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

[gert thijs]

The problem with this error is that I do not know where in my scripts things
are going wrong, since there is no trace given like in other errors. 
I go several times through the same genbank file in several consecutive
scripts, so maybe I am doing something wrong in my scripts. I will have to
print more debugging messages on screen to see when this error is produced. 
I will keep you informed.

Gert


Jason Stajich wrote:
> 
> 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);
> >
> >
> >
> > _______________________________________________
> > Bioperl-guts-l mailing list
> > Bioperl-guts-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-guts-l
> >
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center
> http://www.chg.duke.edu/

-- 
+ Gert Thijs              
+ 
+ email: gert.thijs@esat.kuleuven.ac.be 
+ homepage: http://www.esat.kuleuven.ac.be/~thijs
+ 
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