Re: [Gusdev-gusdev] GI Number

[Deborah F. P. <pi...@pc...>]

Sorry, I missed that. GBParser does store cds information for cds features 
in the dots.transcript table including the source_id in the protein_id 
column but not other identifiers as GI number.

                                                     Debbie

On Mon, 27 Sep 2004, Jinal Jhaveri wrote:

> Deborah,
>
> Actually the GI number in externasequence is only for the whole sequence. I
> was talking about the one related to each cds
>
>
> thank you
> --Jinal
> On Monday 27 September 2004 08:17 am, Deborah F. Pinney wrote:
>> The GBParser puts GI:Number into the secondary_identifier field of
>> dots.externalnasequence.
>>
>>                                             -Deborah
>>
>> On Fri, 24 Sep 2004, Jinal Jhaveri wrote:
>>> Ed,
>>>
>>> You need to look into
>>> dots.nafeatureimp (or dots.nafeature
>>> view/dots.transcript/dots.rnafeature....views.)
>>> dots.nalocation,
>>> dots.nasequence,
>>> dots.nagene,
>>> dots.naentry,
>>> dots.nafeaturecomment,
>>> dots.nafeaturenagene,
>>> dots.naprotein,
>>> dots.nafeaturenaprotein,
>>> dots.nasequenceorganelle
>>> tables.
>>>
>>> for entried made by gbparser
>>>
>>> On Friday 24 September 2004 01:52 pm, Ed Robinson wrote:
>>>> Yes, please pass any extra scripts along.  To your recollection, which
>>>> features does it import?
>>>>
>>>> thanks
>>>> -Ed
>>>>
>>>>> From: Jinal Jhaveri <jjh...@vb...>
>>>>> Date: 2004/09/24 Fri PM 01:40:12 EDT
>>>>> To: ed_...@be...
>>>>> Subject: Re: [Gusdev-gusdev] Plugin for GenBank files
>>>>>
>>>>> Hi Ed,
>>>>>
>>>>> I haven't done development, but I have been using this since a long
>>>>> time. GBparser will work in most cases . I used the word "most cases"
>>>>> because it failes for some newly introduced field in the genbank.
>>>>> Though one thing it doesn't parse is the GI: Number. I have written a
>>>>> small bioperl script as an addendum to gbparser, if you want the GI
>>>>> number too
>>>>>
>>>>>
>>>>> --Jinal
>>>>>
>>>>> On Friday 24 September 2004 01:29 pm, Ed Robinson wrote:
>>>>>> I've found GBParser.pm which seems to do the trick.  It calls on some
>>>>>> CBIL packages which parse GenBank files.  Nice, elegant PERL (elegant
>>>>>> is not normally a word I associate with PERL).  If anyone out there
>>>>>> has done development on these, I'd like to chat a bit to make sure I
>>>>>> have a full grasp on these packages before I start trying to parse
>>>>>> data.
>>>>>>
>>>>>> thanks
>>>>>> -Ed
>>>>>>
>>>>>>> From: Ed Robinson <ed_...@be...>
>>>>>>> Date: 2004/09/24 Fri PM 01:10:06 EDT
>>>>>>> To: <gus...@li...>
>>>>>>> Subject: [Gusdev-gusdev] Plugin for GenBank files
>>>>>>>
>>>>>>> Has anyone written a (partial) plugin for extracting data from
>>>>>>> GenBank data?  I have a copy of the annotated Crypto data I pulled
>>>>>>> via the NCBI seq viewer and I want to load this data into GUS.
>>>>>>> Please let me know if there is anything ready to use to load any part
>>>>>>> of this data.
>>>>>>>
>>>>>>> thanks in advance,
>>>>>>> -Ed
>>>>>>>
>>>>>>>
>>>>>>> Ed Robinson
>>>>>>> 255 Deerfield Rd
>>>>>>> Bogart, GA 30622
>>>>>>> (706)425-9181
>>>>>>> http://www.electedrobinson.com
>>>>>>>
>>>>>>> --Learn more about the face of your neighbor, and less about your
>>>>>>> own. -Sargent Shriver
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>> Ed Robinson
>>>>>> 255 Deerfield Rd
>>>>>> Bogart, GA 30622
>>>>>> (706)425-9181
>>>>>> http://www.electedrobinson.com
>>>>>>
>>>>>> --Learn more about the face of your neighbor, and less about your own.
>>>>>>          -Sargent Shriver
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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