[Bioperl-l] Error message

George Tzotzos G.Tzotzos at unido.org
Tue Jun 20 12:21:32 EDT 2006


Brian

Neither <swiss> nor <swissprot> work. However, your suggestion does  
work fine. So does Chandan's.  Many thanks to both.

Cheers

George



On 20 Jun 2006, at 18:13, Brian Osborne wrote:

> George,
>
> The docs I'm reading say to use 'swiss', not 'swissprot' but I  
> think there's
> some other problem that may be specific to SwissProt. Can you  
> retrieve from
> GenBank? E.g.:
>
> my $seq_object = get_sequence('genbank', 2);
>
> Brian O.
>
>
> On 6/20/06 7:36 AM, "George Tzotzos" <G.Tzotzos at unido.org> wrote:
>
>> I'm a BioPerl novice. I used CPAN to install BioPerl and run the
>> following script to test the installation:
>>
>> use Bio::Perl;
>> use strict;
>> use warnings;
>>
>> my $seq_object = get_sequence('swissprot', "P09651");
>>
>> write_sequence(">roa1.fasta", 'fasta', $seq_object);
>>
>> I used as argument both "ROA1_HUMAN" and "P09651". In both cases I
>> get the message below.
>>
>> Any help on the nature of the problem and how to overcome it would be
>> greatly appreciated.
>>
>> Thanks
>>
>> George
>>
>>
>> ------------- EXCEPTION  -------------
>> MSG: swissprot stream with no ID. Not swissprot in my book
>> STACK Bio::SeqIO::swiss::next_seq /Library/Perl/5.8.6/Bio/SeqIO/
>> swiss.pm:179
>> STACK Bio::DB::WebDBSeqI::get_Seq_by_id /Library/Perl/5.8.6/Bio/DB/
>> WebDBSeqI.pm:153
>> STACK Bio::Perl::get_sequence /Library/Perl/5.8.6/Bio/Perl.pm:513
>> STACK toplevel tut2.pl:5
>>
>>
>>
>> George T. Tzotzos Ph.D
>> Vienna, Austria
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



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