[khmer] cannot run the latest version of normalize-by-median.py

[C. Titus Brown]

On Aug 27, 2013, at 9:55 PM, "C. Titus Brown" <ctb at msu.edu> wrote:

> On Wed, Aug 28, 2013 at 08:03:57AM +0800, cy_jiang wrote:
>> Hi Titus,
>> 
>> I have downloaded the latest version of khmer and tried to run the normalize-by-median.py (command line:/khmer/scripts/normalize-by-median.py -k 20 -C 20 -x 7.5e9 -N 4 --savehash mh.kh T_allR1R2.py), but it prompted up with the following information:
>> 
>> PARAMETERS:
>> Traceback (most recent call last):
>>  File "/home/work/khmer/scripts/normalize-by-median.py", line 241, in <module>
>>    main()
>>  File "/home/work/khmer/scripts/normalize-by-median.py", line 140, in main
>>    ' - kmer size =    {:d} \t\t(-k)'.format(args.ksize)
>> ValueError: zero length field name in format
>> 
>> This command line ran pretty well with the older version of khmer. Can you give me a clue what is going on there?
> 
> That's weird... you're setting k properly on the command line... hmm.
> 
> What does 'python -V' return?

I'm told that this is a result of using an older version of Python.  We'll implement a fix shortly, OR (and I'm *not* recommending this) you can use python2.7.

apologies,
--titus