[Bioperl-l] trouble to retrieve sequence.. I'm a BEGINNER...

[Jason Stajich]

You need
IO::String and LWP::UserAgent perl modules installed to access  
GenBank remote database.  The FAQ answer you are referring to only  
has to do with bioperl versions before 0.7 - more than 3 years ago so  
it isn't relevant anymore.

-jason
On Dec 5, 2005, at 9:26 AM, 현도윤 wrote:

> Hi,
>
> I'm a bioperl beginner and studying bioperl code according to  
> Beginners HOWTO.
> I have a trouble in section 9. Retrievin a sequence from a database.
> How can I solve this promblem? Please, help me~~
>
> 1. ver. of Bioperl : 1.4
>
> 2. OS : linux
>
> 3. I am trying to retrieve seq. from GenBank.
>
> 4. code
> #!/usr/bin/perl -w
>
> use Bio::DB::GenBank;
> use Bio::DB::Query::GenBank;
>
> $query = "Arabidopsis[ORGN] AND topoisomerase[TITL] an 0:3000[SLEN]";
> $query_obj = Bio::DB::Query::GenBank->new(-db => 'nucleotide',
>                                 -query => $query);
>
> $gb_obj = Bio::DB::GenBank->new;
>
> $stream_obj = $gb_obj->get_Stream_by_query($query_obj);
>
> while ($seq_obj = $stream_obj->next_seq){
>         #do something with the sequence object
>         print $seq_obj->display_id,"\t", $seq_obj->length, "\n";
> }
>
> 5. error messages
>
> Can't locate IO/String.pm in @INC (@INC contains: /usr/lib/ 
> perl5/5.6.0/i386-linux /usr/lib/perl5/5.6.0 /usr/lib/perl5/ 
> site_perl/5.6.0/i386-linux /usr/lib/perl5/site_perl/5.6.0 /usr/lib/ 
> perl5/site_perl .) at /usr/lib/perl5/site_perl/5.6.0/Bio/DB/ 
> WebDBSeqI.pm line 90.
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.0/ 
> Bio/DB/WebDBSeqI.pm line 90.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.6.0/Bio/ 
> DB/NCBIHelper.pm line 82.
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.0/ 
> Bio/DB/NCBIHelper.pm line 82.
> Compilation failed in require at /usr/lib/perl5/site_perl/5.6.0/Bio/ 
> DB/GenBank.pm line 124.
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.6.0/ 
> Bio/DB/GenBank.pm line 124.
> Compilation failed in require at query.pl line 3.
> BEGIN failed--compilation aborted at query.pl line 3.
>
> ps. I read the FAQ pages. I found this answer.
> "NCBI changed the web CGI script that provided this access. You  
> must be using bioperl <= 0.7.2. The developer release 0.9.3  
> contains this fix as does the 1.0 release."
> I cant't understand what it means....
>
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> Bioperl-l at portal.open-bio.org
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12