[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1216 (fwd)

[BHurwitz@twt.com]

  > Thank you so much for your reply.  I took a closer look at the output
from
  > blastn and megablast and the only difference is that the order of three
  > lines are switched around at the top of the hit result.  The
information is
  > the same but the order is reversed.  It seems to me that the output
from
  > blastall, whether it be blast or megablast should be the same format.
I
  > just wrote to NCBI and asked them if they were planning on changing the
  > format of output from megablast to match blastn.  Depending on their
reply,
  > I can write a new parser for megablast switching the order, but I hope
they
  > can fix it on their end since it seems kind of silly to have slightly
  > different output format from the same program (blastall).  Below is an
  > example of the lines that are switched in the output.

> Don't hold your breath - it is probably easier for us to fix it on our
end
> if it is really as simple as detecting the two - note that we can't
> parse blastcl3 output becuase it (again) deviates from their
> stablished BLAST format.

> I'm tracking differences in the different XML tag output from different
> versions of BLAST so will take a look at this as well.

That would be great.  I agree, I will probably be holding my breath for a
long time
if I wait for NCBI to fix this.  What's the best course of action?  Should
I just tweak
the BPlite.pm parser to handle this?  What does StandAloneBlast.pm use for
parsing?  Is it
Blast.pm?

   > PS.  I just started using bioperl and so far I love it!  One question,
I
   > noticed that the "-n" option in blastall (for megablast) is not
supported

> - it is an easy add - you just put it in the StandAloneBlast

> just just add a 'n' to the @BLASTALL_PARAMS, so in your code:
> use Bio::Tools::Run::StandAloneBlast;

> push @Bio::Tools::Run::StandAloneBlast::BLASTALL_PARAMS, 'n';

> I guess there is no reason we can't add it to the source file itsself if
> indeed this works.

> If you are interested in wrapping around megablast would need to create a
> megablast() method and the corresponding @MEGABLAST_PARAMS array to make

just adding "push @Bio::Tools::Run::StandAloneBlast::BLASTALL_PARAMS, 'n';"
in my script resulted in the following error.
------------- EXCEPTION  -------------
MSG: Unallowed parameter: n !
STACK Bio::Tools::Run::StandAloneBlast::AUTOLOAD
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:375
STACK toplevel ./besthit_footprint.pl:144

--------------------------------------

But when I added "n" to @BLASTALL_PARAMS in StandAloneBlast.pm it worked
just fine.  So, I think we just need to add "n" to @BLASTALL_PARAMS.  I
wonder if it is necessary to create a megablast() method since megablast is
a blastall parameter?

Thanks for all of your help!
Bonnie