[Bioperl-l] Genbank to gff3 conversion problem

Chris Fields cjfields at illinois.edu
Thu Jan 29 08:39:10 EST 2009


On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote:

> 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.

Yes, but does it unflatten properly, or check GO for the correct terms  
(both important with GFF3)?

chris


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