[Bioperl-l] Barry's challenge

[Jay Hannah]

On Nov 7, 2005, at 8:53 AM, Barry Moore wrote:
> Jason Stajich, who has been one of the lead developers in bioperl for
> many years now, mentioned last week that:
>
> "Tools::StandAloneBlast  could DEFINITELY be improved and needs people
> to adopt it...."

I'll try. :)

> P.S.  Write a script to use bioperl to blast search the following
> sequence against a local copy of the nr database and decide what 
> protein
> it is from and why this protein was your friend last Friday night.
> MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA

Thanks for the challenge!! Sweet!

... A little help? -grin-

I installed bioperl, blast, and 2.6GB of nr*

~/src/blast-2.2.12/data $ du -k -c nr*
826904  nr.00.phr
22664   nr.00.pin
43776   nr.00.pnd
172     nr.00.pni
22664   nr.00.ppd
92      nr.00.ppi
593320  nr.00.psd
12920   nr.00.psi
976564  nr.00.psq
33252   nr.01.phr
964     nr.01.pin
1756    nr.01.pnd
8       nr.01.pni
964     nr.01.ppd
4       nr.01.ppi
21068   nr.01.psd
460     nr.01.psi
42436   nr.01.psq
4       nr.pal
2599992 total

And then threw your challenge in a file

$ cat barry.txt
MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA

But then my program (1) sees barry.txt, but isn't reading it...?

$ cat j.pl

use Bio::Tools::Run::StandAloneBlast;
$ENV{BLASTDIR} = '/Users/jhannah/src/blast-2.2.12';

@params = ('database' => 'nr.00','outfile' => 'j.out');

$factory = Bio::Tools::Run::StandAloneBlast->new(@params);

$str = Bio::SeqIO->new(-file=>'barry.txt' ,
                        -format => 'Fasta' );
$input = $str->next_seq();
$input2 = $str->next_seq();
$blast_report = $factory->blastall($input);

$ perl j.pl

-------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet []
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------

So since I have no idea what I'm doing I'm hoping you can help.

Thanks! I'm 2.6GB+ bio-smarter than I was last week. -laugh-

j