[Bioperl-l] =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=20basic=20questions?=

Pengcheng Yang pengchy at yahoo.com.cn
Tue Jun 12 10:33:15 EDT 2007



I got the same questions.

I guess that the swissprote database has some problems!

code:
use Bio::DB::SwissProt;
$sp = new Bio::DB::SwissProt;
$seq = $sp->get_Seq_by_id('KPY1_ECOLI'); 
print ref($seq),"\t",$seq->display_id,"\n"

the mesage:

------------- EXCEPTION  -------------
MSG: swissprot stream with no ID. Not swissprot in my book
STACK Bio::SeqIO::swiss::next_seq C:/perl/site/lib/Bio\SeqIO\swiss.pm:180
STACK Bio::DB::WebDBSeqI::get_Seq_by_id
C:/perl/site/lib/Bio/DB/WebDBSeqI.pm:154

STACK toplevel t.pl:7

--------------------------------------



--- L Xu <ryanx07 at hotmail.com>дµÀ:

> Here is the code:
> 
> use Bio::Perl;
> $seq_object = get_sequence('swiss',"ROA1_HUMAN");
> print STDERR ref($seq_object), "\t", $seq_object->display_id, "\n";
> write_sequence(">roa1.fasta",'fasta',$seq_object);
> 
> The output looks like the same as the previous version:
> 
> Microsoft Windows XP [Version 5.1.2600]
> (C) Copyright 1985-2001 Microsoft Corp.
> 
> C:\~Scripts>perl test.pl
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: swissprot stream with no ID. Not swissprot in my book
> STACK: Error::throw
> STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:350
> STACK: Bio::SeqIO::swiss::next_seq
> C:/Perl/site/lib/Bio\SeqIO\swiss.pm:178
> STACK: Bio::DB::WebDBSeqI::get_Seq_by_id 
> C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:15
> 3
> STACK: Bio::Perl::get_sequence C:/Perl/site/lib/Bio/Perl.pm:510
> STACK: test.pl:7
> -----------------------------------------------------------
> 
> Thanks.
> 
> 
> 
> 
> 
> >From: David Messina <dmessina at wustl.edu>
> >To: L Xu <ryanx07 at hotmail.com>
> >CC: BioPerl list <bioperl-l at lists.open-bio.org>
> >Subject: Re: [Bioperl-l] basic questions
> >Date: Mon, 11 Jun 2007 13:48:23 -0500
> >
> >Hi,
> >
> >Please use 'Reply All' so everyone on the list can follow the 
> discussion.
> >
> >Try adding the following line after the line that starts with 
> $seq_object:
> >
> >	print STDERR ref($seq_object), "\t", $seq_object->display_id, "\n";
> >
> >And then run the program again. What do you get? Could you post a 
> complete 
> >printout of what you're doing?
> >
> >
> >Dave
> >
> >
> >On Jun 11, 2007, at 11:45 AM, L Xu wrote:
> >>I used WinXP with BioPerl Inst_version 2.1.8 (Bioperl 1.5.2) and  
> >>activeperl 5.8.8.819 Thank you very much.
> >
> 
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Best wishes!

Sincerely, Pengcheng


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