Re: ePCR fetch

[Saira Hussain <saira.h0213@zoho.com>]

On 6/24/19 2:55 PM, Andreas Tille wrote:
> Hi Saira,
Hi Andreas,
> 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.
That's great. I will edit the heading and add some more steps in that 
script.
> > 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
> happening?
>   
Finally! I solved my problem after two days of trying different things. 
The problem is that to do an re-PCR comparison there need to be 
generated a few different files (starting from fasta and converting it 
using different tools such as fahash/famap etc). One of the files need 
to be the input primer for the ePCR process (short single-stranded 
nucleic acid).

As you will see on the new files pushed my primer is the following:
rbcL1/rbcLA     TTGGCAGCATTYCGAGTAACTCC         CCTTTRTAACGATCAAGRC

Alas, the space between the sequences isn't a space (or spaces) as I 
expected but a TAB! This resulted in the error I was getting:

vagrant@contrib-testing:~/or-debian-19/epcr/debian/tests$ ../../re-PCR 
-S ginko.hash -n 5 -g 0 -d 100-300 -o rbcL5.rePCR rbcL-primer.txt
! Fatal: format error in file rbcL-primer.txt

Finally I went through the source and find the problem!

I am going to send more files for review till the end of the day and 
hopefully finalise this test after quite some effort and pain :) 
Hopefully the next one would be way faster :)

Best
SH
> > 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
> helpful).
>   
> > 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
>
>         Andreas.
>
> [1] https://salsa.debian.org/med-team/community/package_template/blob/master/debian/tests/run-unit-test