[Bioperl-l] Hi! everyone

Mon Mar 20 00:10:12 UTC 2006

On Mar 19, 2006, at 8:39 AM, r93626012 at ntu.edu.tw wrote:

>  Hi!I am a graduate student of National Taiwan University. My name  
> is scott. I had some probelms when i using bioperl module. I wanted  
> to get a sequence from "swissprot" database and blast with nr  
> database of NCBI automatically by bioperl module. This is my program:
>
> #!/usr/bin/perl -w
> use strict;
> use Bio::Perl;
>
> my $seq_object = get_sequence('swissport',"ROA1_HUMAN");

'swissport' should be 'swissprot', though I get this script to work  
when spelled either way (well, I get some BLAST results back).  This  
error was, I believe, fixed in a recent version of Bioperl; I would  
upgrade from CVS.   However, the major problem I see is that the  
formatting from Bioperl is completely messed up now; it looks like  
the entire BLAST report is globbed together at the 'Query=' line.   
I'm sure this is an issue related to the recent blast changes at  
NCBI.  I'll look into this tomorrow.

Chris

>
> my $blast_result = blast_sequence($seq_object);
>
> write_blast(">roa1.blast",$blast_result);
>
> exit;
>
> then i could get the sequence successfully, however, it could not  
> produce any results of blast. The error message as follow:
>
> ------------- EXCEPTION  -------------
> MSG: WebDBSeqI Request Error:
> 501 Protocol scheme 'http' is not supported
> Content-Type: text/plain
> Client-Date: Sun, 19 Mar 2006 06:25:06 GMT
> Client-Warning: Internal response
>
> 501 Protocol scheme 'http' is not supported
>
> STACK Bio::DB::WebDBSeqI::_stream_request /usr/lib/perl5/5.8.3/Bio/ 
> DB/WebDBSeqI.pm:728
> STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/lib/perl5/5.8.3/Bio/ 
> DB/WebDBSeqI.pm:460
> STACK Bio::DB::WebDBSeqI::get_Stream_by_id /usr/lib/perl5/5.8.3/Bio/ 
> DB/WebDBSeqI.pm:287
> STACK Bio::DB::WebDBSeqI::get_Seq_by_id /usr/lib/perl5/5.8.3/Bio/DB/ 
> WebDBSeqI.pm:153
> STACK Bio::Perl::get_sequence /usr/lib/perl5/5.8.3/Bio/Perl.pm:511
> STACK toplevel test2.txt:6
>
> --------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: id (ROA1_HUMAN) does not exist
> ---------------------------------------------------
> Use of uninitialized value in concatenation (.) or string at /usr/ 
> lib/perl5/site_perl/5.8.3/Bio/Tools/Run/RemoteBlast.pm line 392.
>
> -------------------- WARNING ---------------------
> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.4
> Content-Length: 178
> Content-Type: application/x-www-form-urlencoded
>
> DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&QUERY=%3Eblast- 
> sequence-temp-id+% 
> 0A&EXPECT=1e-10&SERVICE=plain&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L 
> &CDD_SEARCH=off&PROGRAM=blastp
>
> <HTML>
> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
> <BODY>
> <H1>An Error Occurred</H1>
> 501 Protocol scheme 'http' is not supported
> </BODY>
> </HTML>
>
> ---------------------------------------------------
> Submitted Blast for [blast-sequence-temp-id] i had copy the "http"  
> module and "HTML" module from other sever, but it still tell me  
> that it could not find anything in the folder. Perhaps you can tell  
> me what thing wrong or just i am missing something. Thank you for  
> your reading and i will very glad of get your answers.
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign