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

David Breimann david.breimann at gmail.com
Tue Aug 17 09:44:08 EDT 2010


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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