[Bioperl-l] StandAloneBlast and blast->to_html etc

[Dan Kortschak]

Hi All, I am having befuddlement trying to get a micro local blast server
set up for our lab.

I have looked through StandAloneBlast.pm and can see that all the
appropriate paramters are being passed and that a blast report is being
generated (at least the hash ref is there), but I get no HTML output. I am
not sure that blastall is actually being called (there is no indication of
load when jobs are submitted), but the parts do work in other CL scripts
that I have written.

I'm using bioperl release 1.0.2 (yeah I know, but there are things I've
written which will break if I upgrade - I just know it).

Any help/suggestions were to look would be appreciated.

Dan



#!/usr/bin/perl -w

use CGI qw (:standard);
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
use Bio::Tools::Blast qw(:obj);

my $sequence=param('SEQUENCE');
my $program=param('PROGRAM');
my $matrix=param('MATRIX');
my $filter=param('FILTER');
my $expect=param('EXPECT');
my $strand=param('STRAND');
my $desc=param('DESCRIPTIONS');
my $align=param('ALIGNMENTS');
my $advanced=param('ADVANCED');

print header,start_html("Blast Results"),h1("Blast Results");

my $fasta=1 if $sequence=~/^>/;
$sequence=~s/^>(.*)/$1/;
my @sequence=split('>',$sequence);

my @query;

foreach (@sequence) {
   my ($id, at seq);
   if ($fasta) {
      ($id, at seq)=split(" ");
   } else {
     ($id, at seq)=('',split(" "));
   }

   my $query=new Bio::Seq(-id=>$id,-seq=>join('', at seq));
   push (@query,$query);
}


my @params = ('program' => $program,
              'd' => '/usr/share/ncbi/data/coral.EST.clusters',
              'b' => $align,
              'v' => $desc,
              'expect' => $expect,
              '_READMETHOD' => 'Blast');

my $blastfactory = new Bio::Tools::Run::StandAloneBlast (@params);

if ($strand eq 'both') {
   $blastfactory->S(3);
} elsif ($strand eq 'top') {
   $blastfactory->S(1);
} elsif ($strand eq 'bottom') {
   $blastfactory->S(2);
}

if ($filter eq 'default') {
   $blastfactory->F(T);
} elsif ($filter eq 'none') {
   $blastfactory->F(F);
} elsif ($filter eq 'SEG') {
   $blastfactory->F(T);
}

unless ($matrix eq 'BLOSUM62') {
   $blastfactory->M($matrix);
}

my $report=$blastfactory->blastall(@query);

$report->to_html;

print end_html;

-- 
_____________________________________________________________   .`.`o
                                                         o| ,\__ `./`r
  Dan Kortschak    kortschak at rsbs.anu.spanner.edu.au     <\/    \_O> O
                                                          "|`...'.\
      Rejecting the primacy of appearance over             `      :\
      substance for more than thirty years.                       : \


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