[Bioperl-l] Can't locate object method "seq" via package "Bio::DB::Query::GenBank"

Brian Osborne briano at bioteam.net
Fri Feb 24 09:58:58 EST 2012


Casandra,

BioPerl questions should be directed to the bioperl-l mailing list, that's where they will get the most attention. I'm CC'ing the list here.

Brian O.



On Feb 24, 2012, at 7:07 AM, Casandra wrote:

> Hi, 
> I was training with "Retrieving multiple sequences from a database" 
> use Bio::DB::Query::GenBank;
>  
> $query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and 0:3000[SLEN]";
> $query_obj = Bio::DB::Query::GenBank->new(-db    => 'nucleotide', -query => $query )
> but I'm stuck in the print step. This is what I wrote:
> 
> #!/bin/perl -w
> 
> use Bio::DB::Query::GenBank;
> use Bio::Seq;
> use Bio::SeqIO;
> 
> $query = "Arabidopsis[ORGN] AND topoisomerase[TITL]";
> $query_obj = Bio::DB::Query::GenBank->new(-db =>'nucleotide', -query => $query);
> 
> #$seqio_obj = Bio::SeqIO->new(-file =>'>Arab46.gb', -format =>'genbank');
> #$seqio_obj->write_seq($query_obj);
> 
> print $query_obj->accession_number,"\n";
> 
> I've tried to print it to a file with seqio and to print it through terminal with the following:
> print $query_obj->accession_number,"\n";
> print $query_obj->seq,"\n";
> print $query_obj->division,"\n";
> 
> But the error message I get when I try to print it to a file is:
> --------------------- WARNING ---------------------
> MSG:  Bio::DB::Query::GenBank=HASH(0x965010) is not a SeqI compliant module. Attempting to dump, but may fail!
> ---------------------------------------------------
> Can't locate object method "seq" via package "Bio::DB::Query::GenBank" at /Library/Perl/5.8.8/Bio/SeqIO/genbank.pm line 760.
> 
> And when I try to print it normally:
> Can't locate object method "seq" via package "Bio::DB::Query::GenBank" at bp_seq4.pl line 15.
> 
> 
> I went to cpan to check for this module 
> Bio::DB::Query::GenBank
> I install Bioperl again the one that was following "Bio::DB::Query::GenBank".
> But no change in the message error.
> 
> could you help me?
> 
> Thank you very much.

Brian O.
--
Brian Osborne, PhD
BioTeam: http://bioteam.net
email: briano at bioteam.net
mobile: 978-317-3101




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