[Bioperl-l] BLAST parsing Question

[Wiepert, Mathieu]

Hi,

I believe the class to use is now Bio::SearchIO?  I'll send you a longwinded
program that has an example, or check out
http://docs.bioperl.org/releases/bioperl-1.0/Bio/SearchIO.html




my $searchio = new Bio::SearchIO(-format => 'blast',
                                 -file => 'blast.out');

-Mat

-----Original Message-----
From: Leonardo Marino-Ramirez [mailto:marino@tofu.tamu.edu]
Sent: Thursday, May 09, 2002 6:34 AM
To: Simon K. Chan
Cc: Bioperl Help
Subject: Re: [Bioperl-l] BLAST parsing Question


Dear Simon,

I encourage you to read the bioperl tutorial

http://bio.perl.org/Core/bptutorial.html

The module to use is BPlite. For usage see:

http://docs.bioperl.org/releases/bioperl-1.0/Bio/Tools/BPlite.html

Leonardo

On Wed, 8 May 2002, Simon K. Chan wrote:

> My fellow BioPerl-ers,
>
> It took me a couple of hours to realize that what I
> need to do is EXTREMELY common and that it's already
> been done.  D'oh!! :-0
>
> So, I made a fasta database by using the formatdb
> command.  I have a fasta file with a bunch of
> sequences.
>
> Example:
>
> fasta file: seq A, seq B, seq C
> db made with formatdb: seq 1, seq 2, seq 3
>
> I blast the sequences in the file against the
> database.
> So, let's say that seq A only hits seq 1 with a P
> value of 10e-100 and seq B only hits seq 1 with a P
> value of 2e-15.  Seq C hits nothing.  How would I pull
> out that Seq A matches Seq1 and that Seq C AND Seq B
> match nothing?
>
> I tried to do this with hashes where the keys were the
> matches from the db and the values were arrays with
> the P value and query name. But it go real messy.
> Yuck!  Does anyone know of a module or some other
> quick way of doing this?
>
> Thanks, all.
>
> =====
>
> #################
>
> Warmest Regards,
>
> Simon K. Chan - bioinformatics_rocks@yahoo.com
>
> "Great spirits have always encountered violent opposition from mediocre
minds."
>
> - Albert Einstein
>
>
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-- 

___ _/ _______________________________________________________________
   _/
  _/    _/      _/_/_/    Leonardo Marino-Ramirez   lmarino@tamu.edu
 _/    _/_/  _/_/    _/  Biochemistry Department, Texas A&M University
_/_/_/_/  _/  _/_/_/    2128 TAMU, College Station, TX 77843-2128, USA
     _/      _/     _/ Voice: (979) 862-4055   Fax: (979) 845-9274
___ _/      _/     _/ ________________________________________________

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