[Bioperl-l] basic questions

L Xu ryanx07 at hotmail.com
Tue Jun 12 07:30:09 EDT 2007


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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