[Bioperl-l] searchio/blast

Chris Fields cjfields at uiuc.edu
Thu Jan 31 07:39:46 EST 2008

The easiest way to take care of these (so we don't forget about them  
and can track changes) is to add them as BioPerl bugs/enhancement  
requests to bugzilla, along with example reports and code.


On Jan 31, 2008, at 4:48 AM, Bernd Web wrote:

> Hi,
> I noticed that the HTMLWriter output for a BLAST report may not be
> correct if more than one sequence was "blasted".
> After the BLAST report of the first sequence the report is ended with:
> Search Parameters
> Parameter	Value
> Search Statistics
> Statistic	Value
> Produced by Bioperl module Bio::SearchIO::Writer::HTMLResultWriter on
> Thu Jan 31 11:35:51 2008
> Revision: $Id: HTMLResultWriter.pm,v 1.41 2006/10/02 04:45:37  
> tseemann Exp $
> Then the second HTML blast report follows.
> Although maybe generally 1 sequence is blasted by a user requiring
> HTML output, this may be nice to fix?
> Also for the HTML Writer of FastA reports the statistics section is  
> empty,
> An additional issue with HTMLWriter  containing more than 1 BLAST
> report is the following:
> When a sequence ID occurs more than once, the link (on the E-value) is
> to the first occurrence since it is not report specific.
> In case the above is regarded as unwanted, I'd be happy to make a
> concise example with code.
> Best regards,
> Bernd
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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