[Bioperl-l] Genbank to gff3 conversion problem

Chris Fields cjfields at illinois.edu
Thu Jan 29 16:20:27 EST 2009


On Jan 29, 2009, at 3:15 PM, Chris Mungall wrote:

>
> On Jan 29, 2009, at 5:39 AM, Chris Fields wrote:
>
>>
>> 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)?
>
> I think you mean SO :-)

Yes, I stand corrected.

chris


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