[Bioperl-l] get html-output on my prompt

ak2083 ankh.egypt.public at googlemail.com
Sun Jun 24 06:29:00 EDT 2012


Hello,

i try to blast a protein sequence (in sequence.fasta) against the blast-db.
If i parse this
with the command 'perl file.pl', then the programm displayed html-code on my
prompt and the out-file
was not created. What could i do so that the results write into the
out-file?

my $report = $blast_obj->submit_blast('sequence.fasta');
my $x = 0;
print STDERR "waiting..." if ($x > 0);

while (my @rids = $blast_obj->each_rid() && $x == 5)
{
	foreach my $rid (@rids)
	{
		my $rc = $blast_obj->retrieve_blast($rid);
		if (!ref($rc))
		{
			if ($rc < 0)
			{ $blast_obj->remove_rid($rid); }
			print STDERR "." if ($x > 0);
			sleep 5;
		}
		else
		{
			my $result   = $rc->next_result();
			my $filename = $result->query_name(), '\.out';
			$blast_obj->save_output($filename);
			$blast_obj->remove_rid($rid);
			print "\nQuery Name: ", $result->query_name();
			
			while (my $hit = $result->next_hit())
			{
				next unless ($x > 0);
				print "\thit name is ", $hit->name, "\n";
		
				while (my $hsp = $hit->next_hsp())
				{
					print "\t\tscore is ", $hsp->score(), "\n";
				}
			}
		}
	}
} 
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