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

[Jens-Konrad Preem]

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
>
> On Wed, Apr 10, 2013 at 08:08:39PM -0400, Eric McDonald wrote:
>> I believe that the 'filter-below-abund.py' script trims sequences. So, your
>> Perl script may need to also truncate the quality scores line down to the
>> length of the trimmed sequences.
>>
>> By the way, we are working on getting the scripts to output FASTQ if they
>> receive FASTQ inputs, but that functionality is not ready yet. You're
>> definitely not the only person interested in that functionality. ;-)
>>
>> Hope that helps,
>>    Eric
>>
>>
>>
>> On Wed, Apr 10, 2013 at 8:13 AM, Jens-Konrad Preem <jpreem at ut.ee> wrote:
>>
>>> Hi,
>>> I have just a quick question. Filter-below-abund takes a fastq file and
>>> outputs a fasta file.
>>> Can I make use of a Perl script that would take the names from the
>>> resulting file and add the quality scores from the previous file. As I
>>> understand nothing happens to the names or sequences - some of them just
>>> get culled.
>>>
>>> I want to try out the normalized data with some paired end reads
>>> assemblers that use quality scores/fastq files.
>>> I think its easier for me to write such Perl script than to modify
>>> filter-below-abund.py to output fastq.
>>>
>>> Not much of a python guy - though it seems that there shouldn't be too
>>> much work on replacing screed.fasta with screed.fastq etc., but I find it
>>> is quite often easier to write a few lines than to parse what someone else
>>> wrote and why and then try to modify it :D.
>>>
>>> Jens-Konrad Preem, MSc., University of Tartu
>>>
>>>
>>>
>>>
>>> ______________________________**_________________
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>>> khmer at lists.idyll.org
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>>>
>>
>>
>> -- 
>> Eric McDonald
>> HPC/Cloud Software Engineer
>>    for the Institute for Cyber-Enabled Research (iCER)
>>    and the Laboratory for Genomics, Evolution, and Development (GED)
>> Michigan State University
>> P: 517-355-8733
>> _______________________________________________
>> khmer mailing list
>> khmer at lists.idyll.org
>> http://lists.idyll.org/listinfo/khmer
>
So if I clone and build from the git page, those two scripts should now 
put out fastq as their output?
Or do they need some extra tags at the start time?.
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.
Jens