[khmer] Unique reverse-complement

[Bintu, Bogdan]

Dear Titus,

Thanks for the prompt reply.

Tried what you suggested but sadly it did not solve it.

Any other suggestion?

Regards,

Bogdan



From: C. Titus Brown<mailto:ctbrown at ucdavis.edu>
Sent: Wednesday, December 7, 2016 3:32 PM
To: Bintu, Bogdan<mailto:bbintu at fas.harvard.edu>
Cc: khmer at lists.idyll.org<mailto:khmer at lists.idyll.org>
Subject: Re: [khmer] Unique reverse-complement



On Wed, Dec 07, 2016 at 08:18:31PM +0000, Bintu, Bogdan wrote:
> Dear Dr. Brown,
>
> I am a graduate student using your khmer package.
> I am trying to construct a khmer.Countgraph which is not degenerate between a sequence and its reverse complement.
> More explicitly, in python when running:
>
> import Khmer
> ht = khmer.Countgraph(17,10,1)
> ht.consume('GGCTTGCTCCAGCCATG')
> ht.get('CATGGCTGGAGCAAGCC')
>
> I would like the last line to return 0.
>
> As suggested in a different thread I tired modifying NO_UNIQUE_RC=0 to NO_UNIQUE_RC=1 in lib/Makefile and then run python setup.py install.
> But this did not solve my issue.
>
> Any help would be appreciated.

Hi Bogdan,

thanks for the email!

Can you try doing:

make clean
python setup.py install

after the modification?  That should work.

thanks,
--titus
--
C. Titus Brown, ctbrown at ucdavis.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/khmer/attachments/20161207/db8a371d/attachment.htm>