[Gmod-help] Loading sequences with no GI in chado

[Scott Cain]

Hi Paul,

My best suggestion for you is to ask on the BioPerl mailing list if
the GenBank parser could be modified to work with this sort of input.
When you ask, I would suggest that you explain that you got this input
from someone else who will not reformat it into something a little
easier to use.

Failing getting BioPerl to work, I guess this would have to be handled
with a custom parser.

Scott


On Sat, Sep 26, 2009 at 3:51 AM, Paul Visendi <P.Visendi at cgiar.org> wrote:
> Hii Scott,
>
> Thanks for your quick reply.
>
> I had tried to do that but the parser did not work.i know i missed
> something.
>
> The files were from a sequencing project but the sequence has not been
> submitted to genbank.
>
> i have an original sample file in embl/genbank format with no headers too
>  ;-)
>
> I had removed the "FT" declarations so that that section resembles genbank
> files. and added header sections
>
> how would i best transform this file into a genbank file so that i can parse
> it as below with
>
> bp_genbank2gff3.pl so as to be able to load it into the database (Chado) as
> below?
>
>
>          bp_genbank2gff3.pl -noCDS -s chr_1.gb
>
> please find attached the file
>
>
> On Sep 25, 2009, at 4:17 PM, Scott Cain wrote:
>
>> Or, would it be possible to add text to it to make it look more like a
>> GenBank file so the BioPerl parser would be able to work with it?
>>
>>
>> On Fri, Sep 25, 2009 at 9:16 AM, Scott Cain <scott at scottcain.net> wrote:
>>>
>>> Hi Paul,
>>>
>>> So what you have is files formatted like GenBank files, but not actual
>>> GenBank files?  Where did the data come from?  If converting those
>>> isn't working properly, it is really a BioPerl problem (though still
>>> ultimately our problem :-)
>>>
>>> What does happen?  Would it be possible to go back to the originator
>>> of this file to get it in some other format?
>>>
>>> Scott
>>>
>>>
>>>
>>>
>>> On Fri, Sep 25, 2009 at 2:06 AM, Paul Visendi <P.Visendi at cgiar.org>
>>> wrote:
>>>>
>>>> Halo Help desk,
>>>>
>>>> We at the International Livestock Research Institute have sequenced a
>>>> strain
>>>> of Theileria parva .
>>>>
>>>> we have set up chado on postgresql and we are trying to store this
>>>> sequence
>>>> information in the chado schema.
>>>>
>>>> converting this sequence files to GFF3 has been a problem. How can this
>>>> be
>>>> done since the files we  have are in genbank format without accession
>>>> numbers, GI identifiers etc
>>>>
>>>> only the features section exists
>>>>
>>>> Thank you in advance,
>>>>
>>>> visendi
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research