[Bioperl-l] Fwd: [Bioperl-guts-l] [Bug 3031] Unable to parse algorithm_reference from BLAST reports using Bio::SearchIO

[Smithies, Russell]

It's not really a bug if it was never implemented and it probably wasn't implemented because it wasn't needed.
Is there actually a use case where you'd programmatically need to access the algorithm reference from Blast results??
I'm sure I can't think of one.


--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Razi Khaja
> Sent: Tuesday, 23 March 2010 1:56 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [Bug 3031] Unable to parse
> algorithm_reference from BLAST reports using Bio::SearchIO
> 
> Hello All,
> 
> I've submitted a patch (blast.pm.diff) to bugzilla to enhance
> Bio/SearchIO/
> blast.pm to be able to parse the algorithm_reference from BLAST reports.
> I've also submitted a patch (blast.t.diff) of 26 additional tests to parse
> the algorithm_reference from many of the BLAST reports in the t/data dir
> in
> bioperl-live.
> 
> I'd like to get the patch into bioperl-live and would like someone to
> review
> the patch and tests.
> 
> If the architecture for BLAST report parsing is changing, can someone let
> me
> know and I can contribute my efforts there.
> 
> Below are links to bugzilla.
> 
> Thanks,
> 
> Razi Khaja
> 
> ---------- Forwarded message ----------
> From: <bugzilla-daemon at portal.open-bio.org>
> Date: Fri, Mar 19, 2010 at 11:25 AM
> Subject: [Bioperl-guts-l] [Bug 3031] Unable to parse algorithm_reference
> from BLAST reports using Bio::SearchIO
> To: bioperl-guts-l at bioperl.org
> 
> 
> http://bugzilla.open-bio.org/show_bug.cgi?id=3031
> 
> 
> 
> 
> 
> ------- Comment #2 from razi.khaja at gmail.com  2010-03-19 11:25 EST -------
> Created an attachment (id=1462)
>  --> (http://bugzilla.open-bio.org/attachment.cgi?id=1462&action=view)
> patch for t/SearchIO/blast.t to perform 26 additional tests to parse
> algorithm_reference from many BLAST report files
> 
> 
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