gusdev-gusdev — Topics concerning GUS development

Re: Re: [Gusdev-gusdev] GI Number

[Ed R. <ed_...@be...>]

I modified the views using Oracle Enterprise Manager.  I did not make the modifications through a GUS Build.  I have only done a straight GUS install, so I am not sure where to make the modifications in the project_home to make these changes correctly.

Sorry, I'm still a newbie to GUS, and there isn't much documentation beyond he straight-forward installation docs.

-Ed


> 
> From: Jinal Jhaveri <jjh...@vb...>
> Date: 2004/09/27 Mon PM 01:00:14 EDT
> To: Ed Robinson <ed_...@be...>
> CC: gus...@li...
> Subject: Re: [Gusdev-gusdev] GI Number
> 
> They are created automatically when you compile or build gus
> 
> On Monday 27 September 2004 12:50 pm, you wrote:
> > What about the PERL objects in Model/ ?  Do we need to modify any of those
> > so they will work with the modified views?
> >
> > -Ed
> >
> > > From: "Deborah F. Pinney" <pi...@pc...>
> > > Date: 2004/09/27 Mon PM 12:28:38 EDT
> > > To: Angel Pizarro <an...@pc...>
> > > CC: Ed Robinson <ed_...@be...>,
> > >         Jinal Jhaveri <jjh...@vb...>,
> > >         gus...@li...
> > > Subject: Re: [Gusdev-gusdev] GI Number
> > >
> > > Angel is correct. locus_tag is a relatively new (new to the GBParser)
> > > qualifier for existing features, including gene which is already mapped
> > > to dots.GeneFeature. Therefore, my advise was wrong, it should not be
> > > added to the mapping list in the perl module. Adding this field to the
> > > view should fix the problem for "gene" features.
> > >
> > > As genbank adds features and qualifiers and since the parser was tailored
> > > for genbank records, we are going to encounter this problem again. A
> > > compounding problem is that a qualifier is generally not exclusive to a
> > > single feature. In this case, locus_id really should be added to many
> > > views.
> > >
> > >                                                    -Debbie
> > >
> > > On Mon, 27 Sep 2004, Angel Pizarro wrote:
> > > > Deborah F. Pinney wrote:
> > > >> locus_tag is not in the list of features in the GBParser. It will have
> > > >> to be added with a table(actually view) destination. Which view is
> > > >> appropriate for this feature? What are the attributes (from the
> > > >> Genbank feature table) for this feature? I'll gladly add this and you
> > > >> can test it or you can add it and test and then commit to cvs.
> > > >
> > > > Let me clarify. "locus_tag" is not a GenBank feature, it is a feature
> > > > attribute of the GenBank "gene" feature. The feature is belongs to is
> > > > being mapped to DoTS::GeneFeature. Here is the example from the GB
> > > > record for this feature attribute, available here :
> > > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=462293
> > > >67
> > > >
> > > > gene
> > > > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819
> > > >&view=gbwithparts> complement(<6844..>9270)
> > > >                    /locus_tag="cgd7_10"
> > > >
> > > >
> > > > Thomas' suggestion of adding the attribute "locus_tag" to the
> > > > GeneFeature view and recompiling the objects will work in this case,
> > > > but be a problem for anyone else trying to capture this feature
> > > > attribute.
> > > >
> > > > The GBParser has several known problems, this being one of them. Maybe
> > > > we should start up a wiki for it to aid in development and
> > > > documentation.
> > > >
> > > > Angel
> > > >
> > > >> It should be added  >line 808, following my %featureNameTableMapping =
> > > >> (
> > > >>
> > > >> If the attributes are correct in the mapped table (match the genbank
> > > >> attributes), this should work. If this table is not in the
> > > >> %classChildList, it should also be added to the appropriate line also.
> > > >>
> > > >>                                                -Deborah
> > > >>
> > > >> On Mon, 27 Sep 2004, Ed Robinson wrote:
> > > >>> So far, down here, I can tell that it is parsing the files for crypto
> > > >>> correctly, but I is giving me the following error:
> > > >>>
> > > >>>
> > > >>> ********GEtting loc below6844
> > > >>>
> > > >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
> > > >>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::     
> > > >>> cgd7_10
> > > >>>
> > > >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
> > > >>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::     
> > > >>> cgd7_10
> > > >>>
> > > >>> Do you have any ideas why it is disliking my locus_tags?  I am
> > > >>> running this without the commit on, if it is looking for this again
> > > >>> in the database.
> > > >>>
> > > >>> Thanks for all the help on this.  I don't want to change anything
> > > >>> that is working, just figure out how to use it.
> > > >>>
> > > >>> -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
> > > >>
> > > >> -------------------------------------------------------
> > > >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > > >> Project Admins to receive an Apple iPod Mini FREE for your judgement
> > > >> on who ports your project to Linux PPC the best. Sponsored by IBM.
> > > >> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > > >> _______________________________________________
> > > >> Gusdev-gusdev mailing list
> > > >> Gus...@li...
> > > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> > 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
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

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

Re: [Gusdev-gusdev] GI Number

[Jinal J. <jjh...@vb...>]

They are created automatically when you compile or build gus

On Monday 27 September 2004 12:50 pm, you wrote:
> What about the PERL objects in Model/ ?  Do we need to modify any of those
> so they will work with the modified views?
>
> -Ed
>
> > From: "Deborah F. Pinney" <pi...@pc...>
> > Date: 2004/09/27 Mon PM 12:28:38 EDT
> > To: Angel Pizarro <an...@pc...>
> > CC: Ed Robinson <ed_...@be...>,
> >         Jinal Jhaveri <jjh...@vb...>,
> >         gus...@li...
> > Subject: Re: [Gusdev-gusdev] GI Number
> >
> > Angel is correct. locus_tag is a relatively new (new to the GBParser)
> > qualifier for existing features, including gene which is already mapped
> > to dots.GeneFeature. Therefore, my advise was wrong, it should not be
> > added to the mapping list in the perl module. Adding this field to the
> > view should fix the problem for "gene" features.
> >
> > As genbank adds features and qualifiers and since the parser was tailored
> > for genbank records, we are going to encounter this problem again. A
> > compounding problem is that a qualifier is generally not exclusive to a
> > single feature. In this case, locus_id really should be added to many
> > views.
> >
> >                                                    -Debbie
> >
> > On Mon, 27 Sep 2004, Angel Pizarro wrote:
> > > Deborah F. Pinney wrote:
> > >> locus_tag is not in the list of features in the GBParser. It will have
> > >> to be added with a table(actually view) destination. Which view is
> > >> appropriate for this feature? What are the attributes (from the
> > >> Genbank feature table) for this feature? I'll gladly add this and you
> > >> can test it or you can add it and test and then commit to cvs.
> > >
> > > Let me clarify. "locus_tag" is not a GenBank feature, it is a feature
> > > attribute of the GenBank "gene" feature. The feature is belongs to is
> > > being mapped to DoTS::GeneFeature. Here is the example from the GB
> > > record for this feature attribute, available here :
> > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=462293
> > >67
> > >
> > > gene
> > > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819
> > >&view=gbwithparts> complement(<6844..>9270)
> > >                    /locus_tag="cgd7_10"
> > >
> > >
> > > Thomas' suggestion of adding the attribute "locus_tag" to the
> > > GeneFeature view and recompiling the objects will work in this case,
> > > but be a problem for anyone else trying to capture this feature
> > > attribute.
> > >
> > > The GBParser has several known problems, this being one of them. Maybe
> > > we should start up a wiki for it to aid in development and
> > > documentation.
> > >
> > > Angel
> > >
> > >> It should be added  >line 808, following my %featureNameTableMapping =
> > >> (
> > >>
> > >> If the attributes are correct in the mapped table (match the genbank
> > >> attributes), this should work. If this table is not in the
> > >> %classChildList, it should also be added to the appropriate line also.
> > >>
> > >>                                                -Deborah
> > >>
> > >> On Mon, 27 Sep 2004, Ed Robinson wrote:
> > >>> So far, down here, I can tell that it is parsing the files for crypto
> > >>> correctly, but I is giving me the following error:
> > >>>
> > >>>
> > >>> ********GEtting loc below6844
> > >>>
> > >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
> > >>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::     
> > >>> cgd7_10
> > >>>
> > >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER
> > >>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::     
> > >>> cgd7_10
> > >>>
> > >>> Do you have any ideas why it is disliking my locus_tags?  I am
> > >>> running this without the commit on, if it is looking for this again
> > >>> in the database.
> > >>>
> > >>> Thanks for all the help on this.  I don't want to change anything
> > >>> that is working, just figure out how to use it.
> > >>>
> > >>> -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
> > >>
> > >> -------------------------------------------------------
> > >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > >> Project Admins to receive an Apple iPod Mini FREE for your judgement
> > >> on who ports your project to Linux PPC the best. Sponsored by IBM.
> > >> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > >> _______________________________________________
> > >> Gusdev-gusdev mailing list
> > >> Gus...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
> 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

Re: Re: [Gusdev-gusdev] GI Number

[Ed R. <ed_...@be...>]

What about the PERL objects in Model/ ?  Do we need to modify any of those so they will work with the modified views?

-Ed


> 
> From: "Deborah F. Pinney" <pi...@pc...>
> Date: 2004/09/27 Mon PM 12:28:38 EDT
> To: Angel Pizarro <an...@pc...>
> CC: Ed Robinson <ed_...@be...>, 
>         Jinal Jhaveri <jjh...@vb...>, 
>         gus...@li...
> Subject: Re: [Gusdev-gusdev] GI Number
> 
> Angel is correct. locus_tag is a relatively new (new to the GBParser) 
> qualifier for existing features, including gene which is already mapped 
> to dots.GeneFeature. Therefore, my advise was wrong, it should not be 
> added to the mapping list in the perl module. Adding this field to the 
> view should fix the problem for "gene" features.
> 
> As genbank adds features and qualifiers and since the parser was tailored 
> for genbank records, we are going to encounter this problem again. A 
> compounding problem is that a qualifier is generally not exclusive to a 
> single feature. In this case, locus_id really should be added to many 
> views.
> 
>                                                    -Debbie
> 
> On Mon, 27 Sep 2004, Angel Pizarro wrote:
> 
> > Deborah F. Pinney wrote:
> >
> >> locus_tag is not in the list of features in the GBParser. It will have to 
> >> be added with a table(actually view) destination. Which view is 
> >> appropriate for this feature? What are the attributes (from the Genbank 
> >> feature table) for this feature? I'll gladly add this and you can test it 
> >> or you can add it and test and then commit to cvs.
> >> 
> > Let me clarify. "locus_tag" is not a GenBank feature, it is a feature 
> > attribute of the GenBank "gene" feature. The feature is belongs to is being 
> > mapped to DoTS::GeneFeature. Here is the example from the GB record for this 
> > feature attribute, available here :
> > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46229367
> >
> > gene 
> > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819&view=gbwithparts> 
> > complement(<6844..>9270)
> >                    /locus_tag="cgd7_10"
> >
> >
> > Thomas' suggestion of adding the attribute "locus_tag" to the GeneFeature 
> > view and recompiling the objects will work in this case, but be a problem for 
> > anyone else trying to capture this feature attribute.
> >
> > The GBParser has several known problems, this being one of them. Maybe we 
> > should start up a wiki for it to aid in development and documentation.
> >
> > Angel
> >
> >
> >> It should be added  >line 808, following my %featureNameTableMapping = (
> >> 
> >> If the attributes are correct in the mapped table (match the genbank 
> >> attributes), this should work. If this table is not in the 
> >> %classChildList, it should also be added to the appropriate line also.
> >> 
> >>                                                -Deborah
> >> 
> >> On Mon, 27 Sep 2004, Ed Robinson wrote:
> >> 
> >>> So far, down here, I can tell that it is parsing the files for crypto 
> >>> correctly, but I is giving me the following error:
> >>> 
> >>> 
> >>> ********GEtting loc below6844
> >>> 
> >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER 
> >>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
> >>> 
> >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER 
> >>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
> >>> 
> >>> Do you have any ideas why it is disliking my locus_tags?  I am running 
> >>> this without the commit on, if it is looking for this again in the 
> >>> database.
> >>> 
> >>> Thanks for all the help on this.  I don't want to change anything that 
> >>> is working, just figure out how to use it.
> >>> 
> >>> -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
> >>> 
> >>> 
> >>> 
> >> 
> >> 
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> >> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> >> who ports your project to Linux PPC the best. Sponsored by IBM.
> >> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
> 

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

Re: [Gusdev-gusdev] GI Number

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

Angel is correct. locus_tag is a relatively new (new to the GBParser) 
qualifier for existing features, including gene which is already mapped 
to dots.GeneFeature. Therefore, my advise was wrong, it should not be 
added to the mapping list in the perl module. Adding this field to the 
view should fix the problem for "gene" features.

As genbank adds features and qualifiers and since the parser was tailored 
for genbank records, we are going to encounter this problem again. A 
compounding problem is that a qualifier is generally not exclusive to a 
single feature. In this case, locus_id really should be added to many 
views.

                                                   -Debbie

On Mon, 27 Sep 2004, Angel Pizarro wrote:

> Deborah F. Pinney wrote:
>
>> locus_tag is not in the list of features in the GBParser. It will have to 
>> be added with a table(actually view) destination. Which view is 
>> appropriate for this feature? What are the attributes (from the Genbank 
>> feature table) for this feature? I'll gladly add this and you can test it 
>> or you can add it and test and then commit to cvs.
>> 
> Let me clarify. "locus_tag" is not a GenBank feature, it is a feature 
> attribute of the GenBank "gene" feature. The feature is belongs to is being 
> mapped to DoTS::GeneFeature. Here is the example from the GB record for this 
> feature attribute, available here :
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46229367
>
> gene 
> <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819&view=gbwithparts> 
> complement(<6844..>9270)
>                    /locus_tag="cgd7_10"
>
>
> Thomas' suggestion of adding the attribute "locus_tag" to the GeneFeature 
> view and recompiling the objects will work in this case, but be a problem for 
> anyone else trying to capture this feature attribute.
>
> The GBParser has several known problems, this being one of them. Maybe we 
> should start up a wiki for it to aid in development and documentation.
>
> Angel
>
>
>> It should be added  >line 808, following my %featureNameTableMapping = (
>> 
>> If the attributes are correct in the mapped table (match the genbank 
>> attributes), this should work. If this table is not in the 
>> %classChildList, it should also be added to the appropriate line also.
>> 
>>                                                -Deborah
>> 
>> On Mon, 27 Sep 2004, Ed Robinson wrote:
>> 
>>> So far, down here, I can tell that it is parsing the files for crypto 
>>> correctly, but I is giving me the following error:
>>> 
>>> 
>>> ********GEtting loc below6844
>>> 
>>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER 
>>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
>>> 
>>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER 
>>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
>>> 
>>> Do you have any ideas why it is disliking my locus_tags?  I am running 
>>> this without the commit on, if it is looking for this again in the 
>>> database.
>>> 
>>> Thanks for all the help on this.  I don't want to change anything that 
>>> is working, just figure out how to use it.
>>> 
>>> -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
>>> 
>>> 
>>> 
>> 
>> 
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>> Project Admins to receive an Apple iPod Mini FREE for your judgement on
>> who ports your project to Linux PPC the best. Sponsored by IBM.
>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>

Re: [Gusdev-gusdev] GI Number

[Angel P. <an...@pc...>]

Deborah F. Pinney wrote:

> locus_tag is not in the list of features in the GBParser. It will have 
> to be added with a table(actually view) destination. Which view is 
> appropriate for this feature? What are the attributes (from the 
> Genbank feature table) for this feature? I'll gladly add this and you 
> can test it or you can add it and test and then commit to cvs.
>
Let me clarify. "locus_tag" is not a GenBank feature, it is a feature 
attribute of the GenBank "gene" feature. The feature is belongs to is 
being mapped to DoTS::GeneFeature. Here is the example from the GB 
record for this feature attribute, available here :
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46229367

 gene <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819&view=gbwithparts>            complement(<6844..>9270)
                     /locus_tag="cgd7_10"


Thomas' suggestion of adding the attribute "locus_tag" to the 
GeneFeature view and recompiling the objects will work in this case, but 
be a problem for anyone else trying to capture this feature attribute.

The GBParser has several known problems, this being one of them. Maybe 
we should start up a wiki for it to aid in development and documentation.

Angel


> It should be added  >line 808, following my %featureNameTableMapping = (
>
> If the attributes are correct in the mapped table (match the genbank 
> attributes), this should work. If this table is not in the 
> %classChildList, it should also be added to the appropriate line also.
>
>                                                -Deborah
>
> On Mon, 27 Sep 2004, Ed Robinson wrote:
>
>> So far, down here, I can tell that it is parsing the files for crypto 
>> correctly, but I is giving me the following error:
>>
>>
>> ********GEtting loc below6844
>>
>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       
>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
>>
>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       
>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
>>
>> Do you have any ideas why it is disliking my locus_tags?  I am 
>> running this without the commit on, if it is looking for this again 
>> in the database.
>>
>> Thanks for all the help on this.  I don't want to change anything 
>> that is working, just figure out how to use it.
>>
>> -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
>>
>>
>>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: Re: [Gusdev-gusdev] GI Number

[Ed R. <ed_...@be...>]

Yeah, it's not in the mapping.  I added it to the view GeneFeature on NaFeatureImp.  I'll make a modification to the mapping in the plugin here.  I'll keep notes on what I've done and once our stuff is in, I'll make the changes known and you can decide if you want to put it in the CVS.

-Ed


> 
> From: "Deborah F. Pinney" <pi...@pc...>
> Date: 2004/09/27 Mon AM 11:08:12 EDT
> To: Ed Robinson <ed_...@be...>
> CC: Jinal Jhaveri <jjh...@vb...>,  gus...@li...
> Subject: Re: Re: [Gusdev-gusdev] GI Number
> 
> locus_tag is not in the list of features in the GBParser. It will have to 
> be added with a table(actually view) destination. Which view is 
> appropriate for this feature? What are the attributes (from the Genbank 
> feature table) for this feature? I'll gladly add this and you can test it 
> or you can add it and test and then commit to cvs.
> 
> It should be added  >line 808, following my %featureNameTableMapping = (
> 
> If the attributes are correct in the mapped table (match the genbank 
> attributes), this should work. If this table is not in the 
> %classChildList, it should also be added to the appropriate line also.
> 
>                                                 -Deborah
> 
> On Mon, 27 Sep 2004, Ed Robinson wrote:
> 
> > So far, down here, I can tell that it is parsing the files for crypto correctly, but I is giving me the following error:
> >
> >
> > ********GEtting loc below6844
> >
> > Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
> >
> > Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
> >
> > Do you have any ideas why it is disliking my locus_tags?  I am running this without the commit on, if it is looking for this again in the database.
> >
> > Thanks for all the help on this.  I don't want to change anything that is working, just figure out how to use it.
> >
> > -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
> >
> >
> >
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

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

Re: Re: [Gusdev-gusdev] GI Number

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

locus_tag is not in the list of features in the GBParser. It will have to 
be added with a table(actually view) destination. Which view is 
appropriate for this feature? What are the attributes (from the Genbank 
feature table) for this feature? I'll gladly add this and you can test it 
or you can add it and test and then commit to cvs.

It should be added  >line 808, following my %featureNameTableMapping = (

If the attributes are correct in the mapped table (match the genbank 
attributes), this should work. If this table is not in the 
%classChildList, it should also be added to the appropriate line also.

                                                -Deborah

On Mon, 27 Sep 2004, Ed Robinson wrote:

> So far, down here, I can tell that it is parsing the files for crypto correctly, but I is giving me the following error:
>
>
> ********GEtting loc below6844
>
> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
>
> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
>
> Do you have any ideas why it is disliking my locus_tags?  I am running this without the commit on, if it is looking for this again in the database.
>
> Thanks for all the help on this.  I don't want to change anything that is working, just figure out how to use it.
>
> -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
>
>
>

Re: [Gusdev-gusdev] GI Number

[Thomas O. <ot...@fi...>]

Hi,

that means, that in the views Genefeature and Transcript, the column 
locus_tag does not exist.

My workaround:
I added them to the views (in the oracle), and recompiled them the perl 
modules for the tables
touch $PROJECT_HOME/GUS/Model/schema/VERSION
build GUS/Model install -append # takes time, but easier, would be 
sufficient just the recompile the two changed views
 
Cheers,
Thomas

>So far,
>
> down here, I can tell that it is parsing the files for crypto correctly, but I is giving me the following error:
>
> 
>********GEtting loc below6844
> 
>Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
> 
>Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
>
>Do you have any ideas why it is disliking my locus_tags?  I am running this without the commit on, if it is looking for this again in the database.
>
>Thanks for all the help on this.  I don't want to change anything that is working, just figure out how to use it.
>
>-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
>
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>Project Admins to receive an Apple iPod Mini FREE for your judgement on
>who ports your project to Linux PPC the best. Sponsored by IBM.
>Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>  
>

Re: Re: [Gusdev-gusdev] GI Number

[Ed R. <ed_...@be...>]

So far, down here, I can tell that it is parsing the files for crypto correctly, but I is giving me the following error:

 
********GEtting loc below6844
 
Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
 
Mon Sep 27 10:13:09 2004        INVALID QUALIFIER       GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10

Do you have any ideas why it is disliking my locus_tags?  I am running this without the commit on, if it is looking for this again in the database.

Thanks for all the help on this.  I don't want to change anything that is working, just figure out how to use it.

-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

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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -------------------------------------------------------
>>>>>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>>>>>>> Project Admins to receive an Apple iPod Mini FREE for your judgement
>>>>>>> on who ports your project to Linux PPC the best. Sponsored by IBM.
>>>>>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>>>>>>> _______________________________________________
>>>>>>> Gusdev-gusdev mailing list
>>>>>>> Gus...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------
>>>>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>>>>>> Project Admins to receive an Apple iPod Mini FREE for your judgement
>>>>>> on who ports your project to Linux PPC the best. Sponsored by IBM.
>>>>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>>>>>> _______________________________________________
>>>>>> Gusdev-gusdev mailing list
>>>>>> Gus...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>>>> Project Admins to receive an Apple iPod Mini FREE for your judgement on
>>>> who ports your project to Linux PPC the best. Sponsored by IBM.
>>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>>> Project Admins to receive an Apple iPod Mini FREE for your judgement on
>>> who ports your project to Linux PPC the best. Sponsored by IBM.
>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>> Project Admins to receive an Apple iPod Mini FREE for your judgement on
>> who ports your project to Linux PPC the best. Sponsored by IBM.
>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] GI Number

[Jinal J. <jjh...@vb...>]

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
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> -------------------------------------------------------
> >>>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> >>>>> Project Admins to receive an Apple iPod Mini FREE for your judgement
> >>>>> on who ports your project to Linux PPC the best. Sponsored by IBM.
> >>>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> >>>>> _______________________________________________
> >>>>> Gusdev-gusdev mailing list
> >>>>> Gus...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>> 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
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> -------------------------------------------------------
> >>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> >>>> Project Admins to receive an Apple iPod Mini FREE for your judgement
> >>>> on who ports your project to Linux PPC the best. Sponsored by IBM.
> >>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> >>>> _______________________________________________
> >>>> Gusdev-gusdev mailing list
> >>>> Gus...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> >> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> >> who ports your project to Linux PPC the best. Sponsored by IBM.
> >> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > Project Admins to receive an Apple iPod Mini FREE for your judgement on
> > who ports your project to Linux PPC the best. Sponsored by IBM.
> > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Plugin for GenBank files

[Jinal J. <jjh...@vb...>]

Thanks Deborah,
Uptil now I and some other users didn't know about this. Infact there was also 
a mail sent to the group regarding the same

thanks
--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
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> -------------------------------------------------------
> >>>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> >>>>> Project Admins to receive an Apple iPod Mini FREE for your judgement
> >>>>> on who ports your project to Linux PPC the best. Sponsored by IBM.
> >>>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> >>>>> _______________________________________________
> >>>>> Gusdev-gusdev mailing list
> >>>>> Gus...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>> 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
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> -------------------------------------------------------
> >>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> >>>> Project Admins to receive an Apple iPod Mini FREE for your judgement
> >>>> on who ports your project to Linux PPC the best. Sponsored by IBM.
> >>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> >>>> _______________________________________________
> >>>> Gusdev-gusdev mailing list
> >>>> Gus...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> >> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> >> who ports your project to Linux PPC the best. Sponsored by IBM.
> >> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > Project Admins to receive an Apple iPod Mini FREE for your judgement on
> > who ports your project to Linux PPC the best. Sponsored by IBM.
> > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>>>>> Project Admins to receive an Apple iPod Mini FREE for your judgement
>>>>> on who ports your project to Linux PPC the best. Sponsored by IBM.
>>>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>>>> Project Admins to receive an Apple iPod Mini FREE for your judgement on
>>>> who ports your project to Linux PPC the best. Sponsored by IBM.
>>>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
>> Project Admins to receive an Apple iPod Mini FREE for your judgement on
>> who ports your project to Linux PPC the best. Sponsored by IBM.
>> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] Plugin for GenBank files

[Jinal J. <jjh...@vb...>]

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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > > > Project Admins to receive an Apple iPod Mini FREE for your judgement
> > > > on who ports your project to Linux PPC the best. Sponsored by IBM.
> > > > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > > > _______________________________________________
> > > > Gusdev-gusdev mailing list
> > > > Gus...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> > > 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
> > >
> > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > > Project Admins to receive an Apple iPod Mini FREE for your judgement on
> > > who ports your project to Linux PPC the best. Sponsored by IBM.
> > > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: Re: [Gusdev-gusdev] Plugin for GenBank files

[Ed R. <ed_...@be...>]

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
> > >
> > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > > Project Admins to receive an Apple iPod Mini FREE for your judgement on
> > > who ports your project to Linux PPC the best. Sponsored by IBM.
> > > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> > 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
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> > Project Admins to receive an Apple iPod Mini FREE for your judgement on
> > who ports your project to Linux PPC the best. Sponsored by IBM.
> > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] Plugin for GenBank files

[Ed R. <ed_...@be...>]

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
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

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

[Gusdev-gusdev] tableinfo

[Jinal J. <jjh...@vb...>]

I have a view which fetches data from several tables. How should my entry be 
in the tableinfo?
currently when I make an entry with table_type "standard" or "many to many", 
and superclass set as null, the build process fails with following message:

[exec] Illegal className '' (not in schema::table form) 
at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 696

[exec]     
GUS::ObjRelP::DbiDatabase::getFullTableClassName('GUS::ObjRelP::DbiDatabase=HASH(0x84345f8)','undef') 
called at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 189
     [exec]     
GUS::ObjRelP::DbiDatabase::getTable('GUS::ObjRelP::DbiDatabase=HASH(0x84345f8)','undef') 
called at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiTable.pm line 359
     [exec]     
GUS::ObjRelP::DbiTable::getParentRelations('GUS::ObjRelP::DbiTable=HASH(0x89ce168)') 
called at /home/gus/gushome/lib/perl/GUS/ObjRelP/Generator/TableGenerator.pm 
line 43
     [exec]     
GUS::ObjRelP::Generator::TableGenerator::_getParents('GUS::ObjRelP::Generator::PerlTableGenerator=HASH(0x850ab64)') 
called 
at /home/gus/gushome/lib/perl/GUS/ObjRelP/Generator/PerlTableGenerator.pm 
line 75
     [exec]     
GUS::ObjRelP::Generator::PerlTableGenerator::_genChildAndParentLists('GUS::ObjRelP::Generator::PerlTableGenerator=HASH(0x850ab64)','GUS::Model::DoTS::VBIgeneedit') 
called 
at /home/gus/gushome/lib/perl/GUS/ObjRelP/Generator/PerlTableGenerator.pm 
line 56
     [exec]     
GUS::ObjRelP::Generator::PerlTableGenerator::_genDefaultParams('GUS::ObjRelP::Generator::PerlTableGenerator=HASH(0x850ab64)') 
called 
at /home/gus/gushome/lib/perl/GUS/ObjRelP/Generator/PerlTableGenerator.pm 
line 26
     [exec]     
GUS::ObjRelP::Generator::PerlTableGenerator::generate('GUS::ObjRelP::Generator::PerlTableGenerator=HASH(0x850ab64)','undef') 
called at /home/gus/gushome/lib/perl/GUS/ObjRelP/Generator/Generator.pm line 
108
     [exec]     
GUS::ObjRelP::Generator::Generator::generate('GUS::ObjRelP::Generator::Generator=HASH(0x8434604)','undef') 
called at /home/gus/gushome/bin/generateGusObjects line 67

[Gusdev-gusdev] Plugin for GenBank files

[Ed R. <ed_...@be...>]

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

[Gusdev-gusdev] new GUS tables for phylogenetic profiles

[John I. <io...@pc...>]

Folks,

Shailesh and I are planning to add the phylogenetic profile data he has
generated (http://apropos.icmb.utexas.edu/plex/plex.html) to PlasmoDB. 
This will require storing the data somewhere in GUS.  We propose four
new tables, described below, to do this.

The technique involves creating a "profile" for a gene by BLASTing it
against each sequenced genome.  A matrix is created with the rows
labelled by genes and the column by organisms.  In each cell is stored
the E value of the best BLAST hit from searching the column's organism's
genome with the row's gene's sequence.  For pairs of profiles (i.e.
pairs of genes), a mutual information score is calculated; genes with a
high mutual information score are likely to be part of the same pathway.

For GUS purposes, I propose to call a row of the matrix (i.e. the
"profile" of one gene) a "PhylogeneticProfile", and an entire run a
"PhylogeneticProfileSet".  One element of a row is a
"PhylogeneticProfileMember".  I propose the "MutualInformationScore"
table to store the relative score of two genes.  This operation is not
associative, so that table has a primary_profile_id and
secondary_profile_id, together with a numeric mutual_information_score. 
This means that the full name of this last-mentioned column will be the
somewhat awkward "DoTS.MutualInformationScore.mutual_information_score".

The schema is below.  Thanks in advance for any comments you can offer.

John

---------------------------------------------------------------

create table PhylogeneticProfileSet (
 phylogenetic_profile_set_id NUMBER(10) primary key,
 description varchar2(255),
 modification_date DATE NOT NULL,
 user_read NUMBER(1) NOT NULL,
 user_write NUMBER(1) NOT NULL,
 group_read NUMBER(1) NOT NULL,
 group_write NUMBER(1) NOT NULL,
 other_read NUMBER(1) NOT NULL,
 other_write NUMBER(1) NOT NULL,
 row_user_id NUMBER(12) NOT NULL,
 row_group_id NUMBER(3) NOT NULL,
 row_project_id NUMBER(4) NOT NULL,
 row_alg_invocation_id NUMBER(12) NOT NULL
);

create table PhylogeneticProfile (
 phylogenetic_profile_id NUMBER(10) primary key,
 na_feature_id NUMBER(10) not null,
 phylogenetic_profile_set_id NUMBER(10) not null,
 minus_log_entropy NUMBER(10),
 modification_date DATE NOT NULL,
 user_read NUMBER(1) NOT NULL,
 user_write NUMBER(1) NOT NULL,
 group_read NUMBER(1) NOT NULL,
 group_write NUMBER(1) NOT NULL,
 other_read NUMBER(1) NOT NULL,
 other_write NUMBER(1) NOT NULL,
 row_user_id NUMBER(12) NOT NULL,
 row_group_id NUMBER(3) NOT NULL,
 row_project_id NUMBER(4) NOT NULL,
 row_alg_invocation_id NUMBER(12) NOT NULL,
 CONSTRAINT PhylogeneticProfile_fk01
   FOREIGN KEY (na_feature_id)
   REFERENCES DoTS.NaFeatureImp (na_feature_id),
 CONSTRAINT PhylogeneticProfile_fk02
   FOREIGN KEY (phylogenetic_profile_set_id)
   REFERENCES PhylogeneticProfileSet (phylogenetic_profile_set_id)
   );

create table PhylogeneticProfileMember (
 phylogenetic_profile_member_id NUMBER(10) primary key,
 phylogenetic_profile_id NUMBER(10) not null,
 taxon_id NUMBER(10) not null,
 minus_log_e_value NUMBER(10),
 modification_date DATE NOT NULL,
 user_read NUMBER(1) NOT NULL,
 user_write NUMBER(1) NOT NULL,
 group_read NUMBER(1) NOT NULL,
 group_write NUMBER(1) NOT NULL,
 other_read NUMBER(1) NOT NULL,
 other_write NUMBER(1) NOT NULL,
 row_user_id NUMBER(12) NOT NULL,
 row_group_id NUMBER(3) NOT NULL,
 row_project_id NUMBER(4) NOT NULL,
 row_alg_invocation_id NUMBER(12) NOT NULL,
 CONSTRAINT PhylogeneticProfileMember_fk01
   FOREIGN KEY (taxon_id)
   REFERENCES SRes.Taxon (taxon_id)
);

create table MutualInformationScore (
 primary_profile_id NUMBER(10) primary key,
 secondary_profile_id NUMBER(10) not null,
 mutual_information_score NUMBER(10) not null,
 modification_date DATE NOT NULL,
 user_read NUMBER(1) NOT NULL,
 user_write NUMBER(1) NOT NULL,
 group_read NUMBER(1) NOT NULL,
 group_write NUMBER(1) NOT NULL,
 other_read NUMBER(1) NOT NULL,
 other_write NUMBER(1) NOT NULL,
 row_user_id NUMBER(12) NOT NULL,
 row_group_id NUMBER(3) NOT NULL,
 row_project_id NUMBER(4) NOT NULL,
 row_alg_invocation_id NUMBER(12) NOT NULL,
 CONSTRAINT MutualInformationScore_fk01
   FOREIGN KEY (primary_profile_id)
   REFERENCES PhylogeneticProfile (phylogenetic_profile_id),
 CONSTRAINT MutualInformationScore_fk02
   FOREIGN KEY (secondary_profile_id)
   REFERENCES PhylogeneticProfile (phylogenetic_profile_id)
);

Re: Re: [Gusdev-gusdev] SEQ_BROWSER_FEATS

[John I. <io...@pc...>]

Ed,

Here are some statistics about what's in there:

15:47:35 SQL> select count(*) from plasmodb_41.seq_browser_feats;

  COUNT(*)
----------
    219813

Elapsed: 00:00:00.98
15:47:55 SQL> select seq_taxon_name, count(*) from
plasmodb_41.seq_browser_feats group by seq_taxon_name;

SEQ_TAXON_NAME                   COUNT(*)
------------------------------ ----------
Plasmodium falciparum              183502
Plasmodium vivax                    20339
Plasmodium yoelii                   15972

Elapsed: 00:00:00.39
15:48:12 SQL> select count(distinct feat_source_id) from
plasmodb_41.seq_browser_feats;

COUNT(DISTINCTFEAT_SOURCE_ID)
-----------------------------
                        38005

Elapsed: 00:00:07.15

It isn't a materialized view, so it must have been populated by some
script(s).  I'll look around to see if I can find it; it should probably
be re-run anyway.

Meanwhile, I'll see about getting you an export of the data.

John


On Tue, 2004-09-14 at 15:37, Ed Robinson wrote:
> Thanks for the quick reply.  We have a copy of the empty table.  What we need is information on what goes in it and how is it being used?  It is not referenced anywhere else in the modules so we can't make heads or tails of what to put there to make the modules return correctly.
> 
> In the long run, this is not a big deal.  We are anxiously awaiting the new Struts WDK so all of this work will go away shortly.  But we want to have as good looking a T cruzi site as possible in the meantime.
> 
> Thanks!
> -Ed
> 
> 
> 
> > 
> > From: John Iodice <io...@pc...>
> > Date: 2004/09/14 Tue PM 03:27:12 EDT
> > To: Ed Robinson <ed_...@be...>
> > CC: gus...@li...
> > Subject: Re: [Gusdev-gusdev] SEQ_BROWSER_FEATS
> > 
> > Ed,
> > 
> > SEQ_BROWSER_FEATS is a table in the PLASMODB_41 schema of our database. 
> > Here's a description:
> > SQL> desc plasmodb_41.seq_browser_feats
> > Name                                      Null?    Type
> > ----------------------------------------- --------
> > ----------------------------
> > SEQ_TAXON_NAME                            NOT NULL VARCHAR2(30)
> > SEQ_SOURCE_ID                             NOT NULL VARCHAR2(30)
> > START_MIN                                 NOT NULL NUMBER(12)
> > END_MAX                                   NOT NULL NUMBER(12)
> > STRAND                                             VARCHAR2(1)
> > FEAT_TABLE_NAME                           NOT NULL VARCHAR2(30)
> > FEAT_ROW_ID                               NOT NULL NUMBER(12)
> > FEAT_SOURCE_ID                                     VARCHAR2(50)
> > FEAT_PREDICTION_ALGORITHM                          VARCHAR2(50)
> > SPAN_ORDER_NUM                            NOT NULL NUMBER(12)
> > 
> > I think your guess that it's a materialized view is likely correct.  If
> > so, it's likely overdue for refreshing.
> > 
> > John
> > 
> > On Tue, 2004-09-14 at 14:22, Ed Robinson wrote:
> > > We are trying to get parts of the WDK classic up for a release this week, and I am tryning to get the view-contig tool working.  Everything seems good, until you get all the way down into GUSGenomicSequenceTransducer.
> > > 
> > > Suddenly, we are calling on a table named SEQ_BROWSER_FEATS, and try as we might, we just can't comment this sub out.
> > > 
> > > Does anyone know what SEQ_BROWSE_FEATS is?  Is it a temporary table I can make on the fly or is it storing a set of browser display colors?  Any help would be much appreciated.
> > > 
> > > -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
> > > 
> > > 
> > > 
> > > 
> > > 
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by: thawte's Crypto Challenge Vl
> > > Crack the code and win a Sony DCRHC40 MiniDV Digital Handycam
> > > Camcorder. More prizes in the weekly Lunch Hour Challenge.
> > > Sign up NOW http://ad.doubleclick.net/clk;10740251;10262165;m
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > 
> > 
> 
> 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
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: thawte's Crypto Challenge Vl
> Crack the code and win a Sony DCRHC40 MiniDV Digital Handycam
> Camcorder. More prizes in the weekly Lunch Hour Challenge.
> Sign up NOW http://ad.doubleclick.net/clk;10740251;10262165;m
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: Re: [Gusdev-gusdev] SEQ_BROWSER_FEATS

[Ed R. <ed_...@be...>]

Thanks for the quick reply.  We have a copy of the empty table.  What we need is information on what goes in it and how is it being used?  It is not referenced anywhere else in the modules so we can't make heads or tails of what to put there to make the modules return correctly.

In the long run, this is not a big deal.  We are anxiously awaiting the new Struts WDK so all of this work will go away shortly.  But we want to have as good looking a T cruzi site as possible in the meantime.

Thanks!
-Ed



> 
> From: John Iodice <io...@pc...>
> Date: 2004/09/14 Tue PM 03:27:12 EDT
> To: Ed Robinson <ed_...@be...>
> CC: gus...@li...
> Subject: Re: [Gusdev-gusdev] SEQ_BROWSER_FEATS
> 
> Ed,
> 
> SEQ_BROWSER_FEATS is a table in the PLASMODB_41 schema of our database. 
> Here's a description:
> SQL> desc plasmodb_41.seq_browser_feats
> Name                                      Null?    Type
> ----------------------------------------- --------
> ----------------------------
> SEQ_TAXON_NAME                            NOT NULL VARCHAR2(30)
> SEQ_SOURCE_ID                             NOT NULL VARCHAR2(30)
> START_MIN                                 NOT NULL NUMBER(12)
> END_MAX                                   NOT NULL NUMBER(12)
> STRAND                                             VARCHAR2(1)
> FEAT_TABLE_NAME                           NOT NULL VARCHAR2(30)
> FEAT_ROW_ID                               NOT NULL NUMBER(12)
> FEAT_SOURCE_ID                                     VARCHAR2(50)
> FEAT_PREDICTION_ALGORITHM                          VARCHAR2(50)
> SPAN_ORDER_NUM                            NOT NULL NUMBER(12)
> 
> I think your guess that it's a materialized view is likely correct.  If
> so, it's likely overdue for refreshing.
> 
> John
> 
> On Tue, 2004-09-14 at 14:22, Ed Robinson wrote:
> > We are trying to get parts of the WDK classic up for a release this week, and I am tryning to get the view-contig tool working.  Everything seems good, until you get all the way down into GUSGenomicSequenceTransducer.
> > 
> > Suddenly, we are calling on a table named SEQ_BROWSER_FEATS, and try as we might, we just can't comment this sub out.
> > 
> > Does anyone know what SEQ_BROWSE_FEATS is?  Is it a temporary table I can make on the fly or is it storing a set of browser display colors?  Any help would be much appreciated.
> > 
> > -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
> > 
> > 
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: thawte's Crypto Challenge Vl
> > Crack the code and win a Sony DCRHC40 MiniDV Digital Handycam
> > Camcorder. More prizes in the weekly Lunch Hour Challenge.
> > Sign up NOW http://ad.doubleclick.net/clk;10740251;10262165;m
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 

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

Re: [Gusdev-gusdev] SEQ_BROWSER_FEATS

[John I. <io...@pc...>]

Ed,

SEQ_BROWSER_FEATS is a table in the PLASMODB_41 schema of our database. 
Here's a description:
SQL> desc plasmodb_41.seq_browser_feats
Name                                      Null?    Type
----------------------------------------- --------
----------------------------
SEQ_TAXON_NAME                            NOT NULL VARCHAR2(30)
SEQ_SOURCE_ID                             NOT NULL VARCHAR2(30)
START_MIN                                 NOT NULL NUMBER(12)
END_MAX                                   NOT NULL NUMBER(12)
STRAND                                             VARCHAR2(1)
FEAT_TABLE_NAME                           NOT NULL VARCHAR2(30)
FEAT_ROW_ID                               NOT NULL NUMBER(12)
FEAT_SOURCE_ID                                     VARCHAR2(50)
FEAT_PREDICTION_ALGORITHM                          VARCHAR2(50)
SPAN_ORDER_NUM                            NOT NULL NUMBER(12)

I think your guess that it's a materialized view is likely correct.  If
so, it's likely overdue for refreshing.

John

On Tue, 2004-09-14 at 14:22, Ed Robinson wrote:
> We are trying to get parts of the WDK classic up for a release this week, and I am tryning to get the view-contig tool working.  Everything seems good, until you get all the way down into GUSGenomicSequenceTransducer.
> 
> Suddenly, we are calling on a table named SEQ_BROWSER_FEATS, and try as we might, we just can't comment this sub out.
> 
> Does anyone know what SEQ_BROWSE_FEATS is?  Is it a temporary table I can make on the fly or is it storing a set of browser display colors?  Any help would be much appreciated.
> 
> -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
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: thawte's Crypto Challenge Vl
> Crack the code and win a Sony DCRHC40 MiniDV Digital Handycam
> Camcorder. More prizes in the weekly Lunch Hour Challenge.
> Sign up NOW http://ad.doubleclick.net/clk;10740251;10262165;m
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] SEQ_BROWSER_FEATS

[Ed R. <ed_...@be...>]

We are trying to get parts of the WDK classic up for a release this week, and I am tryning to get the view-contig tool working.  Everything seems good, until you get all the way down into GUSGenomicSequenceTransducer.

Suddenly, we are calling on a table named SEQ_BROWSER_FEATS, and try as we might, we just can't comment this sub out.

Does anyone know what SEQ_BROWSE_FEATS is?  Is it a temporary table I can make on the fly or is it storing a set of browser display colors?  Any help would be much appreciated.

-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

Re: [Gusdev-gusdev] error loading data using plugin

[Steve F. <sfi...@pc...>]

it needs to be in the TableInfo table.   and, you probably need to 
regenerate the perl objects.  to do so, touch the file 
$PROJECT_HOME/GUS/Model/schema/VERSION and then do a "build GUS install 
-append"

steve

D. Brent Weatherly wrote:

>Hello folks.
>
>This is probably an easy question, but I'm unable to use a
>plugin on our most recent GUS instance that worked fine on a
>previous instance. The table in question is:
>
>Dots.MassSpecSummary 
>
>which we had to manually add to Oracle. The
>"MassSpecSummary.pm" perl module does exist in
>GUS::Common::DoTS.  Do these modules need a special
>initialization that we've yet to perform?
>
>Thanks for any help!
>
>Brent Weatherly
>
>
>
>[brentw@mkiwi brentw]$ ga
>GUS::Common::Plugin::LoadTcruziDBMassSpecSummary
>--filename=/scratch/brentw/TcruziDB_data/TSKTSC_ver3_proteome_TcruziDB_data.txt
>--loadSummary --verbose --veryVerbose
>Thu Sep  9 08:55:46 2004        ALGINVID        10254
>Thu Sep  9 08:55:46 2004        COMMIT  commit off
>Thu Sep  9 08:55:46 2004        ARGS    algoinvo        1
>Thu Sep  9 08:55:46 2004        ARGS    algorithm       PROVALT
>Thu Sep  9 08:55:46 2004        ARGS    algorithmId     82
>Thu Sep  9 08:55:46 2004        ARGS    comment
>Thu Sep  9 08:55:46 2004        ARGS    commit
>Thu Sep  9 08:55:46 2004        ARGS    debug
>Thu Sep  9 08:55:46 2004        ARGS    extDbRelId      222
>Thu Sep  9 08:55:46 2004        ARGS    filename       
>/scratch/brentw/TcruziDB_data/TSKTSC_ver3_proteome_TcruziDB_data.txt
>Thu Sep  9 08:55:46 2004        ARGS    forceLookUp
>Thu Sep  9 08:55:46 2004        ARGS    gfExtDbRelId    208
>Thu Sep  9 08:55:46 2004        ARGS    group
>Thu Sep  9 08:55:46 2004        ARGS    gusconfigfile  
>/home/brentw/brentw/.gus.properties
>Thu Sep  9 08:55:46 2004        ARGS    loadSpans       0
>Thu Sep  9 08:55:46 2004        ARGS    loadSummary     1
>Thu Sep  9 08:55:46 2004        ARGS    lookUpFile
>Thu Sep  9 08:55:46 2004        ARGS    project TcruziDB3.0
>Thu Sep  9 08:55:46 2004        ARGS    projectId       22
>Thu Sep  9 08:55:46 2004        ARGS    restart
>Thu Sep  9 08:55:46 2004        ARGS    sqlVerbose
>Thu Sep  9 08:55:46 2004        ARGS    testnumber
>Thu Sep  9 08:55:46 2004        ARGS    usage
>Thu Sep  9 08:55:46 2004        ARGS    user
>Thu Sep  9 08:55:46 2004        ARGS    verbose 1
>Thu Sep  9 08:55:46 2004        ARGS    veryVerbose     1
>COMMIT TURNED OFF
>Thu Sep  9 08:55:46 2004        II parsing entry:
>Peptide Group: 1        TOP     11788.t00001    alpha tubulin
>          3919
>
>
>PepGroup: Peptide Group: 1, Source: TOP, GeneID: 11788.t00001,
>GeneName: alpha tubulin, Tot Score: 
>
>
>
>PepGroup: Peptide Group: 1, Source: TOP, GeneID: 11788.t00001,
>GeneName: alpha tubulin, Tot Score: 
>
>Thu Sep  9 08:55:46 2004        II      got new protein (count
>0)  with geneId: 11788.t00001...
>select tas.* from dots.genefeature gf, dots.rnafeature rnaf,
>dots.translatedaafeature taf, dots.translatedaasequence tas 
>           where gf.external_database_release_id = 208 
>           and rnaf.parent_id = gf.na_feature_id 
>           and rnaf.na_feature_id = taf.na_feature_id
>           and taf.aa_sequence_id = tas.aa_sequence_id 
>           and gf.source_id='11788.t00001' 
>Thu Sep  9 08:55:58 2004        II aa_sequence_id for
>11788.t00001 is 4276057
>
>INFO: 4276057  
>MREAICIHIGQAGCQVGNACWELFCLEHGIQPDGAMPSDKTIGVEDDAFNTFFSETGAGKHVPRAVFLDLEPTVVDEIRTGTYRQLFHPEQLISGKEDAANNYARGHYTIGKEIVDLCLDRIRKLADNCTGLQGFLVYHAVGGGTGSGLGALLLERLSVDYGKKSKLGYTVYPSPQVSTAVVEPYNSVLSTHSLLEHTDVAAMLDNEAIYDLTRRNLDIERPTYTNLNRLIGQVVSALTASLRFDGALNVDLTEFQTNLVPYPRIHFVLTSYAPVISAEKAYHEQLSVSEISNAVFEPASMMTKCDPRHGKYMACCLMYRGDVVPKDVNAAVATIKTKRTIQFVDWSPTGFKCGINYQPPTVVPGGDLAKVQRAVCMIANSTAIAEVFARIDHKFDLMYSKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGAESADMEGEEDVEEY
>
>II      parsing:
>Amastigote      2064    255     38      57
>
>Here: 4276057   Amastigote      38      208     82      38   
>  255     451     1       0       57
>
>
>Can't locate object method "new" via package "_Table" (perhaps
>you forgot to load "_Table"?) at 
>
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line
>201, <F> line 2.
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by BEA Weblogic Workshop
>FREE Java Enterprise J2EE developer tools!
>Get your free copy of BEA WebLogic Workshop 8.1 today.
>http://ads.osdn.com/?ad_id=5047&alloc_id=10808&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] error loading data using plugin

[D. B. W. <db...@ug...>]

Hello folks.

This is probably an easy question, but I'm unable to use a
plugin on our most recent GUS instance that worked fine on a
previous instance. The table in question is:

Dots.MassSpecSummary 

which we had to manually add to Oracle. The
"MassSpecSummary.pm" perl module does exist in
GUS::Common::DoTS.  Do these modules need a special
initialization that we've yet to perform?

Thanks for any help!

Brent Weatherly



[brentw@mkiwi brentw]$ ga
GUS::Common::Plugin::LoadTcruziDBMassSpecSummary
--filename=/scratch/brentw/TcruziDB_data/TSKTSC_ver3_proteome_TcruziDB_data.txt
--loadSummary --verbose --veryVerbose
Thu Sep  9 08:55:46 2004        ALGINVID        10254
Thu Sep  9 08:55:46 2004        COMMIT  commit off
Thu Sep  9 08:55:46 2004        ARGS    algoinvo        1
Thu Sep  9 08:55:46 2004        ARGS    algorithm       PROVALT
Thu Sep  9 08:55:46 2004        ARGS    algorithmId     82
Thu Sep  9 08:55:46 2004        ARGS    comment
Thu Sep  9 08:55:46 2004        ARGS    commit
Thu Sep  9 08:55:46 2004        ARGS    debug
Thu Sep  9 08:55:46 2004        ARGS    extDbRelId      222
Thu Sep  9 08:55:46 2004        ARGS    filename       
/scratch/brentw/TcruziDB_data/TSKTSC_ver3_proteome_TcruziDB_data.txt
Thu Sep  9 08:55:46 2004        ARGS    forceLookUp
Thu Sep  9 08:55:46 2004        ARGS    gfExtDbRelId    208
Thu Sep  9 08:55:46 2004        ARGS    group
Thu Sep  9 08:55:46 2004        ARGS    gusconfigfile  
/home/brentw/brentw/.gus.properties
Thu Sep  9 08:55:46 2004        ARGS    loadSpans       0
Thu Sep  9 08:55:46 2004        ARGS    loadSummary     1
Thu Sep  9 08:55:46 2004        ARGS    lookUpFile
Thu Sep  9 08:55:46 2004        ARGS    project TcruziDB3.0
Thu Sep  9 08:55:46 2004        ARGS    projectId       22
Thu Sep  9 08:55:46 2004        ARGS    restart
Thu Sep  9 08:55:46 2004        ARGS    sqlVerbose
Thu Sep  9 08:55:46 2004        ARGS    testnumber
Thu Sep  9 08:55:46 2004        ARGS    usage
Thu Sep  9 08:55:46 2004        ARGS    user
Thu Sep  9 08:55:46 2004        ARGS    verbose 1
Thu Sep  9 08:55:46 2004        ARGS    veryVerbose     1
COMMIT TURNED OFF
Thu Sep  9 08:55:46 2004        II parsing entry:
Peptide Group: 1        TOP     11788.t00001    alpha tubulin
          3919


PepGroup: Peptide Group: 1, Source: TOP, GeneID: 11788.t00001,
GeneName: alpha tubulin, Tot Score: 



PepGroup: Peptide Group: 1, Source: TOP, GeneID: 11788.t00001,
GeneName: alpha tubulin, Tot Score: 

Thu Sep  9 08:55:46 2004        II      got new protein (count
0)  with geneId: 11788.t00001...
select tas.* from dots.genefeature gf, dots.rnafeature rnaf,
dots.translatedaafeature taf, dots.translatedaasequence tas 
           where gf.external_database_release_id = 208 
           and rnaf.parent_id = gf.na_feature_id 
           and rnaf.na_feature_id = taf.na_feature_id
           and taf.aa_sequence_id = tas.aa_sequence_id 
           and gf.source_id='11788.t00001' 
Thu Sep  9 08:55:58 2004        II aa_sequence_id for
11788.t00001 is 4276057

INFO: 4276057  
MREAICIHIGQAGCQVGNACWELFCLEHGIQPDGAMPSDKTIGVEDDAFNTFFSETGAGKHVPRAVFLDLEPTVVDEIRTGTYRQLFHPEQLISGKEDAANNYARGHYTIGKEIVDLCLDRIRKLADNCTGLQGFLVYHAVGGGTGSGLGALLLERLSVDYGKKSKLGYTVYPSPQVSTAVVEPYNSVLSTHSLLEHTDVAAMLDNEAIYDLTRRNLDIERPTYTNLNRLIGQVVSALTASLRFDGALNVDLTEFQTNLVPYPRIHFVLTSYAPVISAEKAYHEQLSVSEISNAVFEPASMMTKCDPRHGKYMACCLMYRGDVVPKDVNAAVATIKTKRTIQFVDWSPTGFKCGINYQPPTVVPGGDLAKVQRAVCMIANSTAIAEVFARIDHKFDLMYSKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGAESADMEGEEDVEEY

II      parsing:
Amastigote      2064    255     38      57

Here: 4276057   Amastigote      38      208     82      38   
  255     451     1       0       57


Can't locate object method "new" via package "_Table" (perhaps
you forgot to load "_Table"?) at 

/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line
201, <F> line 2.