Changing type of seqlen column in feature table to 'bigint'

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Changing type of seqlen column in feature table to 'bigint'

Mara Kim-2
Hello everyone,

I am currently trying to change the type of the seqlen column in the
feature table to 'bigint', in order to store lengths of very long
features.  However, it seems that there are many views in the so.*
schema that depend on this column.  Is there a way to drop these views
and recreate them en masse?

Thank you,
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


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Re: Changing type of seqlen column in feature table to 'bigint'

adf_ncgr
Hi Mara-
I'm no expert, but it looks like the script:
create-so-bridge.pl
in the chado distribution will probably do what you want (see the --drop
option).

HTH

Andrew Farmer

On 6/12/14 12:31 PM, Mara Kim wrote:

> Hello everyone,
>
> I am currently trying to change the type of the seqlen column in the
> feature table to 'bigint', in order to store lengths of very long
> features.  However, it seems that there are many views in the so.*
> schema that depend on this column.  Is there a way to drop these views
> and recreate them en masse?
>
> Thank you,
> Mara Kim
>
> Ph.D. Candidate
> Computational Biology
> Vanderbilt University
> Nashville, TN
>
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

--
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche


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Re: Changing type of seqlen column in feature table to 'bigint'

Mara Kim-3
Hi Andrew,

This looks like exactly what I needed.

However, there appear to be a few more dependencies outside the SO
layer.  Specifically the  chado.fnr_type, chado.f_loc, chado.f_type,
chado.protein_coding_gene, chado.gff3view  VIEWs.  Are these views
part of chado proper?  In that case, I think manually dropping and
creating them would be reasonable.

On Thu, Jun 12, 2014 at 3:07 PM, Andrew Farmer <[hidden email]> wrote:

> Hi Mara-
> I'm no expert, but it looks like the script:
> create-so-bridge.pl
> in the chado distribution will probably do what you want (see the --drop
> option).
>
> HTH
>
> Andrew Farmer
>
> On 6/12/14 12:31 PM, Mara Kim wrote:
>> Hello everyone,
>>
>> I am currently trying to change the type of the seqlen column in the
>> feature table to 'bigint', in order to store lengths of very long
>> features.  However, it seems that there are many views in the so.*
>> schema that depend on this column.  Is there a way to drop these views
>> and recreate them en masse?
>>
>> Thank you,
>> Mara Kim
>>
>> Ph.D. Candidate
>> Computational Biology
>> Vanderbilt University
>> Nashville, TN
>>
>>
>> ------------------------------------------------------------------------------
>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
>> Find What Matters Most in Your Big Data with HPCC Systems
>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>> http://p.sf.net/sfu/hpccsystems
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> --
> ...all concepts in which an entire process is semiotically concentrated
> elude definition; only that which has no history is definable.
>
> Friedrich Nietzsche
>
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema



--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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Re: Changing type of seqlen column in feature table to 'bigint'

adf_ncgr
Hi again-
these do seem to be defined with "CREATE OR REPLACE VIEW" stanzas in the
file that
I guess would be considered "chado proper", ie ./modules/default_schema.sql
(although the so.* views seem be in there too, so perhaps it's not
_that_ proper...)

hope this isn't a case of the blind leading the blind... ;) in any case,
I guess you
ought to be able to get the little extra you need from there one way or
another.

Andrew


On 6/12/14 3:26 PM, Mara Kim wrote:

> Hi Andrew,
>
> This looks like exactly what I needed.
>
> However, there appear to be a few more dependencies outside the SO
> layer.  Specifically the  chado.fnr_type, chado.f_loc, chado.f_type,
> chado.protein_coding_gene, chado.gff3view  VIEWs.  Are these views
> part of chado proper?  In that case, I think manually dropping and
> creating them would be reasonable.
>
> On Thu, Jun 12, 2014 at 3:07 PM, Andrew Farmer <[hidden email]> wrote:
>> Hi Mara-
>> I'm no expert, but it looks like the script:
>> create-so-bridge.pl
>> in the chado distribution will probably do what you want (see the --drop
>> option).
>>
>> HTH
>>
>> Andrew Farmer
>>
>> On 6/12/14 12:31 PM, Mara Kim wrote:
>>> Hello everyone,
>>>
>>> I am currently trying to change the type of the seqlen column in the
>>> feature table to 'bigint', in order to store lengths of very long
>>> features.  However, it seems that there are many views in the so.*
>>> schema that depend on this column.  Is there a way to drop these views
>>> and recreate them en masse?
>>>
>>> Thank you,
>>> Mara Kim
>>>
>>> Ph.D. Candidate
>>> Computational Biology
>>> Vanderbilt University
>>> Nashville, TN
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
>>> Find What Matters Most in Your Big Data with HPCC Systems
>>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>>> http://p.sf.net/sfu/hpccsystems
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> --
>> ...all concepts in which an entire process is semiotically concentrated
>> elude definition; only that which has no history is definable.
>>
>> Friedrich Nietzsche
>>
>>
>> ------------------------------------------------------------------------------
>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
>> Find What Matters Most in Your Big Data with HPCC Systems
>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>> http://p.sf.net/sfu/hpccsystems
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>

--
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche


------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
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Re: Changing type of seqlen column in feature table to 'bigint'

Karl O. Pinc
On 06/12/2014 04:50:35 PM, Andrew Farmer wrote:

> Hi again-
> these do seem to be defined with "CREATE OR REPLACE VIEW" stanzas in
> the
> file that
> I guess would be considered "chado proper", ie
> ./modules/default_schema.sql
> (although the so.* views seem be in there too, so perhaps it's not
> _that_ proper...)
>
> hope this isn't a case of the blind leading the blind... ;) in any
> case,
> I guess you
> ought to be able to get the little extra you need from there one way
> or
> another.

I also don't know what I'm doing.  But I suspect that
the views you need are all defined in the default_schema.sql
file.  The problem is that there's no way to grep them
out.

There's likewise no way to grep out the views from
all the sql in the modules directory.

(I've thought of a better way to do chado installs.
If anyone wants to talk about it I think a phone
call would be best.  I've no plans of actually doing
the work....)

It might be eaiser to use pg to get the views out.
You could, for example, use the pg "information" (iirc?)
schema to get a list of all the views.  Then take
that list and transform it into a pg_dump command
with a -t for each view.  Dump as sql.

You might also need to take the list of views and
put a "DROP VIEW" in front of each and feed the
result to psql before restore.

Regards,


Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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