[Bioperl-l] searchio/blast

Bernd Web bernd.web at gmail.com
Thu Jan 31 05:48:15 EST 2008


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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