[Bioperl-l] changing matrix parameter on blastp

[incenp24@netscape.net]

Thanks Brian,
I hadn't got an uptodate examples directory but have found the
standaloneblast.pl script  now.
this works fine e.g.,
my @params = ('prog' => $progname,
        'data' => $database_name,
        'MATRIX' => 'BLOSUM45',
        'GAP' => 11,
        'EXTENSION' => 1);
A factory object also has set methods for these e.g, $factory->MATRIX('BLOSUM45');
So it was just the capitalization of the parameters that was needed .
BUT
this doesn't work for remote blast, it still ignores the change in 
matrix settings. 
Very grateful for any more ideas!
Thank you
Richard

Dr Richard Adams
Molecular Medicine Centre
University of Edinburgh UK

 "Brian Osborne" <brian_osborne@cognia.com> wrote:

>Richard,
>
>I can't say I know the answer but have you looked at the script
>standaloneblast.pl in the examples/ directory? It contains code that
>attempts to set the matrix. I'd be curious to know if this code works for
>you.
>
>Brian O.
>
>PS Here is how I traverse a Unix directory tree searching for text files
>containing a particular word in a case-insensitive manner (obviously I'm
>looking for *.pl files containing the word 'matrix'):
>
>find . -name '*.pl' | xargs grep -i -l matrix
>
>My apologies if you knew this already.
>
>-----Original Message-----
>From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
>Behalf Of incenp24@netscape.net
>Sent: Wednesday, July 10, 2002 6:38 AM
>To: bioperl-l@bioperl.org
>Subject: [Bioperl-l] changing matrix parameter on blastp
>
>Hello,
>I'm fairly new to BioPerl so I hope this isn't a dumb question.
>I'm trying to alter blastp to be like the "blast 2 short nearly identical
>peptides' option. I can change the expect value fine but am having problems
>changing the matrix/gapopen/gapextend parameters, and to swithc off repeat
>masking.
>I'm trying to change the matrix parameter from the default
>BLOSUM62 to PAM30 for both standalone and remoteblast searches.
>Using -M PAM30 has always worked from the command line,
>but using
>my $factory = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp',
>                          -data => 'nr',
>                         -matrix => 'PAM30')
>and then accessing the matrix from the report
>print "matrix is ", $result->get_parameter('matrix'), "\n";
>shows the matrix to be unchanged. I've tried various permutations
>of -matrix, matrix, -m, m etc with no success.
>
>with standaloneblast, any attempt to change the matrix results in
>"blastallcrashed" with errors reported in StandAloneBlast.pm at 600, 456 and
>567. Otherwise it works fine if  I don't attempt to alter the matrix values.
>Firstly, am I declaring the parmeter wrongly? I've been unable to find
>a list of settable parameters in documentation outside of the tutorial
>examples.
>I would greatly apprciate any help/pointers in the right direction.
>Thank you.
>
>Dr Richard Adams
>Molecular Medicine Centre
>University of Edinburgh UK
>
>
>
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