[Bioperl-l] getting sequences from external databank

[geo rose]

Hi Bioperl,

In the past, I have been able to retrieve sequences from an external
databank, but my scripts are not working anymore.
I am afraid that I may have broken my Bioperl installation while updating my
Fedora7 machine with yum update.

Below is an example of what happens.

The script is from
http://www.faculty.uaf.edu/ffnt/teaching/programming/bioperl/node2.html and
it works.
(I used it on an older machine with Bioperl and MacOS Tiger)

__________________________________________________________________________________
#!/usr/bin/perl -w

use Bio::SeqIO;
use Bio::DB::GenBank;

$genBank = new Bio::DB::GenBank;  # This object knows how to talk to GenBank

my $seq = $genBank->get_Seq_by_acc('AF060485');  # get a record by accession


my $seqOut = new Bio::SeqIO(-format => 'genbank');

$seqOut->write_seq($seq);


_________________________________________________________________________________________
This is the error I get
_________________________________________________________________________________________

[home at home Desktop]# perl final-seq-db-test1.pl
Bio::SeqIO: genbank cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::SeqIO::genbank. Weak references are not
implemented in the version of perl at
/usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91
BEGIN failed--compilation aborted at
/usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91.
Compilation failed in require at
/usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172.
BEGIN failed--compilation aborted at
/usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172.
Compilation failed in require at
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 425.

STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Root::Root::_load_module
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:427
STACK: Bio::SeqIO::_load_format_module
/usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:555
STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376
STACK: Bio::DB::WebDBSeqI::get_seq_stream
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/WebDBSeqI.pm:458
STACK: Bio::DB::NCBIHelper::get_Stream_by_acc
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/NCBIHelper.pm:361
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/WebDBSeqI.pm:172
STACK: final-seq-db-test1.pl:8
-----------------------------------------------------------

For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: acc AF060485 does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc
/usr/lib/perl5/site_perl/5.8.8/Bio/DB/WebDBSeqI.pm:173
STACK: final-seq-db-test1.pl:8
-----------------------------------------------------------
[home at home Desktop]# Use of uninitialized value in concatenation (.) or
string at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Scalar/Util.pm
line 30.

[home at home Desktop]#


________________________________________________________________________________________


Before I mess things up further I thought I'd ask:
Can I fix this problem by reinstalling some part of Bioperl or Perl?

Thanks,

George