[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1216 (fwd)
Fri, 21 Jun 2002 10:33:21 -0500
> Thank you so much for your reply. I took a closer look at the output
> 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
> the same but the order is reversed. It seems to me that the output
> blastall, whether it be blast or megablast should be the same format.
> 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
> I can write a new parser for megablast switching the order, but I hope
> 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
> 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
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
> PS. I just started using bioperl and so far I love it! One question,
> noticed that the "-n" option in blastall (for megablast) is not
> - 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 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!