[BioSQL-l] Timing importing GenBank files into BioSQL

Peter biopython at maubp.freeserve.co.uk
Mon Aug 18 17:41:58 UTC 2008


Peter wrote:
>>> I'm wondering if the BioPerl time is typical (I hope not), and if
>>> there are any computationally intensive or otherwise slow things it
>>> does that BioPython might be skipping (checksums? fetching taxonomy?)

Nick wrote:
>> I also found that BioPython was faster than BioPerl at importing the same
>> GenBank file.

If anyone else with at least two of BioPerl, BioJava, BioRuby and
Biopython installed could try this example, and report their findings,
that would be interesting.
i.e. time importing the small NC_005213.1 and medium sized NC_000913.2
genbank files linked to at the start of this thread into an empty
BioSQL database.

Thanks,

Peter



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