[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1073 (fwd)

[Jason Stajich]

Hmm - you don't report your version of bioperl that you are running -
This works for me with the 0.9.3 release.  It may indeed work with the
0.7.2 release - I would make sure you at least have bioperl 0.7.2
installed.

-jason

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

---------- Forwarded message ----------
Date: Tue, 29 Jan 2002 21:46:48 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1073

JitterBug notification

new message incoming/1073

Message summary for PR#1073
	From: glen-charydczak@sugen.com
	Subject: Bio::DB::GenBank returns error for some accession numbers
	Date: Tue, 29 Jan 2002 21:46:38 -0500
	0 replies 	0 followups

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

>From glen-charydczak@sugen.com Tue Jan 29 21:46:47 2002
Received: from localhost (localhost [127.0.0.1])
	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g0U2kcit015785
	for <bioperl-bugs@pw600a.bioperl.org>; Tue, 29 Jan 2002 21:46:47 -0500
Date: Tue, 29 Jan 2002 21:46:38 -0500
Message-Id: <200201300246.g0U2kcit015785@pw600a.bioperl.org>
From: glen-charydczak@sugen.com
To: bioperl-bugs@bioperl.org
Subject: Bio::DB::GenBank returns error for some accession numbers

Full_Name: Glen Charydczak
Module: Bio::DB::GenBank
Version: unknown
PerlVer: 5.00503
OS: IRIX 6.5
Submission from: (NULL) (65.197.179.125)


Hi,

Some genbank accession numbers produce errors.

For instance, using this accession number :


use Bio::DB::GenBank;
use Bio::Seq;
use Bio::SeqIO;

$gb = new Bio::DB::GenBank();
$seq2 = $gb->get_Seq_by_acc('2072959');
$Sequence2 = $seq2->seq();
$Sequence2 = $seq2->display_id() . "\n" .$Sequence2;
print $Sequence2 . "\n";
exit(0);

produces :

HSU93568
GGGGGAGGAGCCAAGATGGCCGAATACGAACAGCTCCGGTCTACAGCTCCCAGCGTGAGCGACGCAGAAGACGGGTGATTTCTGCATTTCCATCTGAGGTACCGGGTTCATCTCACTAGGGAGTCCCAGA
etc...

while using this accession number :

use Bio::DB::GenBank;
use Bio::Seq;
use Bio::SeqIO;

$gb = new Bio::DB::GenBank();
$seq2 = $gb->get_Seq_by_acc('18148431');
$Sequence2 = $seq2->seq();
$Sequence2 = $seq2->display_id() . "\n" .$Sequence2;
print $Sequence2 . "\n";
exit(0);

produces :

-------------------- WARNING ---------------------
MSG: unable to parse location successfully out of AB040129.1:527..646, ignoring
feature (seqid=AB040129S2)
---------------------------------------------------
Can't call method "location" on an undefined value at
/usr/freeware/lib/perl5/site_perl/5.005/Bio/SeqIO/FTHelper.pm line 136.


Thanks!

Glen Charydczak
Programmer, Bioinformatics
SUGEN, Inc.
South San Francisco, CA


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