[Bioperl-l] [Bioperl-guts-l] Bug in genbank.pm?

Chris Fields cjfields at illinois.edu
Fri Jun 5 16:43:04 EDT 2009

(Just so this is going to the correct list)


I'll look into it.  This may have been fixed in between the releases,  

There isn't a PPM available for 1.6 yet (several prereqs were missing  
at the time of the 1.6 release, such as Graphviz and so on).  A bug  
report is in the queue for this, though, as a reminder.  I think those  
are now available, though, so we should *theoretically* be capable of  
getting a PPM ready.  I say 'theoretically' b/c I don't have easy  
access to a PC running Windows (I have moved to OS X).  I'll see what  
I can do about that in the next few weeks.

In the meantime, if you need it you can download 1.6 or the 'nightly  
build' version (nightly snapshots of svn code) and add it to PERL5LIB  
or "use lib 'PATH_TO_BIOPERL';" in your scripts; it should work.

Nightly builds:



On Jun 4, 2009, at 10:17 PM, Barbeitos, Marcos wrote:

> OK, I attached the first record for both files.  These are GenBank  
> flat files that were emailed to us and transferred from Macs to PCs,  
> so I am not sure if the encoding/line terminations got messed up at  
> some point.  I converted the line terminations to Unix and the  
> encoding to Western European Windows, still, it didn't work. May be  
> worth it mention that BioEdit did understand the format after I  
> fixed the encoding.
> The data was erased because my boss is kind of finicky about sharing  
> information.  However, I tested the files attached to this email and  
> got the same results.
> I am still using Bio-Perl 1.5.2_100 in a PC, PPM has not flagged the  
> availability of an upgrade from CPAN, are you releasing the PPD as  
> well?
> Thanks!
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Thu 6/4/2009 8:05 PM
> To: Barbeitos, Marcos
> Cc: bioperl-guts-l at lists.open-bio.org
> Subject: Re: [Bioperl-guts-l] Bug in genbank.pm?
> Marcos,
> We need the GenBank file (or the accession) you are attempting to
> parse.  Also, what version are you using?  We have released v. 1.6 on
> CPAN, and I intend on releasing 1.6.1 soon.
> chris
> On Jun 4, 2009, at 5:57 PM, Marcos S. Barbeitos wrote:
>> Hello.  I am trying to parse the Info from GeneBank flat files using
>> Bio::SeqIO.  I got two file which are virtually identical and one of
>> them
>> gets parsed just fine.  However, in the case of the other, the  
>> program
>> croaks when trying to parse the features and gives me:
>> -------------------- WARNING ---------------------
>> MSG: Unexpected error in feature table for  Skipping feature,
>> attempting to
>> recover
>> ---------------------------------------------------
>> I noticed that it does that after it reads the entry '/organism' in
>> Features.  The only difference I can see between the two files is the
>> presence of the feature ' /organelle' and of the line BASE COUNT in
>> one of
>> them, but the error persists even after I remove these lines.  Apart
>> from
>> that, there are the number of white spaces that precede the
>> beginning of
>> each line.   Any ideas?
>> Thanks!
>> Marcos S. Barbeitos
>> Post-Doc Fellow
>> The University of Kansas
>> Department of Ecology and Evolutionary Biology
>> 2041 Haworth Hall
>> 1200 Sunnyside Avenue
>> Lawrence, Kansas 66045
>> p: 785.864.5887
>> f: 785.864.5860
>> _______________________________________________
>> Bioperl-guts-l mailing list
>> Bioperl-guts-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l
> <BioPerlTest.gb>

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