[Bioperl-l] Bio::Tools::Run::Alignment::Clustalw. Alignment doesn't
print out in CGI.
tariq_shafi75 at hotmail.com
Sat May 29 11:25:50 EDT 2004
Got a major problem using BioPerl and can't figure out the solution!
I am trying to make an alignment in Clustalw and print out the results to a
CGI page, with no luck.
When I print out to the console it prints out, but it doesn't work in the
Here is the code:
# Filename: DoAlignment.pl
use CGI qw(:standard);
$query = new CGI;
# The dbh connection works fine. (I have changed the names here for
$dbh = DBI->connect('dbi:mysql:dbname=db;host=host.domain.;port=9999', 'me',
'my password') or die("connection not made:\n");
for ($i = 1; $i < 4; $i++)
$seq = Bio::Seq->new(-seq => 'ATCGT',
-desc => 'Sample sequence',
-id => 'something' . $i,
-accession_number => 'GB_ID'
print $seq->seq(), br();
print $seq->id(), br();
push @sequences, $seq;
# Prints out '3' to web page, which is fine
print scalar @sequences, br();
@params = ('ktuple'=>2, 'matrix' => 'BLOSUM');
$aligner = Bio::Tools::Run::Alignment::Clustalw->new(@params);
# This prints out to web page
print "Here!", br();
$alignment = $aligner->align(\@sequences);
#This does NOT print out to web page
print "Here again!", br();
On the web page, this executable script types the following:
But there is no ClustalW alignment printed out and not even the 'Here
Again!' after the Clustalw operation. Everything works fine when I test
./DoAlignment.pl on the console.
Many thanks for your help in advance
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