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

[Razi Khaja]

Nope, not a bug, It's an enhancement though ;)  I implemented it so that I
could do a loss less transformation from BLAST report format to other
formats. You could consider that a use case. I also have additional patches
that parse other details from BLAST reports that aren't currently
implemented in Bio::SearchIO, and I'd like to contribute those as well,
however, I thought I'd start with this one.

Razi



On Mon, Mar 22, 2010 at 9:26 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> 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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