[Bioperl-l] Why cannot I get sequences for some entries?

[Jason Stajich]

No idea why, but it appears broken though you are right. The genpept tests are still working so I don't know what is wrong - you probably should submit it as a bug.

On Aug 21, 2013, at 8:06 PM, cacaucenturion2 <cacaucenturion2 at gmail.com> wrote:

> Hi,
>  
> Thanks for your help! I used GenPept but it did not work (also did not work when I was using Bio::DB::GenPept). I am pasting the code as follows.
>  
> use Bio::DB::GenPept;
> $gb = Bio::DB::GenPept->new();
> $seq = $gb->get_Seq_by_id('162138530');
> print $seq->seq."\n";
>  
> But it would work if I want to get the id of this sequence by typing
> print $seq->display_id."\n"
>  
> 发件人： Jason Stajich
> 发送时间： 2013-08-23 01:01
> 收件人： cacaucenturion2
> 抄送： Bioperl-l
> 主题： Re: [Bioperl-l] Why cannot I get sequences for some entries?
> are you using Bio::DB::GenPept as your object since it is a protein ID.
>  
> On Aug 19, 2013, at 1:31 AM, cacaucenturion2 <cacaucenturion2 at gmail.com> wrote:
>  
> > Hi all, 
> > 
> > I tried 
> > 
> > my $seq = $gb->get_Seq_by_gi('162138530');
> >                print $seq->seq."\n";
> > 
> > I am sure that the sequence whose GI is 162138530 does exist in the database (http://www.ncbi.nlm.nih.gov/protein/162138543). However, no sequences could be given. Has anyone encountered the similar problem? Thanks.
> > 
> > Sincerely yours,
> > Cacau
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>  
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org