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

Casandra kasandrah at gmail.com
Fri Feb 24 10:24:05 EST 2012


I saw my mistake but thank you anyway : )


El 24/02/2012, a las 15:58, Brian Osborne escribió:

> 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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