[khmer] questions about khmer utilities

Michael R. Crusoe mcrusoe at msu.edu
Mon Aug 19 18:24:48 PDT 2013

Hello Ken,

Did you install khmer from the master branch or the bleeding-edge branch?

Can you share with us the four complete command lines you executed?

On Mon, Aug 19, 2013 at 8:50 PM, Kenlee Nakasugi <
kenlee.nakasugi at sydney.edu.au> wrote:

> Hi,
> I'm just starting to do some kmer-type analyses on my read data.
> I am trying to compare/find any differences in two different read
> datasets, and am trying to get some basic k-mer stats, but more importantly
> trying to figure out what would be the best type of comparison to do.
> I have already generated the hash (.kh) and hist (.hist) via the
> load-into-counting.py and abundance-dist.py scripts from khmer v0.4.
> Now from http://khmer.readthedocs.org/en/latest/blog-posts.html , i
> wanted to get the abundance by position, and hi-lo kmer distributions, but
> are the scripts listed there (and found in sandbox directory in khmer
> distribution) compatible with the output from 'load-into-counting.py and
> abundance-dist.py' ?
> I tried inputting the .hist and hash tables but getting errors like:
> ##
> python /usr/local/bin/khmer/sandbox/abundance-hist-by-position.py
> R1.k32.hist
> ... 0
> Traceback (most recent call last):
>   File "/usr/local/bin/khmer/sandbox/abundance-hist-by-position.py", line
> 15, in <module>
>     countSum[i] += int(tok[i])
> ValueError: invalid literal for int() with base 10: '0.617'
> ##
> Do I need to run these scripts from
> http://khmer.readthedocs.org/en/latest/blog-posts.html from scratch ?
> And any other types of comparisions useful?
> Any advice appreciated!
> Cheers,
> Ken
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Michael R. Crusoe     Software Engineer     mcrusoe at msu.edu
 @ the lab for Genomics, Evolution, and Development (GED)
  home of the Khmer software suite   http://ged.msu.edu/
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