[Bioperl-l] Call to users/developers -- user cases that bring Bioperl to its knees

Albert Vilella avilella at gmail.com
Wed Feb 25 09:00:07 EST 2009


Any parameters in particular for the script?

Can you give me yours?

On Wed, Feb 25, 2009 at 6:11 AM, Charles Plessy
<charles-listes+bioperl at plessy.org> wrote:
> Le Mon, Feb 23, 2009 at 04:06:21PM +0000, Albert Vilella a écrit :
>> Can interested users/developers provide a URL with a dataset that
>> brings bioperl to its knees in
>> terms of CPU usage for say, about 1h?
> Dear Albert,
> I do not know if it fits your requirements, but I found that bp_seqconvert or
> bp_sreformat are not fast enough to be used efficiently with million of
> sequences in fastq format.
> You can download an example file here (that I have chosen randomly):
> ftp://ftp.era.ebi.ac.uk/vol1/fastq/ERR002/ERR002479/ERR002479_2.fastq.gz
> This file will give an error as the sequence name is not duplicated in the
> quality header, but I compared with a local file that does not have this
> problem, and confirmed that the error is not the slowing factor.
> (Unfortunately, I could not find public fastq files in which the file name is
> given in both the sequence and quality header, probably because it makes the
> file heavier).
> Have a nice day,
> --
> Charles Plessy
> Tsurumi, Kanagawa, Japan
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