[Bioperl-l] Bemusement with get_seq_by_gi in a CGI script

Mark Wilkinson markw at illuminae.com
Wed Aug 20 10:48:00 EDT 2003


Hi all, 

I've been banging my head for days on this problem, but I can't make heads
nor tails of it.  The solution must be obvious, but I can't see it.

The following script is running at 
http://mobycentral.cbr.nrc.ca/cgi-bin/testseq.cgi

===============================================
use lib '/usr/local/apache/cgi-bin/bioperl/core';
print "Content-type: text/plain\n\n";
use Bio::DB::GenBank;
$d = Bio::DB::GenBank->new();
$seq = $d->get_Seq_by_gi('163483');
print "I didn't print the sequence!\n";
===============================================

If you look at the output you see that the genbank record is printed to the
screen, but the last print statement is not!  If I run the same code from 
the command line I don't see the record, and the last print statement prints.

??!??  I'm at my wit's end trying to work out what is happening.  This started 
shortly after upgrading to mod_perl, so it might be associated
with that somehow, but I need some direction in trying to find my mistake.

Any advice appreciated - if only to save my sanity :-)

Cheers!

Mark









More information about the Bioperl-l mailing list