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

[Kevin Clancy]

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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