[Bioperl-l] Bio::Tools::Run::Alignment::Clustalw. Alignment d
oesn't print out in CGI.
Davis, Sean (NIH/NHGRI)
sdavis2 at mail.nih.gov
Sat May 29 19:52:08 EDT 2004
I'm not an expert, but you might check the server error log. It may be
that the user under which the CGI is running does not have privileges for
executing clustalw or writing necessary temp files.
From: Tariq Shafi
To: bioperl-l at portal.open-bio.org
Sent: 5/29/2004 11:25 AM
Subject: [Bioperl-l] Bio::Tools::Run::Alignment::Clustalw. Alignment doesn't
print out in CGI.
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
CGI page, with no luck.
When I print out to the console it prints out, but it doesn't work in
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
$dbh = DBI->connect('dbi:mysql:dbname=db;host=host.domain.;port=9999',
'my password') or die("connection not made:\n");
for ($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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