[Bioperl-l] How to fix "blast_report is undefined"??
Huizhuan Wu
wuhuizhu at mail.eecis.udel.edu
Tue Jul 6 13:59:55 EDT 2004
Here is the msg I got:
Here is blast_report: Bio::SearchIO::blast=HASH(0x9ac3e0)
Can't call method "next_result" on an undefined value at
/Users/wuhuizhuan/Sites/CGI-BIN/bl.cgi line 73.
Here is my code:
#!/usr/bin/perl -w -T
$ENV{BLASTMAT} = '/usr/local/BLAST/data';
$ENV{'BLASTDB'} ='/Users/huizhuan/myWork/learnBlast';
$ENV{PATH} = '/usr/local/bin:/usr/ucb:/usr/bin:/sbin:/usr/sbin';
$ENV{IFS} = "" if $ENV{IFS} ne "";
# This script gets sequence from grape MPSS page and perform blastn
against
# contig_fastaforNevada.txt database.
# Modules to use.
use CGI qw(:all);
use CGI::Carp qw(warningsToBrowser fatalsToBrowser);
use CGI::Carp qw(fatalsToBrowser carpout);
use strict;
use warnings;
use Getopt::Long;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SeqIO;
print header;
print start_html("BLAST RESULT");
my ($query, $seq);
my $db = "/Users/huizhuan/myWork/learnBlast/data.txt";
my $maxEval = 1.0e-10;
$query = "233fff";
my $seq = "GATCGGTTAATGGGCCATGGGGGG";
my $seqobj = Bio::Seq->new( '-id' => $query,
'-seq' => $seq);
my @params = ('program'=>'blastn', 'outfile'=>'blast.out',
'_READMETHOD'=>'Blast', 'F'=>'F','W'=>17,'g'=>'F',
'database'=>$db);
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
$factory->e($maxEval);
my $blast_report = $factory->blastall($seqobj);
print "Here is blast_report: $blast_report";
my $result = $blast_report->next_result;
print end_html;
Any help is highly appreciated!
huizhuan
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