From GeneBank to .GFF

[ThePresident]

Hello everyone,

I'm working with an organism that doesn't have a proper .gff annotated file available on NCBI. However, I can have a full GeneBank file. Does anyone know how to "convert" or extract the information in order to create .gff from GeneBank? My organism has about 52 genes (a virus), so I guess I could almost do it manually, but still...

I have no true skills in programming, so... Any "easy" way of doing it?

TP

[mastal]

Have a look at the following links:

http://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

http://www.hpa-bioinformatics.org.uk/biosnippets/snippets/115

http://www.raetschlab.org/suppl/gff-tools

I have not used any of the scripts, though.

[ThePresident]

I used the first one and wow... It seemed to work perfectly in a fraction of a second! I'll try to use it in HTseq-count, but I think it should work.

Thanks a lot!!! I screened the web but missed this one!

[amitbik]

Hi There,
I am having error while converting genebank file to gff format.
I am using genbank2gff.pl perl script but i am getting following error

------------- EXCEPTION -------------
MSG: type_map values must be scalar or CODE ref. You said: ARRAY(0x19c5050) for type: tRNA
STACK Bio::SeqFeature::Tools::TypeMapper::map_types /usr/local/share/perl/5.14.2/Bio/SeqFeature/Tools/TypeMapper.pm:194
STACK main::unflatten_seq genbank2gff.pl:891
STACK toplevel genbank2gff.pl:395

Can any body help me to find out the error..?

Thanks in advance..