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

[Albert Vilella]

Hi Kevin,

Can you provide with a script and an input file or a pointer to one?

On Wed, Feb 25, 2009 at 5:05 PM, Kevin Clancy <kpclancy at hotmail.com> wrote:
>
> Hello Albert
>
>
>
> I recently had a  project involving finding all the restriction sites for a SAGE cutter on chromosome 21. This seemed to take a very long period of time to complete. In the end I had to take another approach to find these sites involving regular expressions.
>
>
>
> kevin
>
>> Date: Wed, 25 Feb 2009 15:11:57 +0900
>> From: charles-listes+bioperl at plessy.org
>> To: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] Call to users/developers -- user cases that bring Bioperl to its knees
>>
>> 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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