[Bioperl-l] dealing with large files

Amir Karger akarger at CGR.Harvard.edu
Thu Dec 20 13:52:51 EST 2007

> Amir Karger wrote:
> >> It would be nice to code up a lazy sequence object and related  
> >> parsers; maybe for the next dev release.
> > 
> > Also, BLAST parsing. Blasting the proteome against the 
> genome makes for
> > rather large result files.
> This has already been done. Use Bio::SearchIO::blast_pull. In a 
> situation like yours I dropped run time from 20223s to
> 951s (~20x faster) and memory usage from over 8GB to less 
> than 5GB (~40%
> less).

Not in 1.5.1. Is it in 1.5.2 or just in cvs? Is there a single file I
can put in my own perl lib for this, or does it require large bunches of
new code? (I'm guessing the latter.) We're about to upgrade to 1.5.2
here, but I don't see our whole center using CVS Bioperl.


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