[Bioperl-l] Genbank to gff3 conversion problem

shafeeq rim hsa_rim at yahoo.co.in
Wed Jan 28 23:23:25 EST 2009


Hi,

I was trying my hands on  bp_genbank2gff3.pl script
in Bioperl but getting lots of errors. I first tried with .gbk file in
genbank and then .gbs file but still no success. I actually want Human
genome annotation file in gff3 format for my application. Is there any other
software or script for gff3 conversion from genbank format apart from
this bioperl script? Readseq utility is there but it converts only into
gff2.
I extracted and removed problematic file but still of no use NT_011512. 

I am getting errors like this :- 
I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk
##########################################################
STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549
STACK (eval) bp_genbank2gff3.pl:378
STACK main::unflatten_seq bp_genbank2gff3.pl:377
STACK toplevel bp_genbank2gff3.pl:229

--------------------------------------

Possible gene unflattening error withNT_011512: consult STDERR

------------- EXCEPTION  -------------
MSG: seq_id must be set
STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id
/usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242
STACK main::generic_features bp_genbank2gff3.pl:353
STACK toplevel bp_genbank2gff3.pl:254
#####################################################

Thanks in advance
Regards
Shafeeq


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