[Bioperl-l] Fwd: BIoPerl and user complaints.

Jason Stajich jason.stajich at duke.edu
Tue Sep 6 10:11:22 EDT 2005

Begin forwarded message:

> From: "Mcginnis, Scott (NIH/NLM/NCBI)" <mcginnis at ncbi.nlm.nih.gov>
> Date: September 6, 2005 9:38:10 AM EDT
> To: "'Barry Moore'" <bmoore at genetics.utah.edu>,  
> "'jason at bioperl.org'" <jason at bioperl.org>
> Subject: BIoPerl and user complaints.
> Dear Jason and Barry:
> We recently received an e-mail from a user complaining that a small  
> change
> to the format of the BLAST output resulted in a problem with the  
> BPLite
> parser.
> BPLite appears to be parsing the plain text output of the BLAST  
> results and
> simple change such as removing a colon form the output causes it to  
> not work
> properly.
> NCBI does not advocate the use of the plain text or HTML of BLAST  
> output as
> a means of accurately parsing the data. We reserve the right to  
> alter the
> appearance of "human readable" formats precisely to make them more  
> usable to
> human readers of the results. It's not convenient for us to tie the  
> human
> readable results down to a software compatible format.
> To this effect we make the ASN.1 and XML outputs available for  
> parsing the
> BLAST output. We support these formats and we will not alter or  
> change them
> without ample forewarning and support.
> You may wish to repair your BPLite program, but can I also ask that  
> you put
> some sort of disclaimer in it that it relies on a format which is  
> subject to
> change with out advanced notice.
> Thanks,
> Scott McGinnis.

Jason Stajich
Duke University

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