[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/930

[Jason Stajich]

Hmm, I am pretty sure this behaviour was fixed already -- but of course
not in the 0.7 release and and I have not propigated fix to 07 branch yet
because I wanted to test it some more.  I probably need to get moving on
putting it on the branch....

I run the following code on the live branch and do not get any errors.
#!/usr/local/bin/perl -w
use strict;

use Bio::SeqIO;

my $seqio = new Bio::SeqIO(-format => 'genbank',
                           -file => 'AP000413.gb');

while( my $seq = $seqio->next_seq ) {
    print "name is ", $seq->display_id(), "\n";
    foreach my $feature ( $seq->top_SeqFeatures ) {
        print "feature=", $feature->primary_tag, ",",
        $feature->start, "..", $feature->end, "\n";
    }
}

% perl test.pl
name is AP000413
feature=source,1..65047
feature=CDS,963..1631
feature=CDS,6390..11243
feature=CDS,13262..13496
feature=CDS,14090..15288
feature=CDS,15962..16674
feature=CDS,18333..19733
feature=CDS,20115..20747
feature=CDS,23635..24161
feature=CDS,24545..26104
feature=CDS,27042..27701
feature=CDS,31773..33020
feature=CDS,33699..34562
feature=CDS,38249..39115
feature=CDS,39507..41796
feature=CDS,46741..48373
feature=CDS,48818..51971
feature=CDS,54094..54909
feature=CDS,56217..57022
feature=CDS,57696..58130
feature=CDS,59757..59981
feature=CDS,60316..60816
feature=exon,63349..63420
feature=exon,63938..64093
feature=exon,64184..64939
feature=exon,65025..65047

-Jason

On Wed, 21 Mar 2001 bioperl-bugs@bioperl.org wrote:

> JitterBug notification
>
> new message incoming/930
>
> Message summary for PR#930
> 	From: gert.thijs@esat.kuleuven.ac.be
> 	Subject: calling location on undefined object
> 	Date: Wed, 21 Mar 2001 06:17:46 -0500
> 	0 replies 	0 followups
>
> ====> ORIGINAL MESSAGE FOLLOWS <====
>
> >From gert.thijs@esat.kuleuven.ac.be Wed Mar 21 06:17:46 2001
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.11.2/8.11.2) with ESMTP id f2LBHj223188
> 	for <bioperl-bugs@pw600a.bioperl.org>; Wed, 21 Mar 2001 06:17:46 -0500
> Date: Wed, 21 Mar 2001 06:17:46 -0500
> Message-Id: <200103211117.f2LBHj223188@pw600a.bioperl.org>
> From: gert.thijs@esat.kuleuven.ac.be
> To: bioperl-bugs@bioperl.org
> Subject: calling location on undefined object
>
> Full_Name: Gert Thijs
> Module: SeqIO::FTHelper
> Version: 0.7
> PerlVer: 5.6.0
> OS: Linux RedHat 6.2
> Submission from: cisco-cache-1.kuleuven.ac.be (134.58.253.113)
>
>
> While parsing a genbank file, I got the following error:
>
> Can't call method "location" on an undefined value at
> /users/sista/thijs/perl/lib/site_perl/5.6.0/Bio/SeqIO/FTHelper.pm line 136,
> <GEN0> line 228.
> The code at line 136 in FTHelper.pm there is
> $sf->location($splitlocation);
>
> The problem occurs when there is a problem parsing the location line. The else
> part in the preceding block returns undef for $sf.
>
> adding an extra check seems to solve the problem:
> $sf->location($splitlocation) if defined($sf);
>
>
>
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>

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/