Siddhartha Basu | 7 Feb 17:38 2013
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Re: FASTQ, was Re:BioPerl long-term, was Re: dependencies on perl version

Another approach might be use map-reduce(Hadoop) if possible. I have
seen one implementation in biopython's GFF3 parser.
http://bcbio.wordpress.com/2009/03/22/mapreduce-implementation-of-gff-parsing-for-biopython/

-siddhartha

On Thu, 07 Feb 2013, Aaron Mackey wrote:

> e.g., a pull-based FASTQ parser that did nothing else at the top level but
> "chunk" the file into as-yet-unparsed four-line blobs could appear to work
> very fast, if the user code did nothing but count the number of entries:
> 
>   while (my $seq = $seqio->nextseq) { $ct++ };
> 
> in other words, you defer *everything* except the minimal amount of
> parsing/logic required to detect object boundaries.
> 
> This is, in fact, the exact opposite of the event-based SearchIO "push"
> parsers, which always perform the most parsing possible, despite the user
> never accessing most of the material.
> 
> Lastly, with respect to performance, if the parsing/object building
> operation is not simply IO bound, then parallel parser/object-building CPU
> threads could be considered, which could then dynamically adapt to
> pre-parse attributes (e.g. quality scores) that the calling code was
> actually using.  What's the state of thread-safe Perl these days?
> 
> -Aaron
> 
> 
> On Thu, Feb 7, 2013 at 10:56 AM, Fields, Christopher J <
> cjfields <at> illinois.edu> wrote:
> 
> > This will likely be the approach for more NGS-friendly Bio::Seq class.
> >  Calculation of the PHRED scores could also be deferred until needed.
> >
> > seqtk has some C-based methods that we could possibly take advantage of,
> > but will have to look into it.
> >
> > chris
> >
> > On Feb 7, 2013, at 9:25 AM, Aaron Mackey <amackey <at> virginia.edu> wrote:
> >
> > > You might also want to consider a lazy/pull-based parser to defer
> > parsing/object-building for pieces of the object that don't get used.  This
> > also usually provides some error tolerance.
> > >
> > > -Aaron
> >
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Gmane