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Re: ePCR and data files

Dear Saira,

On Wed, Jun 19, 2019 at 02:12:59PM +0100, Saira Hussain wrote:
> > Seems you started by chance with one of the harder examples.
> > 
> Seems like that as well. I decided to start from the first bug
> (sequentially, maybe that wasn't a great idea!)

I filed the bugs in the sequence of usage measured by the user
popuplarity contest at the time of bug filing.  Once the open
bugs are closed I will provide you with another set of packages
which do not yet have any autopkgtest but some number of users.
You do not need to keep that sequence but you are free to pick
your prefered program (may be due to own use or whatever reason
you might have).

> > As far as I understand these data can be considered free.
> > > My exact search is as following (using Nucleotide):
> > > 
> > > ((chloroplast OR plastid) AND "complete genome" AND Embryophyta NOT (mi-
> > > tochondrion OR mitochondrial)) AND "Ginkgo biloba"[porgn:__txid3311]
> > 
> > I do not have any idea whether that is possible but if the way you
> > created those data is **easily** scriptable I would have a slight
> > preference to have a script that can be run over some data created via
> > web form.  However, if this would require extra work on your side just
> > do what you planed to do and add some README describing what you have
> > done to create that specific data set.
> > 
> No problem. I will try to use the NCBI API and write a script. I'll also use
> a README file describing the process in any case.

Very good!

> Another thing I discovered
> while I stumbled across an error on a database generation is that the
> documentation for the tool has been intentionally remove and the tool is
> deprecated in favour of a new, improved version incorporated with the NCBI
> Blast tool.
> Have a look here:
> https://ncbiinsights.ncbi.nlm.nih.gov/2017/06/28/e-pcr-is-retiring-use-primer-blast/

Yes, that is known (mentioned in the long description of the package).
However as you can see here


the number of active users (and we do only get the numbers from those
users who agree to submit popcon data) is non-zero.  So we also try to
support those users who for whatever reason are using deprecated

Kind regards



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