[Bioperl-l] Bio::Blast object question

[Jason Eric Stajich]

My first reaction would be to try using Bio::Tools::BPlite, but this might
not have all the same features that you need for parsing - you'll have to
decide about that.  I'm not sure how much work has been done to calibrate
blast parsing on the patent dbs but if they are weirdly formatted or
contain () or some other weird characters - you could possible fix this by
preprocessing the report before hand - 'sed s/\(/\[/' ... etc

-jason
On Thu, 20 Sep 2001, Zhao, David  [PRI Non J&J] wrote:

> Hi Jason,
> I'm using bioperl 0.7.1, and Bio::Tools:Blast module to parse blast report.
> The sequence database that gave me such as were actually NCBI databases
> (patnt, pataa).
> The description using bioperl module looks like this:
>
> Sequence 1 from patent US
> instead of
> Sequence 1 from patent US 6096507
> The patent number somehow got cut off.
> Thanks,
> David
>
>
> > -----Original Message-----
> > From:	Jason Eric Stajich [SMTP:jason@cgt.mc.duke.edu]
> > Sent:	Thursday, September 20, 2001 6:17 PM
> > To:	Zhao, David  [PRI Non J&J]
> > Cc:	'bioperl-l@bioperl.org'
> > Subject:	Re: [Bioperl-l] Bio::Blast object question
> >
> > David - I've struggled with this sometimes with reports as well when the
> > query database is badly formatted - are you working with a NCBI blastdb or
> > your own ?  I would pull out the line from the db which this hit sequence
> > is from
> > (% grep "^>.*accession") -- where accession is the accession are you
> > are having trouble with.
> >
> > If you can send that information to the list we can probably figure out a
> > way to patch the parser.  To help us better need to know what he Blast
> > module name is (Bio::Tools::Blast or Bio::Tools::BPlite) and what version
> > of bioperl you are using.
> >
> > -jason
> >
> > On Thu, 20 Sep 2001, Zhao, David  [PRI Non J&J] wrote:
> >
> > > Hi all,
> > > When I use $hit->desc() method parsing blast report, sometimes I only
> > get
> > > partial description of the sequence,
> > > what should I do to get the full description?
> > > Thanks,
> > > David
> > >
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
> >
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu