[Bioperl-l] Genbank to gff3 conversion problem

Chris Mungall cjm at berkeleybop.org
Thu Jan 29 16:15:49 EST 2009


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 :-)


>
>
> chris
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