[Bioperl-l] (no subject)

[Simon K. Chan]

Hi All, 

I'm trying to make something similar to the NCBI blast
query form using a CGI script.
I have correctly installed the program and modules and
have read the docs.  The flow fails to enter the while
loop to parse the blast report.  Below is a snippet of
the code.  Any suggestions would be appreciated!

Simon



# StandAloneBlast->exists_blast returns 1
BEGIN {$ENV{BLASTDIR} = '/path/to/blast/'; }


my $seq1 = "AAAAATATCTAACTTACCAAA";
my $seq2 = "AGACTATATCTTACCAGGGAA";

my $seq1_obj = Bio::Seq->new( '-id' => "Sequence1" , 
                             '-seq' => "$seq1");

my $seq2_obj = Bio::Seq->new( '-id' => "Sequence2" , 
                             '-seq' => "$seq2");

# $blast_report is now a BPl2seq object
my $blast_report = $factory->bl2seq($seq1_obj,
seq2_obj);

  while(my $hsp = $blast_report->next_feature) {
         print "In while loop!\n";
}






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