[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1112 (fwd)

[Jason Stajich]

Works for me.  Try upgrading to bioperl 1.0alpha or 1.0alpha2 available
later this week.

-jason

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Sat, 2 Mar 2002 17:41:59 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1112

JitterBug notification

new message incoming/1112

Message summary for PR#1112
	From: wyss@purdue.edu
	Subject: Problem using Bio::DB::Genbank
	Date: Sat, 2 Mar 2002 17:41:58 -0500
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From wyss@purdue.edu Sat Mar  2 17:41:58 2002
Received: from localhost (localhost [127.0.0.1])
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Date: Sat, 2 Mar 2002 17:41:58 -0500
Message-Id: <200203022241.g22MfwkO021731@pw600a.bioperl.org>
From: wyss@purdue.edu
To: bioperl-bugs@bioperl.org
Subject: Problem using Bio::DB::Genbank

Full_Name: Phillip Wyss
Module: Bio::SeqIO::fasta Bio::SeqIO::genbank
Version: 0.7.1
PerlVer: 5.6.0
OS: Linux
Submission from: mac1.chem.purdue.edu (128.210.143.22)


Trying to fetch sequence data from NT_011516
in fasta or genbank format fail using
Bio::DB:GenBank->get_seq_by_id.

Cause (fasta):

Bio::SeqIO::fasta sets the line terminator to
"\n>" which is found in the http response
before the beginning of the sequence and
complains the sequence looks like "<HTML".

Workaround:

my $seqIOobj = get_Stream_by_id([$id]);
if( $format =~ /fasta/i ) {
local $/ = '<pre>'; # data in preformatted HTML
$seqIOobj->_readline();
}
$seqdata = $seqIOobj->next_seq();

Cause?(genbank)

genbank format complains most probably because
there is no actual sequence data in the
genbank format, only header information.


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