[Bioperl-l] the most weird thing I've seen, help please

Guojun Yang gyang at plantbio.uga.edu
Tue Aug 14 15:01:07 EDT 2007


Hi, all,  
I have two subroutines in my code. One is remoteblast and the other local blast. It works well.  
When I decided to change the remoteblast to local blast, I always get the following error. I downloaded nt database from NCBI as preformatted, but it works ok for both subroutines when I use command line blastall -p blastn.... I changed the db name to 'nt', 'nt.00', the same error message was returned. The error says: "program name was not given an argument", but I apparently gave it there.  Can anybody help me? The code for the two subrountines are very similar:  
   
sub search {
    use Bio::Tools::Run::StandAloneBlast;
    use Bio::SearchIO::blast;  
my $query = Bio::Seq -> new ( -seq=>"$_[0]",
                              -id=>"query");
my $len=$query->length();
@db=('nt.nal');
foreach my $db (@db) {
    my $factory = Bio::Tools::Run::StandAloneBlast->new( -program =>"blastn",
                                                         -database =>"$db",
                                                         -e =>"$_[1]");
    my $rc = $factory->blastall($query);  
......  
   
   
sub ancestor {
    use Bio::Tools::Run::StandAloneBlast;
    use Bio::SearchIO::blast;  
my $query = Bio::Seq -> new ( -seq=>"$_[0]",
                              -id=>"test");
my $len=$query->length();
my $long_name=$_[1];
my $long_start=$_[2];
my $long_end=$_[3];
@db=('TNDB');
foreach my $db (@db) {
    my $factory = Bio::Tools::Run::StandAloneBlast->new(-program => "blastx",
                                                        -database => "$db",
                                                        -e => 1e-3,
                                                        );
    my $blast_report = $factory->blastall($query);

  
Thanks a lot!  
Guojun Yang  
Department of Plant Biology  
University of Georgia


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