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

Chris Fields cjfields at illinois.edu
Wed Aug 18 14:24:16 EDT 2010


Okay, will file this as a bug.  Thanks!

chris

On Aug 18, 2010, at 1:46 AM, David Breimann wrote:

> Dear Chris's,
> 
> I tested the updated version on multiple genomes that previously
> returned errors (for future reference: NC_005707, NC_006578,
> NC_007103, NC_007104, NC_007106, NC_007107, NC_008573, NC_008762,
> NC_008763, NC_008785, NC_009457, NC_012040). The script now ends
> normally on all of them. However, as you mentioned, the result GFF3
> file does not comply with GFF3 specifications for circular genomes.
> This in turn causes some unexpected results in other applications.
> 
> Best,
> Dave
> 
> On Wed, Aug 18, 2010 at 6:42 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> 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
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
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