Re: ePCR fetch
Hi Saira,
On Tue, Jun 25, 2019 at 12:50:28PM +0100, Saira Hussain wrote:
> >
> > 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.
:-)
> > 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
Argg, seems to be tricky. But finally its good to know also from a
users perspective.
> 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 :)
No problem. Some things are just more tricky. Keep on your good work
Andreas.
--
http://fam-tille.de
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