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

[C. Titus Brown]

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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> >
> 
> 
> 
> -- 
> 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

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