[Bioperl-l] dealing with large files
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.
> 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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