[khmer] find-knots.py error: what are the 2 arguments?

[C. Titus Brown]

yes!

http://khmer-recipes.readthedocs.org/en/latest/001-extract-reads-by-coverage/index.html

(If you're going to tell us we need better discoverability of our
documentation, we know :)

--titus

On Wed, Jun 03, 2015 at 06:10:23PM +0300, Diane Hatziioanou wrote:
> Thank you very much for the quick responses and tips, I'll battle that
> guide out tomorrow, another dumb question I have is is there any easy way
> to make a graph out of the histograms khmer makes to see if I have neat
> separate peaks of khmer distributions? Here is the sort of thing I'm
> looking for : http://ged.msu.edu/angus/_images/stamps-reads.png
> 
> Thanks in advance!
> Diane
> 
> 
> -- 
> Dr Diane Hatziioanou
> Greek Mobile: (+30)6909403373
> UK Mobile: (+44)7779516625www.linkedin.com/in/dhatziioanou/https://twitter.com/DianeHIoanou
> 
> 
> On 3 June 2015 at 16:50, C. Titus Brown <ctbrown at ucdavis.edu> wrote:
> 
> > Yes, but what I really wanted to do was point Diane at a somewhat more
> > friendly set of instructions --
> >
> > so, here!
> >
> > https://khmer-protocols.readthedocs.org/en/latest/metagenomics/index.html
> >
> > More soon...
> >
> > best,
> > --titus
> >
> > On Wed, Jun 03, 2015 at 09:47:57AM -0400, Ramakrishnan Srinivasan wrote:
> > > Titus,
> > >
> > > Would adding a False to check_space() help?
> > >
> > > --
> > > Ram
> > >
> > > On Wed, Jun 3, 2015 at 9:43 AM, C. Titus Brown <ctbrown at ucdavis.edu>
> > wrote:
> > >
> > > > Hi Diane, sorry, that's a bug in our code :(.
> > > >
> > > > More in a bit --
> > > >
> > > > best,
> > > > --titus
> > > >
> > > > On Wed, Jun 03, 2015 at 04:40:36PM +0300, Diane Hatziioanou wrote:
> > > > >  Hello,
> > > > >
> > > > > I'm using khmer for the first time and have encountered a problem.
> > > > > I'm running khmer version 1.4 and also using screed version 0.8.
> > > > >
> > > > > I have a dataset which is metagenomic-like with excessive coverage
> > which
> > > > I
> > > > > have been following the basic metagenomic pipleline from the khmer
> > page:
> > > > >
> > > > >    1. Apply single-pass digital normalization: normalize-by-median to
> > > > C=20
> > > > >
> > > > >       2. Run filter-below-abund with C=100
> > > > >
> > > > >    1. Partition reads with load-graph, etc. etc.
> > > > >
> > > > > I did the load-graph.py, make-initial-stoptags.py and
> > partition-graph.py
> > > > > successfully following the guide at
> > > > >
> > http://khmer.readthedocs.org/en/latest/user/partitioning-big-data.html
> > > > and
> > > > > no matter what I do I can not make the find-knots.py work.
> > > > >
> > > > > The command I give is:
> > > > >
> > > > > find-knots.py -N 4 -x 8e9 C100Graph2 &
> > > > >
> > > > > I've also tried:
> > > > >
> > > > > find-knots.py C100Graph2 &
> > > > >
> > > > > and:
> > > > >
> > > > > find-knots.py C100Graph2 C100Graph2 &
> > > > >
> > > > > the message I always get is:
> > > > >
> > > > > Traceback (most recent call last):
> > > > >   File "/usr/local/bin/find-knots.py", line 154, in <module>
> > > > >     main()
> > > > >   File "/usr/local/bin/find-knots.py", line 95, in main
> > > > >     check_space(infiles)
> > > > > TypeError: check_space() takes at least 2 arguments (1 given)
> > > > >
> > > > > I can't find any help anywhere which described the two arguments
> > needed,
> > > > > all the examples i've seen only have one! Please let me know if you
> > can
> > > > see
> > > > > what I'm doing wrongor if this is a known problem.
> > > > >
> > > > >
> > > > > Yours sincerely,
> > > > >
> > > > > Artemis
> > > > > --
> > > > > Dr Diane Hatziioanou
> > > > > Greek Mobile: (+30)6909403373
> > > > > UK Mobile: (+44)7779516625
> > > > > www.linkedin.com/in/dhatziioanou/
> > > > > https://twitter.com/DianeHIoanou
> > > >
> > > > > _______________________________________________
> > > > > khmer mailing list
> > > > > khmer at lists.idyll.org
> > > > > http://lists.idyll.org/listinfo/khmer
> > > >
> > > >
> > > > --
> > > > C. Titus Brown, ctbrown at ucdavis.edu
> > > >
> > > > _______________________________________________
> > > > khmer mailing list
> > > > khmer at lists.idyll.org
> > > > http://lists.idyll.org/listinfo/khmer
> > > >
> >
> > --
> > C. Titus Brown, ctbrown at ucdavis.edu
> >

-- 
C. Titus Brown, ctbrown at ucdavis.edu