[Bioperl-l] a question

Chris Fields cjfields at uiuc.edu
Fri Sep 7 10:09:18 EDT 2007


On Sep 7, 2007, at 2:57 AM, ÑîÃÍ£¨ÖÐÐÄʵÑéÊÒ wrote:

> I am a student from China.During my learing the bioperl,I encounter  
> a problem as follows:
>
> I run the program,
>
> use Bio::Perl;
> $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
> write_sequence(">roa1.fasta",'fasta',$seq_object);
>
> But It returns lots of mistake informatiom,

First, always preface problems of this sort with the version of  
BioPerl you are using (there are quite a few versions still being used).

> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: WebDBSeqI Request Error:
> 501 Protocol scheme '' is not supported
> Content-Type: text/plain
> Client-Date: Fri, 07 Sep 2007 07:26:06 GMT
> Client-Warning: Internal response
> 501 Protocol scheme '' is not supported
> STACK: Error::throw
> STACK: Bio::Root::Root::throw D:/perl/site/lib/Bio/Root/Root.pm:359
> STACK: Bio::DB::WebDBSeqI::_request D:/perl/site/lib/Bio/DB/ 
> WebDBSeqI.pm:685
> STACK: Bio::DB::WebDBSeqI::get_seq_stream D:/perl/site/lib/Bio/DB/ 
> WebDBSeqI.pm:4
> 91
> STACK: Bio::DB::WebDBSeqI::get_Stream_by_id D:/perl/site/lib/Bio/DB/ 
> WebDBSeqI.pm
> :275
> STACK: Bio::DB::WebDBSeqI::get_Seq_by_id D:/perl/site/lib/Bio/DB/ 
> WebDBSeqI.pm:14
> 5
> STACK: Bio::Perl::get_sequence D:/perl/site/lib/Bio/Perl.pm:510
> STACK: C:\DOCUME~1\yangmeng\LOCALS~1\Temp\dir13D.tmp\Untitled.pl:6
> -----------------------------------------------------------

This works for me using bioperl from CVS.  There were a few remote  
DbFetch server changes if I recall correctly, so updating from CVS  
may be your best option.

> I don't know the reason of the problem.I have installed the  
> addition perl modules such as bioperl-db,bioperl-network,bioperlgui  
> and almost all "BioPerl Dependencies modules".My network is also  
> OK. It's an annoying promleb to me.
> I have consulted many experts but didn't got a reply. Could you  
> vacuate in your mass business to give me a help?
>
> Thank you!
>
> Best regards!
>
> YangMeng

I think my 'vacuating' is a private matter, let alone doing so in my  
mass business...

http://www.thefreedictionary.com/Vacuate

;>

chris


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