[Bioperl-l] Hi! everyone

r93626012 at ntu.edu.tw r93626012 at ntu.edu.tw
Sun Mar 19 09:39:46 EST 2006


  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");

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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