Re: [Gusdev-gusdev] Plugin for GenBank files

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

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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>
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