[khmer] questions about khmer utilities
kenlee.nakasugi at sydney.edu.au
Mon Aug 19 17:50:22 PDT 2013
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
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!
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