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

Chris Fields cjfields at illinois.edu
Tue Aug 17 23:42:59 EDT 2010


Chris, David, 

The branch is now merged back to trunk.  David, let us know if this helps.

chris (f)

On Aug 17, 2010, at 2:24 PM, Chris Fields wrote:

> 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
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>>> 
>> 
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