[Bioperl-l] bp_genbank2gff3.pl error with circular genomes

Chris Mungall CJMungall at lbl.gov
Tue Aug 17 11:53:15 EDT 2010


You can merge this in. It should allow David to proceed.

I haven't kept up on synchrony between bioperl and GFF on circular  
genomes. The above fix is conservative in that essentially preserves  
the genbank coordinates even when the origin is crossed:

	http://github.com/bioperl/bioperl-live/commit/d752a4cb5168d1bb01f8c80247a57f66b2bd9daf

However, if this is to conform to GFF3 then the resulting coordinates  
that cross the origin should have start/end incremented by the genome  
length

On Aug 17, 2010, at 6:51 AM, Chris Fields wrote:

> I think Chris Mungall has a branch set up for this in bioperl:
>
> http://github.com/bioperl/bioperl-live/tree/circular
>
> Is that correct?  Should we merge that code into the master branch?
>
> chris
>
> On Aug 17, 2010, at 8:44 AM, David Breimann wrote:
>
>> Hello,
>>
>> The following genbank has a gene that runs over the 'end" of the
>> chromosome and into its "beginning", and the script generates an
>> error.
>>
>> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_cereus_ATCC_10987/NC_005707.gbk
>>
>> NC_005707 Unflattening error:
>> Details:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: PROBLEM, SEVERITY==2
>> Ranges not in correct order. Strange ensembl genbank entry? Range:
>> [207497,208369] [1,687]
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/ 
>> Root.pm:473
>> STACK: Bio::SeqFeature::Tools::Unflattener::problem
>> /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:952
>> STACK:  
>> Bio::SeqFeature::Tools::Unflattener::_check_order_is_consistent
>> /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2842
>> STACK: Bio::SeqFeature::Tools::Unflattener::infer_mRNA_from_CDS
>> /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2713
>> STACK: Bio::SeqFeature::Tools::Unflattener::unflatten_seq
>> /usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:1532
>> STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:1023
>> STACK: /usr/local/bin/bp_genbank2gff3.pl:506
>> -----------------------------------------------------------
>>
>> Best,
>> Dave
>> _______________________________________________
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>



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