[khmer] filter-below-abund.py fastq scores from previous file

C. Titus Brown ctb at msu.edu
Sat Apr 20 07:26:58 PDT 2013


On Sat, Apr 20, 2013 at 09:21:04AM +0300, Jens-Konrad Preem wrote:
> OK. The filter-below-abund.py from sandbox did not produce an fastq file  
> (from a fastq file foo.fastq.keep, it produced fasta file  
> foo.fastq.keep.below),
> The khmer was built at 19th of April with git clone  
> git://github.com/ged-lab/khmer.git*, and make clean all. Havent checked  
> filter abund yet.
> Jens
> *should clone the master branch? (Not much of git user)

Yes, that should have worked.  How disappointing :)

The updates were to python/khmer/thread_utils.py; for example, see line
168:

  https://github.com/ged-lab/khmer/blob/master/python/khmer/thread_utils.py#L168

My first guess is that maybe you have multiple versions of khmer lying
around, or some such; could you try

	import khmer
	print khmer

inside of Python, and make sure that the source file from 'khmer' is loaded
is from the right place to have been checked out?  You may need to modify
your PYTHONPATH to get things to work right.

I've added a test for the FASTQ output that is now on master, too;
look for test_filter_abund_3() in tests/test_scripts.py.

Whether or not the PYTHONPATH is your particular problem, I think now that more
people are using khmer, we should start talking about doing installation
better; I still prefer to use it out of a build directory, but I'm a developer
:).  I'll file an issue (now #47).

Here's what I just did:

---
git clone https://github.com/ged-lab/khmer.git
cd khmer
make clean all test
export PYTHONPATH=./python/
python scripts/load-into-counting.py 25k data/25k.fq.gz 
python scripts/filter-abund.py 25k data/25k.fq.gz
head -4 25k.fq.gz.abundfilt
---

the output of the last command is:

@895:1:1:1264:15854/1
CGTGATGATGTGCTTGCGGCCGGAGGGCCTGT
+
``W__ZZ__ZSOJNNNQWSQZ\^X\W__

So it can, at least on one person's computer, work :)

And, Jens, thanks for your patience!

cheers,
--titus

> On 04/19/2013 07:24 PM, C. Titus Brown wrote:
>> On Fri, Apr 19, 2013 at 12:14:48PM +0300, Jens-Konrad Preem wrote:
>>> On 04/17/2013 07:21 AM, C. Titus Brown wrote:
>>>> I have hacked this into ged-lab/master branch for filter-abund and
>>>> filter-below-abund.  Let me know if it works (or doesn't work!)
>>>>
>>>> cheers,
>>>> --titus
>>>>
>>> So if I clone and build from the git page, those two scripts should now
>>> put out fastq as their output?
>> Yes.
>>
>>> Or do they need some extra tags at the start time?.
>> Nope.
>>
>>> As a note - the sandbox scripts do not have the #!/usr/bin/env python
>>> line  and also need to be chmod +x in addition to this to be started.
>>> Don't know if it is so as some thought out design issue/feature or not,
>>> anyway thought I'd mention it.
>> Thanks for pointing this out!
>>
>> --t
>
> -- 
> Jens-Konrad Preem, MSc, University of Tartu
>

-- 
C. Titus Brown, ctb at msu.edu




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