', '14-7.log']
>>> fname1 = ['C-VX3', '15-7', '14-7'
> 
> where fname and fname1 are three typical data files.
> 
> my problem is how do I pass the argument's in the two files from the 
> bash script to the python script? It has been suggested to me that the 
> solution is an implementation of the sys/.argv function but it seems 
> that every reference that I can find goes the other way from python to 
> bash.
> 
> So my question is what question should I be goggling? I am not looking 
> for someone to write the script for me, but pointers in the correct 
> direction.


- over-simplified but useful to gain context,
How to use sys.argv in Python:
https://www.pythonforbeginners.com/system/python-sys-argv

- the recommended* Python library is argparse
https://docs.python.org/3/library/argparse.html
(much of the discussion/tutorial deals with offering 'help' responses to 
incorrect cmdLN instruction, but that can be skipped in a personal 
implementation)


* previous coding-tools have been deprecated, even as they appear more 
frequently in web-tutorials, etc.


May I recommend that you do as much as possible in Python, even 
(assuming I've understood the approach) reading the 'command files' 
there, rather than trying to do more in BASH.


PS I replied to your (previous) personal msg, but SBC's email-blocker, 
blocked!
-- 
Regards =dn