[Bioperl-l] dealing with large files

Sendu Bala bix at sendu.me.uk
Thu Dec 20 13:48:29 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.
> Yes!
> 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%

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