[Bioperl-l] bp_genbank2gff3.pl

David Breimann david.breimann at gmail.com
Sat Jul 24 04:06:19 EDT 2010


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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