[Bioperl-l] bp_genbank2gff3.pl

Chris Mungall cjm at berkeleybop.org
Tue Jul 27 18:14:00 EDT 2010


Hi David

I can't replicate this, but I just pushed a change that gives more  
informative error messages on the 'circular' branch (same branch I  
pushed the unflattener temp fix for circular genomes)

On Jul 24, 2010, at 1:06 AM, David Breimann wrote:

> Hello,
>
> I'm trying to convert some genbank files downloaded from NCBI to GFF3
> format but I keep getting error messages.
>
> My bioperl version (according to perl -MBio::Perl -le 'print
> Bio::Perl->VERSION;') is 1.0069 (I use github live branch).
>
> For example, I am trying to convert CP000249.gbk
> (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk 
> ):
>
> $ bp_genbank2gff3.pl CP000249.gbk
> # Input: CP000249.gbk
> # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia
> sp. CcI3, complete genome.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: must be scalar or CODE ref
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/ 
> Root.pm:473
> STACK: Bio::SeqFeature::Tools::TypeMapper::map_types
> /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195
> STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930
> STACK: /usr/local/bin/bp_genbank2gff3.pl:411
> -----------------------------------------------------------
>
> Thanks,
> David
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