[Bioperl-l] getting sequences from external databank

[Barry Moore]

George,

This is a hideous little bug in Red Hat/Fedora installations of  
perl.  It's happened to me a couple time on upgrades, but it's always  
fixed with

perl -MCPAN -e shell
force install Scalar::Util

http://www.perlmonks.org/?node_id=460411

Barry

On Dec 6, 2007, at 8:28 AM, geo rose wrote:

> 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
> _______________________________________________
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