[Bioperl-l] use threads to get seq file error.

forrest forrest_zhang at 163.com
Mon Mar 1 00:10:31 EST 2010


Hi all,

When I use threads to get Genbank format file, show some error. It is
shown as:

"Can't call method "get_taxon" on unblessed reference at
/opt/local/lib/perl5/site_perl/5.8.9/Bio/Taxon.pm line 671."

=========================================
#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
use Bio::Seq;
use Bio::DB::GenBank;
use threads;


my @id = ("AK287649","AF031249","EZ238383","BLYDHN5","AY895908","EF409493","AY895886","AF181455","AY895930","EF409498");


my $seq_out = Bio::SeqIO->new(-format => "genbank",
                              -file => ">dhn_all.gb");
my @seq;

my $number = @id;

my $max_threads = 6;

for (my $thread_number=0;$thread_number<$number;){
        my %threads_seq_hash;
        
        if ($number - $thread_number > $max_threads){
            for (my $thread=0;$thread<$max_threads;){
                $threads_seq_hash{$thread} = threads->new(sub {
                                        my $gb = Bio::DB::GenBank->new;
                                        my $seq = $gb->get_Seq_by_acc($id[$thread_number]);
                                    });
                $thread_number++;
                $thread++;

            }
        }else{
            my $else_number = $number % $max_threads;
            for (my $thread=0;$thread<$else_number;){
                $threads_seq_hash{$thread} = threads->new(sub {
                                        my $gb = Bio::DB::GenBank->new;
                                        my $seq = $gb->get_Seq_by_acc($id[$thread_number]);
                                    });
                $thread_number++;
                $thread++;
                
            }
            
            
        }
    
    foreach my $thread (sort keys %threads_seq_hash){
        my ($seq) = $threads_seq_hash{$thread}->join;
        push (@seq,$seq);
    } 
}

foreach (@seq){
    $seq_out->write_seq($_);
}
=========================================


How can I fix this error?
Thanks.


Zhang Tao







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