[Bioperl-l] Genbank to gff3 conversion problem

Dan Bolser dan.bolser at gmail.com
Thu Jan 29 06:58:07 EST 2009


2009/1/29 shafeeq rim <hsa_rim at yahoo.co.in>:
> 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.

You could try this one liner:

perl -MBio::SeqIO -e '
 $s = Bio::SeqIO->new( -file => shift )->next_seq;
 print "# ", $s->feature_count, "\n";
 print $_->gff_string, "\n" foreach $s->get_SeqFeatures

' my.gbf > my.gbf.gff

Which is roughly equivalent to the bp_genbank2gff3.pl ;-)


Dan.


> 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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