Multiple location questions

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Multiple location questions

Jieyu Wang
Dear colleges,
I have a question about storing multiple locations for one feature.
Though CHADO schema allows this, I am not sure is there any script
similar to gmod_bulk_load_gff3 would parse this kind of information in
gff file, most probably in the 9 th column.
That is, read the distinct rank and locgroup  information for a single
feature and store them in feature_loc.

It seems current gmod_bulk_load_gff3 doesn't parse information like this.


Thank you all.
Have a great day,


Joy

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Re: Multiple location questions

Scott Cain
Hi Joy,

I think you are asking about the pan genome stuff Jim Hu has been
talking about, right?  Because the answer to that question is that no,
there is not currently a loader that will deal with that.  Added to
that is the problem that there hasn't been a standard developed for
how to deal with that data, so we're a little way away from modifying
the GFF loader to deal with that sort of data. I think the actual
modification should be fairly easy.

If that is not what you are asking about, please disregard the above
paragraph and describe a little better what it is you want to do.
With appropriately designed GFF, you might be able to do it without
too much modification to the loader.

Scott


On Mon, Aug 23, 2010 at 4:45 PM, Jieyu Wang <[hidden email]> wrote:

> Dear colleges,
> I have a question about storing multiple locations for one feature.
> Though CHADO schema allows this, I am not sure is there any script
> similar to gmod_bulk_load_gff3 would parse this kind of information in
> gff file, most probably in the 9 th column.
> That is, read the distinct rank and locgroup  information for a single
> feature and store them in feature_loc.
>
> It seems current gmod_bulk_load_gff3 doesn't parse information like this.
>
>
> Thank you all.
> Have a great day,
>
>
> Joy
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



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

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Re: Multiple location questions

Jieyu Wang
Thank you.
Yes, I am from Dr. Hu's Lab. It may not be difficult for experts like
you to modify the code so that gmod_bulk_load_gff3 can update features
and can "read" rank and loc_group. For me, it may take quite a while.
You know, lazy people always want the easiest way :). So if
gmod_bulk_load_gff3 could have the function of updating feature and
could "read" rank and loc_group, it really help.

Thank you again for your patience.

Joy


2010/8/23 Scott Cain <[hidden email]>:

> Hi Joy,
>
> I think you are asking about the pan genome stuff Jim Hu has been
> talking about, right?  Because the answer to that question is that no,
> there is not currently a loader that will deal with that.  Added to
> that is the problem that there hasn't been a standard developed for
> how to deal with that data, so we're a little way away from modifying
> the GFF loader to deal with that sort of data. I think the actual
> modification should be fairly easy.
>
> If that is not what you are asking about, please disregard the above
> paragraph and describe a little better what it is you want to do.
> With appropriately designed GFF, you might be able to do it without
> too much modification to the loader.
>
> Scott
>
>
> On Mon, Aug 23, 2010 at 4:45 PM, Jieyu Wang <[hidden email]> wrote:
>> Dear colleges,
>> I have a question about storing multiple locations for one feature.
>> Though CHADO schema allows this, I am not sure is there any script
>> similar to gmod_bulk_load_gff3 would parse this kind of information in
>> gff file, most probably in the 9 th column.
>> That is, read the distinct rank and locgroup  information for a single
>> feature and store them in feature_loc.
>>
>> It seems current gmod_bulk_load_gff3 doesn't parse information like this.
>>
>>
>> Thank you all.
>> Have a great day,
>>
>>
>> Joy
>>
>> ------------------------------------------------------------------------------
>> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>> Be part of this innovative community and reach millions of netbook users
>> worldwide. Take advantage of special opportunities to increase revenue and
>> speed time-to-market. Join now, and jumpstart your future.
>> http://p.sf.net/sfu/intel-atom-d2d
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
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Re: Multiple location questions

Scott Cain
Hi Joy,

I don't think it would be difficult for me to modify the loader, and I
imagine I will when the time comes.  The problem is that there is no
specification or standard describing what the GFF should look like, or
how that should be stored in Chado.  Without that, I really can't
modify the loader.  Someone has to write that up (probably as a
collaborative effort on this mailing list, but I don't know enough to
get that ball rolling).

Scott


On Mon, Aug 23, 2010 at 5:28 PM, Jieyu Wang <[hidden email]> wrote:

> Thank you.
> Yes, I am from Dr. Hu's Lab. It may not be difficult for experts like
> you to modify the code so that gmod_bulk_load_gff3 can update features
> and can "read" rank and loc_group. For me, it may take quite a while.
> You know, lazy people always want the easiest way :). So if
> gmod_bulk_load_gff3 could have the function of updating feature and
> could "read" rank and loc_group, it really help.
>
> Thank you again for your patience.
>
> Joy
>
>
> 2010/8/23 Scott Cain <[hidden email]>:
>> Hi Joy,
>>
>> I think you are asking about the pan genome stuff Jim Hu has been
>> talking about, right?  Because the answer to that question is that no,
>> there is not currently a loader that will deal with that.  Added to
>> that is the problem that there hasn't been a standard developed for
>> how to deal with that data, so we're a little way away from modifying
>> the GFF loader to deal with that sort of data. I think the actual
>> modification should be fairly easy.
>>
>> If that is not what you are asking about, please disregard the above
>> paragraph and describe a little better what it is you want to do.
>> With appropriately designed GFF, you might be able to do it without
>> too much modification to the loader.
>>
>> Scott
>>
>>
>> On Mon, Aug 23, 2010 at 4:45 PM, Jieyu Wang <[hidden email]> wrote:
>>> Dear colleges,
>>> I have a question about storing multiple locations for one feature.
>>> Though CHADO schema allows this, I am not sure is there any script
>>> similar to gmod_bulk_load_gff3 would parse this kind of information in
>>> gff file, most probably in the 9 th column.
>>> That is, read the distinct rank and locgroup  information for a single
>>> feature and store them in feature_loc.
>>>
>>> It seems current gmod_bulk_load_gff3 doesn't parse information like this.
>>>
>>>
>>> Thank you all.
>>> Have a great day,
>>>
>>>
>>> Joy
>>>
>>> ------------------------------------------------------------------------------
>>> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>>> Be part of this innovative community and reach millions of netbook users
>>> worldwide. Take advantage of special opportunities to increase revenue and
>>> speed time-to-market. Join now, and jumpstart your future.
>>> http://p.sf.net/sfu/intel-atom-d2d
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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

------------------------------------------------------------------------------
Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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