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

Chris Fields cjfields at illinois.edu
Tue Aug 17 09:51:02 EDT 2010


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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