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Re: ePCR fetch

Hi Saira,

On Mon, Jun 24, 2019 at 02:20:29PM +0100, Saira Hussain wrote:
> I pushed towards the master my python script to be used for fetching data
> from the database in order to be further modified and used for testing of
> the ePCR package.

I confirm your fetch_fasta.py script works (=creates a data file).  I've
added a #! line on top which is more convenient since you can call the
script directly.
> I have one problem down the line, as ePCR isn't happy with my final
> converted file but I am working on it.

Could you please specify your problem?  What command line are you
calling and what is the output of this command?  What error is
> Meanwhile could you give me some feedback? I hope a Python script is fine as
> it's quite comfortable for me to write Python.

This script is not yet the test for ePCR - it just *documents* how the
used data are obtained.  In other words: You can write your
documentation in whatever language you want (some comment in the header
what this script is doing and why the data are fetched that way would be
> Could I write further tests in Python instead of sh or bash scripts are
> preferred?

In principle the tests can be written in any language but I admit I do
not see a big need for it.  In all tests written for Debian Med
maintained packages shell was perfectly sufficient and we have a very
frequently used template[1] where you usually simply add a program call.
I'd consider a Python script unnecessary overkill and you should provide
more reasons why you think in this case some higher level language would
be better.
> Looking forward to your comments and suggestions,

Kind regards


[1] https://salsa.debian.org/med-team/community/package_template/blob/master/debian/tests/run-unit-test 


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