[Bioperl-l] write_sequence cgi perl problem

[Baranidharan P]

Dear all,

The following perl script works fine from the command line....
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use Bio::Perl;

# this script will only work with an internet connection
# on the computer it is run on
$seq_object = get_sequence('genbank',"NM_173283");
#print "$seq_object";
write_sequence(">ILGF1.gb",'genbank',$seq_object);
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but the following cgi-perl script in /var/www/cgi-bin
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#!/usr/bin/perl -w

use strict;
use CGI::Carp qw(fatalsToBrowser);
use CGI qw(:standard);
use Bio::Perl;

# this script will only work with an internet connection on the computer it is run on
my $seq_object = get_sequence('genbank',"NM_173283");
write_sequence(">ILGF1.gb",'genbank',$seq_object);
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returns an error in the browser as
---------------------------------------------------
You have a non object [] passed to write_sequence. It maybe that you want to use new_sequence to make this string into a sequence object? at /usr/lib/perl5/site_perl/5.8.1/Bio/Perl.pm line 283
Bio::Perl::write_sequence('>ILGF1.gb','genbank','undef') called at /var/www/cgi-bin/getgenseq.cgi line 12
----------------------------------------------------

and the /etc/httpd/logs/error_log file says
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[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: , referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: ------------- EXCEPTION -------------, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: MSG: WebDBSeqI Request Error:, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: 500 (Internal Server Error) Can't connect to www.ebi.ac.uk:80 (Bad hostname 'www.ebi.ac.uk'), referer: http://10.22.32.3/ge
tgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: Content-Type:
text/plain, referer: http://10.22.32.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: Client-Date:
Tue, 11 May 2004 04:23:36 GMT, referer: http://10.22.32.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: Client-Warnin
g: Internal response, referer: http://10.22.32.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: , referer: ht
tp://10.22.32.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: 500 Can't con
nect to www.ebi.ac.uk:80 (Bad hostname 'www.ebi.ac.uk'), referer: http://10.22.32.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: , referer: ht
tp://10.22.32.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: , referer: ht
tp://10.22.32.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: STACK Bio::DB
::WebDBSeqI::_stream_request /usr/lib/perl5/site_perl/5.8.1/Bio/DB/WebDBSeqI.pm:728, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/lib/perl5/site_perl/5.8.1/Bio/DB/WebDBSeqI.pm:460, referer: http://10.22.32.3
/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: STACK Bio::DB
::RefSeq::get_seq_stream /usr/lib/perl5/site_perl/5.8.1/Bio/DB/RefSeq.pm:155, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: STACK Bio::DB::WebDBSeqI::get_Stream_by_acc /usr/lib/perl5/site_perl/5.8.1/Bio/DB/WebDBSeqI.pm:312, referer: http://10.22.3
2.3/getgenseq.html [Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: STACK Bio::DB
::WebDBSeqI::get_Seq_by_acc /usr/lib/perl5/site_perl/5.8.1/Bio/DB/WebDBSeqI.pm:181, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: STACK Bio::Perl::get_sequence /usr/lib/perl5/site_perl/5.8.1/Bio/Perl.pm:508, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: STACK toplevel /var/www/cgi-bin/getgenseq.cgi:10, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: , referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: --------------------------------------, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] , referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] -------------------- WARNING ---------------------, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] MSG: acc (NM_173283) does not exist, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] ---------------------------------------------------, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: Use of uninitialized value in length at /usr/lib/perl5/site_perl/5.8.1/Bio/Perl.pm line 271., referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.1/Bio/Perl.pm line 283., referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: You have a non object [] passed to write_sequence. It maybe that you want to use new_sequence to make this string into a sequence object? at /usr/lib/perl5/site_perl/5.8.1/Bio/Perl.pm line 283, referer: http://10.22.32.3/getgenseq.html
[Tue May 11 09:53:36 2004] [error] [client 10.22.32.3] [Tue May 11 09:53:36 2004] getgenseq.cgi: Bio::Perl::write_sequence('>ILGF1.gb','genbank','undef') called at /var/www/cgi-bin/getgenseq.cgi line 12, referer: http://10.22.32.3/getgenseq.html


Please help me to find a solution to this problem ..

Baranidharan P
IITKGP
Baranidharan P
Senior Project Assistant
Bioinformatics Sub-DIC
Dept. of Biotechnology
Indian Institute of Technology
Kharagpur -721302
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