[Bioperl-l] FW: Bioperl 1.4.0(BUG)

[Brian Osborne]

-----Original Message-----
From: lenavarzim at portugalmail.pt [mailto:lenavarzim at portugalmail.pt]
Sent: Tuesday, December 21, 2004 1:01 PM
To: Brian Osborne
Subject: RE: Bioperl 1.4.0(BUG)


This is the message error:


------------ EXCEPTION  -------------
MSG: WebDBSeqI Request Error:
500 (Internal Server Error) Can't connect to eutils.ncbi.nlm.nih.gov:80
(connect: timeout)
Content-Type: text/plain
Client-Date: Tue, 21 Dec 2004 18:18:11 GMT
Client-Warning: Internal response

500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (connect: timeout)

STACK Bio::DB::WebDBSeqI::_stream_request
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:728
STACK Bio::DB::WebDBSeqI::get_seq_stream
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:460
STACK Bio::DB::NCBIHelper::get_Stream_by_acc
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/NCBIHelper.pm:415
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:181
STACK Bio::DB::GenBank::get_Seq_by_acc
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/GenBank.pm:216
STACK Bio::Perl::get_sequence /usr/lib/perl5/site_perl/5.8.0/Bio/Perl.pm:508
STACK main::procuraSeqC menu.pl:312
STACK toplevel menu.pl:69

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

-------------------- WARNING ---------------------
MSG: acc (gb|AE000440) does not exist
---------------------------------------------------




Citando Brian Osborne <brian_osborne at cognia.com>:

 Madalena,

 This works for me, from the command-line:

 >perl -e 'use Bio::Perl; $seq =

get_sequence('Genbank','AE000440');write_sequence(">tests.fa","fasta",$seq);
 '

 Brian O.

 -----Original Message-----
 From: lenavarzim at portugalmail.pt [mailto:lenavarzim at portugalmail.pt]
 Sent: Tuesday, December 21, 2004 12:16 PM
 To: Brian Osborne
 Subject: RE: Bioperl 1.4.0(BUG)




 Brain,
 the accession number is: AE000440 (Escheriachia coli k-12 MG1655 section
330
 of
 400 of the complete genome).
 The program code:
 use Bio::Perl;
 get_Sequence('Genbank','AE000440');
 the problem is on this method (get_Sequence).

 Madalena














 Citando Brian Osborne <brian_osborne at cognia.com>:

  Madalena,

  Please provide your code so we can take a closer look.

  Brian O.

  -----Original Message-----
  From: lenavarzim at portugalmail.pt [mailto:lenavarzim at portugalmail.pt]
  Sent: Tuesday, December 21, 2004 12:03 PM
  To: jason at bioperl.org; brian_osborne at cognia.com; heikki at ebi.ac.uk;
  bioperl-bugs at bio.perl.org
  Subject: Bioperl 1.4.0(BUG)



  Hi!

  I'm using Bioperl 1.4.0 and i have the next problem:


  I'm using Bio::DB::GenBank to query Genbank and I'm certain that the ac
  (accession number) is there but I'm seeing the error "MSG: acc does not
  exist".

  I wait your answer.
  thanks,
  Madalena Varzim (student from University of Minho - Portugal)



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