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

Chris Fields cjfields at illinois.edu
Tue Aug 17 15:24:23 EDT 2010


On Aug 17, 2010, at 10:53 AM, Chris Mungall wrote:

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

Will do.  I'll go ahead and delete the remote branch as well.

> 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

Yes, that is a problem that needs to be addressed.  Might be worth filing a bug report for tracking this; we can use David's example, or the one I recently added for phi-X174.

chris

> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
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