[Bioperl-l] load in biosql a genome genbank file

[Hilmar Lapp]

Which file exactly do you mean? The .gbk I find at NCBI looks like a 
perfectly normal genbank formatted file, and so shouldn't pose a 
problem for bioperl.

Also, you need to post the full error message or otherwise explain what 
you think isn't going the way you thought it should if you want help 
because otherwise I don't know what exactly you mean by 'works not'.

	-hilmar

On Nov 16, 2005, at 11:08 AM, gdi at gbf.de wrote:

> Hi Hilmar,
>
> the ncbi genome files are different from "normal" genbank files eg. for
> one gene. I tried it with the load_seqdatabase.pl, with a) swissprot
> genome file. (eg. LISMO.dat), b) genbank lmo genome file
> a) works
> b) not
>
> Or i am wrong?
>
> Guido
>
>
>> The genome is in genbank format, right? Generally speaking there is
>> little limit on what you can load into BioSQL; if you are referring to
>> load_seqdatabase.pl, it can load any format that's understood by the
>> Bio::SeqIO system in Bioperl.
>>
>> Let me know if you were thinking about something else.
>>
>> 	-hilmar
>>
>> On Nov 8, 2005, at 3:26 AM, Guido Dieterich wrote:
>>
>>> Hi
>>>
>>> is it possible to load into biosql a complete bacterial genome 
>>> genbank
>>> file
>>> from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/
>>>
>>> Best regards
>>>
>>> Guido
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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