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
