[khmer] Extracting kmer sequences from khmer output

[Miller, Ruth]

Hi,

Thanks for getting back to me. I am glad that this functionality is
available.
I downloaded count-kmers.py, but I am having some problems, because it
seems to require a module that I don¹t have, namely load_countgraph,
because I get the error:

hashtable from kmers.g
Traceback (most recent call last):
  File "/usr/local/packages/khmer/khmer/sandbox/count-kmers.py", line 105,
in <module>
    main()
  File "/usr/local/packages/khmer/khmer/sandbox/count-kmers.py", line 79,
in main
    countgraph = khmer.load_countgraph(
AttributeError: 'module' object has no attribute Œload_countgraph'


I have downloaded the latest version of khmer, so I don¹t think that is
the problem.  And I can¹t see a script called load_countgraph in the
sandbox downloads. Is load_countgraph available somewhere?

Thanks,

Ruth

On 2015-09-19, 6:08 AM, "C. Titus Brown" <ctbrown at ucdavis.edu> wrote:

>On Fri, Sep 18, 2015 at 03:25:39PM -0700, Miller, Ruth wrote:
>> Hi,
>> 
>> I am hoping to get a list of the sequence of each kmer identified from
>>my dataset and it?s abundance. This would allow me to compare the
>>abundance of different kmers in my sample set, to see whether certain
>>samples cluster together based on the abundance of kmers present.
>> 
>> Is there a way to do this in khmer?
>> 
>> Thanks,
>> 
>> Ruth
>
>Hi Ruth,
>
>yep! In khmer 2.0 we've added the 'count-kmers.py' and
>'count-kmers-single.py'
>scripts in the sandbox/ directory; you can either do
>
>	load-into-counting.py kmers.g file1.fq file2.fq file3.fq ...
>	sandbox/count-kmers.py kmers.g file1.fq
>
>if you have multiple files, or
>
>	sandbox/count-kmers-single.py file1.fq
>
>The graph size parameters (-M, or -x / -N) still apply for setting the
>size of the kmer countgraph database; see
>
>	http://khmer.readthedocs.org/en/v2.0/user/choosing-table-sizes.html
>
>for more info.
>
>Now, the other problem is that count-kmers.py/count-kmers-single.py aren't
>installed with 'pip install khmer' because they're not yet part of the
>supported scripts.  So you'll need to grab them from the URLs below,
>
>https://github.com/dib-lab/khmer/blob/master/sandbox/count-kmers.py
>https://github.com/dib-lab/khmer/blob/master/sandbox/count-kmers-single.py
>
>(click 'Raw' to download the text file) *or* check out the git repository
>and call them from sandbox.
>
>Let me know if you have any problems --
>
>best,
>--titus
>-- 
>C. Titus Brown, ctbrown at ucdavis.edu