gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] Problem loading Pfam data into GUS

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

madhura-  i am real busy right now, so, quickly, i think the problem is 
that the data has links to medline entries.   the plugin wants to insert 
that link, and do it in a formal way.    we represent external links in 
two tables (the ones mentioned in the error message).    you need to add 
a row in ExternalDatabase for medline, and one in 
ExternalDatabaseRelease.  I'll write shortly with what we have in our db 
for this.

steve

Madhura Sharangpani wrote:

> Hi
>  
> I am trying again to load Pfam data into GUS using LoadPfam plugin, 
> but after registering the LoadPfam plugin successfully, when I try 
> loading data into database, I get the following error:
>
> ***************************************************
> elaine15:~/RA/pfam> ga
> GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz 
> --rele
> ase=13.0
> Reading properties from
> /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop
> Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties
> ImportPfam: COMMIT OFF
> ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz
> 0: PF00244.7
> Unable to find most recent ExternalDatabaseRelease for ExternalDatabase
> medline at
> /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> line 417, <PFAM> line 590.
>
> gunzip: stdout: Broken pipe
> ***************************************************
>
> I have downloaded latest release 13.0 from website
>
> Do I need to also specify external_database_release_id or something in the
> command? 
>
> Thanks!
>
> Madhura

[Gusdev-gusdev] Problem loading Pfam data into GUS

[Madhura S. <sma...@st...>]

Hi

I am trying again to load Pfam data into GUS using LoadPfam plugin, but =
after registering the LoadPfam plugin successfully, when I try loading =
data into database, I get the following error:

***************************************************
elaine15:~/RA/pfam> ga
GUS::Common::Plugin::LoadPfam --parse_only --flat_file=3DPfam-A.full.gz =
--rele
ase=3D13.0
Reading properties from
/afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop
Reading properties from =
/afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties
ImportPfam: COMMIT OFF
ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz
0: PF00244.7
Unable to find most recent ExternalDatabaseRelease for ExternalDatabase
medline at
/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm
line 417, <PFAM> line 590.

gunzip: stdout: Broken pipe
***************************************************

I have downloaded latest release 13.0 from website

Do I need to also specify external_database_release_id or something in =
the
command? =20

Thanks!

Madhura

Re: [Gusdev-gusdev] deleting objects/rows

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

Hi,

DeleteEntries.pl deletes rows using DBI and executing a delete statement.
That is equivalent to doing a delete using sqlplus, for example, and
doesn't put anything in corresponding version tables.  Plugins, that use
objects to delete and don't explicitly avoid versioning, put rows into ver
tables when rows are updated or deleted. 

Version tables allow you to track changes and recover data if necessary 
while deleteEntries is unrecoverable. I don't think we use the version 
tables often but they are an important safeguard.

                                                   Debbie


On Tue, 4 May 2004, Sucheta
Tripathy wrote:

> Hi Terry,
> 
> I think this means that the data which are deleted could be stored in the 
> ver tables. However, I am not sure if this has to be done by the user or 
> the deleteEntries.pl takes care of it. In our case I did not get any 
> version of my deleted records stored in the -ver tables.
> 
> I think Debbie can comment on this.
> 
> Sucheta
> 
> At 03:24 PM 5/4/2004 -0500, you wrote:
> >It sounds like rows that are not intended to be completely cleaned
> >from the database, but the model is to keep a "version" around, is that 
> >right?
> >Could you help to expand on this: What is in that version & what/who uses it?
> >Most of what I know about GUS versioning concepts I have gleaned from reading
> >Perl code in the object layer with occasional comments.
> >Can you (or someone) summarize the in's and out's of GUS
> >versioning, or maybe point to some writeup?
> >
> >many thanks
> >
> >Terry
> >
> >
> >On Tue, May 04, 2004 at 04:14:13PM -0400, Deborah F. Pinney wrote:
> > > We only use deleteEntries.pl in selected cases where there are no
> > > children. DeleteEntries.pl would fail if there were children of a row
> > > being deleted because of foriegn key contraints. In most of the cases that
> > > we want to delete rows with children, we write a plugin using objects.
> > > In that case, unless specified otherwise, deleted rows are versioned. I
> > > don't think there are any examples in the GUS set of plugins but I can
> > > send you an attached text if you need it.
> > >
> > >                                                    Deborah Pinney
> > >
> > >
> > >
> > > On Tue, 4 May
> > > 2004, Gregory Carl Kettler wrote:
> > >
> > > > I was wondering if there's a canonical way to delete rows or objects from
> > > > GUS.  A simple "delete from table where..." would do it, but that can
> > > > easily make orphans of any child objects and doesn't update
> > > > Core::AlgorithmInvocation.  Still, that seems to be what deleteEntries.pl
> > > > does.
> > > > GusRow.pm seems a little more sophisticated, since it can delete
> > > > children and makes use of an object's markedDeleted attribute, but 
> > I'm not
> > > > sure if that attribute is stored in the database or used anywhere else.
> > > > Can I get any insight into how this works?
> > > >
> > > >     Greg Kettler
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > This SF.Net email is sponsored by: Oracle 10g
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> > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > -------------------------------------------------------
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> >
> >
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> 
> 
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Re: [Gusdev-gusdev] deleting objects/rows

[Sucheta T. <su...@vb...>]

Hi Terry,

I think this means that the data which are deleted could be stored in the 
ver tables. However, I am not sure if this has to be done by the user or 
the deleteEntries.pl takes care of it. In our case I did not get any 
version of my deleted records stored in the -ver tables.

I think Debbie can comment on this.

Sucheta

At 03:24 PM 5/4/2004 -0500, you wrote:
>It sounds like rows that are not intended to be completely cleaned
>from the database, but the model is to keep a "version" around, is that 
>right?
>Could you help to expand on this: What is in that version & what/who uses it?
>Most of what I know about GUS versioning concepts I have gleaned from reading
>Perl code in the object layer with occasional comments.
>Can you (or someone) summarize the in's and out's of GUS
>versioning, or maybe point to some writeup?
>
>many thanks
>
>Terry
>
>
>On Tue, May 04, 2004 at 04:14:13PM -0400, Deborah F. Pinney wrote:
> > We only use deleteEntries.pl in selected cases where there are no
> > children. DeleteEntries.pl would fail if there were children of a row
> > being deleted because of foriegn key contraints. In most of the cases that
> > we want to delete rows with children, we write a plugin using objects.
> > In that case, unless specified otherwise, deleted rows are versioned. I
> > don't think there are any examples in the GUS set of plugins but I can
> > send you an attached text if you need it.
> >
> >                                                    Deborah Pinney
> >
> >
> >
> > On Tue, 4 May
> > 2004, Gregory Carl Kettler wrote:
> >
> > > I was wondering if there's a canonical way to delete rows or objects from
> > > GUS.  A simple "delete from table where..." would do it, but that can
> > > easily make orphans of any child objects and doesn't update
> > > Core::AlgorithmInvocation.  Still, that seems to be what deleteEntries.pl
> > > does.
> > > GusRow.pm seems a little more sophisticated, since it can delete
> > > children and makes use of an object's markedDeleted attribute, but 
> I'm not
> > > sure if that attribute is stored in the database or used anywhere else.
> > > Can I get any insight into how this works?
> > >
> > >     Greg Kettler
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by: Oracle 10g
> > > Get certified on the hottest thing ever to hit the market... Oracle 10g.
> > > Take an Oracle 10g class now, and we'll give you the exam FREE.
> > > http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: Oracle 10g
> > Get certified on the hottest thing ever to hit the market... Oracle 10g.
> > Take an Oracle 10g class now, and we'll give you the exam FREE.
> > http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>-------------------------------------------------------
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>Take an Oracle 10g class now, and we'll give you the exam FREE.
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>_______________________________________________
>Gusdev-gusdev mailing list
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>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] deleting objects/rows

[<tw...@cs...>]

It sounds like rows that are not intended to be completely cleaned 
from the database, but the model is to keep a "version" around, is that right?  
Could you help to expand on this: What is in that version & what/who uses it?
Most of what I know about GUS versioning concepts I have gleaned from reading
Perl code in the object layer with occasional comments. 
Can you (or someone) summarize the in's and out's of GUS
versioning, or maybe point to some writeup?

many thanks 

Terry


On Tue, May 04, 2004 at 04:14:13PM -0400, Deborah F. Pinney wrote:
> We only use deleteEntries.pl in selected cases where there are no 
> children. DeleteEntries.pl would fail if there were children of a row 
> being deleted because of foriegn key contraints. In most of the cases that 
> we want to delete rows with children, we write a plugin using objects. 
> In that case, unless specified otherwise, deleted rows are versioned. I 
> don't think there are any examples in the GUS set of plugins but I can 
> send you an attached text if you need it. 
> 
>                                                    Deborah Pinney
> 
> 
> 
> On Tue, 4 May 
> 2004, Gregory Carl Kettler wrote:
> 
> > I was wondering if there's a canonical way to delete rows or objects from
> > GUS.  A simple "delete from table where..." would do it, but that can
> > easily make orphans of any child objects and doesn't update
> > Core::AlgorithmInvocation.  Still, that seems to be what deleteEntries.pl
> > does.
> > GusRow.pm seems a little more sophisticated, since it can delete
> > children and makes use of an object's markedDeleted attribute, but I'm not
> > sure if that attribute is stored in the database or used anywhere else.
> > Can I get any insight into how this works?
> > 
> > 	Greg Kettler
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: Oracle 10g
> > Get certified on the hottest thing ever to hit the market... Oracle 10g. 
> > Take an Oracle 10g class now, and we'll give you the exam FREE.
> > http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g
> Get certified on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
> http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] deleting objects/rows

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

We only use deleteEntries.pl in selected cases where there are no 
children. DeleteEntries.pl would fail if there were children of a row 
being deleted because of foriegn key contraints. In most of the cases that 
we want to delete rows with children, we write a plugin using objects. 
In that case, unless specified otherwise, deleted rows are versioned. I 
don't think there are any examples in the GUS set of plugins but I can 
send you an attached text if you need it. 

                                                   Deborah Pinney



On Tue, 4 May 
2004, Gregory Carl Kettler wrote:

> I was wondering if there's a canonical way to delete rows or objects from
> GUS.  A simple "delete from table where..." would do it, but that can
> easily make orphans of any child objects and doesn't update
> Core::AlgorithmInvocation.  Still, that seems to be what deleteEntries.pl
> does.
> GusRow.pm seems a little more sophisticated, since it can delete
> children and makes use of an object's markedDeleted attribute, but I'm not
> sure if that attribute is stored in the database or used anywhere else.
> Can I get any insight into how this works?
> 
> 	Greg Kettler
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g
> Get certified on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
> http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

[Gusdev-gusdev] deleting objects/rows

[Gregory C. K. <gck...@cs...>]

I was wondering if there's a canonical way to delete rows or objects from
GUS.  A simple "delete from table where..." would do it, but that can
easily make orphans of any child objects and doesn't update
Core::AlgorithmInvocation.  Still, that seems to be what deleteEntries.pl
does.
GusRow.pm seems a little more sophisticated, since it can delete
children and makes use of an object's markedDeleted attribute, but I'm not
sure if that attribute is stored in the database or used anywhere else.
Can I get any insight into how this works?

	Greg Kettler

[Gusdev-gusdev] default java compiling in GUS Build System

[Dave B. <db...@pc...>]

Folks,

I have changed the behavior of the GUS build system to compile java code 
by default.  Gone is the --compileJava flag that a few people might have 
been using before; all java compiling is now done for you.  

This will take effect next time you update your build.xml files.  To try 
it out:

1. % cd $PROJECT_HOME/install/

2. % cvs update (this will update build.xml and bin/build.pl)

3. % cd $PROJECT_HOME/GUS

4. % cvs update build.xml

If you are building the components GUS/ObjRelJ or GUS/WebDevKit, you need 
to have java libraries for those components that are now in cvs.  To get 
those:

1. % cd $PROJECT_HOME/GUS/ObjRelJ(or WebDevKit)

2. % cvs update -d (this will check out the 'lib' directory if you don't 
have it, and the necessary java libaries.)

then build as normal, without the --compileJava flag.

If you are a java developer, please make sure that your java code compiles 
before you check it into CVS, and that any external libraries your 
code depends upon (i.e., those that are not created by the build system, such as oracle or apache 
libraries) are checked into the proper place (the 'lib/java' 
directory for the appropriate component).

Please let me know if you experience any problems or have any questions 
about this new feature.

Dave

Re: [Gusdev-gusdev] about uploading RAD data problem

[Elisabetta M. <man...@pc...>]

Hi Sucheta,

1. .CHP files. These are not in text format, but through MAS 5.0 one can 
generate their corresponding text files, i.e. the Metrics files. These can 
be loaded into RAD. More precisely minor parsing, of the Metrics files is 
needed in order to use them as input of the ArrayResultLoader 
(basically just the header needs to be parsed a bit, see doc for 
this plugin). 
We have recently written another plugin, the BathArrayResult loader, 
which loads in batch results for a group of assays. For this plugin
there is no need of parsing of Metrics files, all needed is an xml 
configuration file. We have not deposited this plugin into the Sanger cvs 
repository yet, but we can make available upon request in the meantime.

2. .CEL files. Up to recently these were in text format and in principle 
could be loaded into RAD using the ArrayResultLoader (and in fact, we have 
loaded a few in our instance of RAD). However we have now opted not to 
load the probe cell data into RAD. We keep the .CEL files on our 
filesystem and store in RAD a pointer to their location (see point 4 
below).

3. For image files like .DAT files (and similarly for .tif files), we 
store in RAD a pointer to their location, but and store the files  in our 
filesystem.

4. Summarizing how we currently deal with a given assay, with files 
myassay.data, myassay.CEL, myassay.CHP (and myassay_Metrics.txt):

a. The assay has one child in RAD3.Acquisition and the 
RAD3.Acquisition.uri of this points to the location of the .DAT file in 
our filesystem.

b. The acquisition in (a) has TWO children in RAD.Quantification (and 
these are related in RAD3.RelatedQuantification): one corresponds to the 
.CEL quantification (i.e. the probe cell analysis) and its uri points to 
the location of the .CEL file in our system, the other corresponds to the 
.CHP (probe set) analysis and its uri points to the location of the 
corresponding Metrics file (or .CHP file) in our file system.

c. We load the results corresponding to the .CHP file (from the Metrics 
file) into the AffymetrixMAS5 view of CompositeElementResultImp. Every 
entry in the latter will have quantification_id pointing to the 
quantification_id of the quantification in (b) corresponding to the probe 
set analysis (.CHP).

Hope this clarifies things a bit,
Elisabetta

On Tue, 4 May 2004, Sucheta Tripathy wrote:

> Hello Elisabetta and Sam,
> 
> I am new to RAD modules in GUS. Now we have some microarray data, which is 
> available in 3 different file formats(.cel,.dat,.CHP). Which of these 3 
> files can be uploaded to RAD tables. None of the tables are in text format.
> 
> Thanks in advance.
> 
> Sucheta
> 
> At 07:55 PM 11/16/2003 -0800, sam wang wrote:
> >Dear Elisabetta,
> >
> >thank you very much for your great help! now I am trying according to your 
> >suggestion, besides, it seems a little complicated :-)
> >
> >Thanks again,
> >Sammy
> >
> >Elisabetta Manduchi <man...@pc...> wrote:
> >Dear Sam,
> >regarding the part of your question referring to the manufacturer_id
> >error, if you look at schemaBrowser for RAD3.Array at
> >http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=RAD3::Array&path=RAD3::Array 
> >
> >you should see that manufacturer_id and platform_type_id are nonnullable.
> >Thus a valid manufacturer_id and a valid platform_type_id must be given
> >when running the ArrayLoader plugin (see also plugin documentation at
> >http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-ArrayLoader.html).
> >This means that before you can load an array, you will need to have
> >entered the manufacturer in the SRes.Contact (this can be done also
> >via the StudyAnnotator Contact form) and you should have in 
> >RAD3.OntologyEntry
> >an entry that describes the platform type. MGED has an ontology available
> >that we use to populate RAD3.OntologyEntry for terms referring to
> >platform types, namely the ontology for class=TechnologyType. The idea is
> >that in RAD3.OntologyEntry we store the instances of this class,
> >all of which have category set to 'TechnologyType". Similarly for
> >SubstrateType, an array entry in RAD3.Array has a substrate_type_id that
> >points to a term in RAd3.OntologyEntry describing the substrate type. For
> >this we use the instances of the MGED SubstrateType class, that is we
> >enter in RAD3.OntologyEntry an entry for each such instance, all having
> >category set to "SubstrateType". To get the MGED instatnces (individuals)
> >for TechnologyType and SubstrateType, you can go to
> >http://mged.sourceforge.net/ontologies/MGEDontology.php#TechnologyType and
> >http://mged.sourceforge.net/ontologies/MGEDontology.php#SubstrateType
> >I believe that, even though substrate_type_id is nullable in RAD3.Array,
> >the ArrayLoader might require that this value is provided in the arguments
> >anyway. Junmin, cc'ed in this email, can confirm this, as he is the author
> >of the ArrayLoader plugin.
> >Elisabetta
> >
> >On Fri, 14 Nov 2003, sam wang wrote:
> >
> > > Dear friends,
> > >
> > > after I download the new version of DbiDbHandle.pm,
> > > though it can go more steps, but there is no any data
> > > in my database, besides, there is an error "ERROR a
> > > VALID -- manufacturer_id must be on the commandline
> > > manufacturer_id = 0", I don't know the meaning and if
> > > it's the problem that I can't upload data? if so, how
> > > can I correct it?
> > >
> > > Thank you very much for your help!
> > > Sammy
> > >
> > >
> > > please check the following error message:
> > >
> > > [oracle@GUS oracle]$ ga GUS::RAD::Plugin::ArrayLoader
> > > --cfg_file
> > > /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> > > --data_file /home/oracle/RADDOTSdataset/assay5quan3
> > > --manufacturer_id 0 --platform_type_id 0
> > > Reading properties from
> > > /opt/gus/gus_home/config/GUS-PluginMgr.prop
> > > Reading properties from /home/oracle/.gus.properties
> > > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > > ::st are not setup, RootClass ignored at
> > > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > > line 152
> > > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > > ::st are not setup, RootClass ignored at
> > > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > > line 152
> > > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > > ::st are not setup, RootClass ignored at
> > > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > > line 152
> > > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > > ::st are not setup, RootClass ignored at
> > > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > > line 152
> > > Fri Nov 14 19:43:23 2003 ALGINVID 3
> > > Fri Nov 14 19:43:23 2003 ARGS algoinvo
> > > 1
> > > Fri Nov 14 19:43:23 2003 ARGS cfg_file
> > > /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> > > Fri Nov 14 19:43:23 2003 ARGS comment
> > > Fri Nov 14 19:43:23 2003 ARGS commit
> > > Fri Nov 14 19:43:23 2003 ARGS data_file
> > > /home/oracle/RADDOTSdataset/assay5quan3
> > > Fri Nov 14 19:43:23 2003 ARGS debug
> > > Fri Nov 14 19:43:23 2003 ARGS group
> > > Fri Nov 14 19:43:23 2003 ARGS gusconfigfile
> > > /home/oracle/.gus.properties
> > > Fri Nov 14 19:43:23 2003 ARGS
> > > manufacturer_id 0
> > > Fri Nov 14 19:43:23 2003 ARGS noWarning
> > > Fri Nov 14 19:43:23 2003 ARGS
> > > platform_type_id 0
> > > Fri Nov 14 19:43:23 2003 ARGS project
> > > Fri Nov 14 19:43:23 2003 ARGS protocol_id
> > > Fri Nov 14 19:43:23 2003 ARGS restart
> > > Fri Nov 14 19:43:23 2003 ARGS sqlVerbose
> > > Fri Nov 14 19:43:23 2003 ARGS
> > > substrate_type_id
> > > Fri Nov 14 19:43:23 2003 ARGS testnumber
> > > Fri Nov 14 19:43:23 2003 ARGS usage
> > > Fri Nov 14 19:43:23 2003 ARGS user
> > > Fri Nov 14 19:43:23 2003 ARGS verbose
> > > Fri Nov 14 19:43:23 2003 ARGS veryVerbose
> > > Fri Nov 14 19:43:23 2003 COMMIT commit off
> > > Fri Nov 14 19:43:23 2003 ERROR a VALID --
> > > manufacturer_id must be on the commandline
> > > manufacturer_id = 0
> > > Fri Nov 14 19:43:23 2003 RESULT
> > > [oracle@GUS oracle]$

Re: [Gusdev-gusdev] about uploading RAD data problem

[Sucheta T. <su...@vb...>]

Hello Elisabetta and Sam,

I am new to RAD modules in GUS. Now we have some microarray data, which is 
available in 3 different file formats(.cel,.dat,.CHP). Which of these 3 
files can be uploaded to RAD tables. None of the tables are in text format.

Thanks in advance.

Sucheta

At 07:55 PM 11/16/2003 -0800, sam wang wrote:
>Dear Elisabetta,
>
>thank you very much for your great help! now I am trying according to your 
>suggestion, besides, it seems a little complicated :-)
>
>Thanks again,
>Sammy
>
>Elisabetta Manduchi <man...@pc...> wrote:
>Dear Sam,
>regarding the part of your question referring to the manufacturer_id
>error, if you look at schemaBrowser for RAD3.Array at
>http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=RAD3::Array&path=RAD3::Array 
>
>you should see that manufacturer_id and platform_type_id are nonnullable.
>Thus a valid manufacturer_id and a valid platform_type_id must be given
>when running the ArrayLoader plugin (see also plugin documentation at
>http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-ArrayLoader.html).
>This means that before you can load an array, you will need to have
>entered the manufacturer in the SRes.Contact (this can be done also
>via the StudyAnnotator Contact form) and you should have in 
>RAD3.OntologyEntry
>an entry that describes the platform type. MGED has an ontology available
>that we use to populate RAD3.OntologyEntry for terms referring to
>platform types, namely the ontology for class=TechnologyType. The idea is
>that in RAD3.OntologyEntry we store the instances of this class,
>all of which have category set to 'TechnologyType". Similarly for
>SubstrateType, an array entry in RAD3.Array has a substrate_type_id that
>points to a term in RAd3.OntologyEntry describing the substrate type. For
>this we use the instances of the MGED SubstrateType class, that is we
>enter in RAD3.OntologyEntry an entry for each such instance, all having
>category set to "SubstrateType". To get the MGED instatnces (individuals)
>for TechnologyType and SubstrateType, you can go to
>http://mged.sourceforge.net/ontologies/MGEDontology.php#TechnologyType and
>http://mged.sourceforge.net/ontologies/MGEDontology.php#SubstrateType
>I believe that, even though substrate_type_id is nullable in RAD3.Array,
>the ArrayLoader might require that this value is provided in the arguments
>anyway. Junmin, cc'ed in this email, can confirm this, as he is the author
>of the ArrayLoader plugin.
>Elisabetta
>
>On Fri, 14 Nov 2003, sam wang wrote:
>
> > Dear friends,
> >
> > after I download the new version of DbiDbHandle.pm,
> > though it can go more steps, but there is no any data
> > in my database, besides, there is an error "ERROR a
> > VALID -- manufacturer_id must be on the commandline
> > manufacturer_id = 0", I don't know the meaning and if
> > it's the problem that I can't upload data? if so, how
> > can I correct it?
> >
> > Thank you very much for your help!
> > Sammy
> >
> >
> > please check the following error message:
> >
> > [oracle@GUS oracle]$ ga GUS::RAD::Plugin::ArrayLoader
> > --cfg_file
> > /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> > --data_file /home/oracle/RADDOTSdataset/assay5quan3
> > --manufacturer_id 0 --platform_type_id 0
> > Reading properties from
> > /opt/gus/gus_home/config/GUS-PluginMgr.prop
> > Reading properties from /home/oracle/.gus.properties
> > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > ::st are not setup, RootClass ignored at
> > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > line 152
> > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > ::st are not setup, RootClass ignored at
> > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > line 152
> > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > ::st are not setup, RootClass ignored at
> > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > line 152
> > DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and
> > ::st are not setup, RootClass ignored at
> > /opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> > line 152
> > Fri Nov 14 19:43:23 2003 ALGINVID 3
> > Fri Nov 14 19:43:23 2003 ARGS algoinvo
> > 1
> > Fri Nov 14 19:43:23 2003 ARGS cfg_file
> > /opt/gus/projects/RAD/DataLoad/config/ArrayLoader.cfg
> > Fri Nov 14 19:43:23 2003 ARGS comment
> > Fri Nov 14 19:43:23 2003 ARGS commit
> > Fri Nov 14 19:43:23 2003 ARGS data_file
> > /home/oracle/RADDOTSdataset/assay5quan3
> > Fri Nov 14 19:43:23 2003 ARGS debug
> > Fri Nov 14 19:43:23 2003 ARGS group
> > Fri Nov 14 19:43:23 2003 ARGS gusconfigfile
> > /home/oracle/.gus.properties
> > Fri Nov 14 19:43:23 2003 ARGS
> > manufacturer_id 0
> > Fri Nov 14 19:43:23 2003 ARGS noWarning
> > Fri Nov 14 19:43:23 2003 ARGS
> > platform_type_id 0
> > Fri Nov 14 19:43:23 2003 ARGS project
> > Fri Nov 14 19:43:23 2003 ARGS protocol_id
> > Fri Nov 14 19:43:23 2003 ARGS restart
> > Fri Nov 14 19:43:23 2003 ARGS sqlVerbose
> > Fri Nov 14 19:43:23 2003 ARGS
> > substrate_type_id
> > Fri Nov 14 19:43:23 2003 ARGS testnumber
> > Fri Nov 14 19:43:23 2003 ARGS usage
> > Fri Nov 14 19:43:23 2003 ARGS user
> > Fri Nov 14 19:43:23 2003 ARGS verbose
> > Fri Nov 14 19:43:23 2003 ARGS veryVerbose
> > Fri Nov 14 19:43:23 2003 COMMIT commit off
> > Fri Nov 14 19:43:23 2003 ERROR a VALID --
> > manufacturer_id must be on the commandline
> > manufacturer_id = 0
> > Fri Nov 14 19:43:23 2003 RESULT
> > [oracle@GUS oracle]$
> >
> >
> >
> > __________________________________
> > Do you Yahoo!?
> > Protect your identity with Yahoo! Mail AddressGuard
> > http://antispam.yahoo.com/whatsnewfree
> >
> >
> > -------------------------------------------------------
> > This SF. Net email is sponsored by: GoToMyPC
> > GoToMyPC is the fast, easy and secure way to access your computer from
> > any Web browser or wireless device. Click here to Try it Free!
> > https://www.gotomypc.com/tr/OSDN/AW/Q4_2003/t/g22lp?Target=mm/g22lp.tmpl
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
>--
>Elisabetta Manduchi
>
>Computational Biology and Informatics Laboratory
>Center for Bioinformatics
>University of Pennsylvania
>1428 Blockley Hall
>423 Guardian Drive
>Philadelphia, PA 19104-6021
>
>phone: 215-573-4408
>fax: 215 573-3111
>email: man...@pc...
>web: http://www.cbil.upenn.edu/~manduchi
>
>---
>
>
>Do you Yahoo!?
><http://antispam.yahoo.com/whatsnewfree>Protect your identity with Yahoo! 
>Mail AddressGuard

[Gusdev-gusdev] plugin bug: memory leak in DBD::Oracle

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

Folks-

we have identified a memory leak in the DBD::Oracle package (this is 
comes from CPAN not CBIL).

if you are running DBD::Oracle verion 1.15 or maybe 1.13 and 1.14, and 
are doing alot of inserts you will get massive memory overruns.

we have filed a bug report, but, don't have much hope of it getting any 
attention:
http://rt.cpan.org/NoAuth/Bug.html?id=5325

we are going to try to revert to 1.12 to see if that is a workaround.

steve

[Gusdev-gusdev] Plugin memory leak w/ Perl 5.8

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

GUS users-

it looks like we are seeing a memory leak in the plugins that coincided 
with our change to Perl 5.8 from 5.6.

it is likely you will have trouble running plugins under Perl 5.8.

we're looking into it now and will keep you posted.

steve

[Gusdev-gusdev] pipeline scripts

[Sucheta T. <su...@vb...>]

Hello,

I have been looking at the pipeline scipts, it seems to me, it requires
some of the programs and modules which does not appear in the
distribution. e.g; "DoTS::DotsBuild::plugin::LoadPredictedAAFeatures",
"parse-predictions" etc.

Can you please tell me where to look for them? Also if I want to run a
fragment of the pipeline(some functions like parseSGPHMMSignalP) can I
pull them out and put in another file and execute?

Thanks

Sucheta

-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] New table: DoTS.DevelopmentalStageLibrary

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

It sounds useful to me. 




On Sat, 24 Apr 2004 
io...@pc... wrote:

> 
> Hey, GUS developers!
> 
> I'm writing to propose a new table, DoTS.DevelopmentalStageLibrary.
> 
> This is a mapping table to associate an EST library in
> DoTS.Library with a developmental stage in
> SRes.DevelopmentalStage. This is analogous to the way
> DoTS.AnatomyLibrary associates a library with an
> anatomy term in SRes.Anatomy.
> 
> Here's the proposed schema:
> 
> create table DoTS.DevelopmentalStageLibrary (
> developmental_stage_library_id number(10) primary key,
> developmental_stage_id references
> SRes.DevelopmentalStage,
> library_id references DoTS.Library,
> 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
> );
> 
> There is also a SourceForge tracker for this change; it's number 941027.
> 
> Please let me know what you think.
> 
> John
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: The Robotic Monkeys at ThinkGeek
> For a limited time only, get FREE Ground shipping on all orders of $35
> or more. Hurry up and shop folks, this offer expires April 30th!
> http://www.thinkgeek.com/freeshipping/?cpg=12297
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

[Gusdev-gusdev] New table: DoTS.DevelopmentalStageLibrary

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

Hey, GUS developers!

I'm writing to propose a new table, DoTS.DevelopmentalStageLibrary.

This is a mapping table to associate an EST library in
DoTS.Library with a developmental stage in
SRes.DevelopmentalStage. This is analogous to the way
DoTS.AnatomyLibrary associates a library with an
anatomy term in SRes.Anatomy.

Here's the proposed schema:

create table DoTS.DevelopmentalStageLibrary (
developmental_stage_library_id number(10) primary key,
developmental_stage_id references
SRes.DevelopmentalStage,
library_id references DoTS.Library,
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
);

There is also a SourceForge tracker for this change; it's number 941027.

Please let me know what you think.

John

Re: [Fwd: [Gusdev-gusdev] dbest.pm plugin]

[Sucheta T. <su...@vb...>]

Hi Debbie,

Thanks.

In my case I need to upload a big file with sequences in genbank format to
EST related tables in GUS. If I were to use dbEST how do I pass on the
input file name.
Is it not the --update_file option?

Sucheta

>
> Hi Sucheta,
>
> I use the dbEST plugin frequently. We have made a few changes in the
> plugin lately so you may want to update it from cvs. The changes all
> relate to the option --taxon_id being changed to taxon_id_list which now
> takes a string (a comma delimited list of taxons) rather than an int (a
> single taxon_id).
>
> We maintain a mirrored dbEST database and this plugin was created to load
> data into GUS from our copy of the dbEST db. I didn't write the plugin and
> have never used the --update_file option, but I think it would be a list
> of id_est's that identify ests in the dbEST mirror that need to be updated
> but not a list of records that can be loaded directly into GUS.
>
> One other point, I don't think you should use = between an option and a
> value. I believe that may be why it is hanging.
>
>                                                      Debbie
>
>
>
>
>
>
> On Thu, 22 Apr 2004, Steve Fischer wrote:
>
>>
>>
>> -------- Original Message --------
>> Subject: 	[Gusdev-gusdev] dbest.pm plugin
>> Date: 	Wed, 21 Apr 2004 18:48:32 -0400 (EDT)
>> From: 	Sucheta Tripathy <su...@vb...>
>> To: 	gus...@li...
>>
>>
>>
>> Hi,
>>
>> has anyone used dbest plugin. I have been trying to upload data with
>> sequence files in genbank format using the following parameter, but it
>> keeps hanging.
>>
>> ga GUS::Common::Plugin::dbEST  --debug --fullupdate
>> --log=/home/apps/oracle/data
>> _load_dbest.log  --restart_number=1 --sqlVerbose --taxon_id=143371
>> --update_fil
>> e=/usr/local/src/gus-related/dbest/tmp >&
>> /home/apps/oracle/gusdev/dbest_err1
>>
>> Any suggestion what file type I should be using etc..
>>
>> Thanks
>>
>> Sucheta
>>
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] Can I put wdk related questions to the forum

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

Sucheta-

i did a recursive grep over the java code and did not see any mention to 
allgenes.gif there.

steve

Sucheta Tripathy wrote:

>Steve,
>
>Thanks, this will help.
>Actually I have been playing around with the servlet-config file a bit,
>and changed some of the images/values etc., but I think if I go to any
>page like the news page where I think the image URL is embedded in the
>java code(or may be not!!), I am unable to get rid of the logo.
>
>However, I will try with simpler versions .
>
>I have some old servlet-config files, can I have any other such files in
>working condition.
>
>Sucheta
>
>  
>
>>Sucheta-
>>
>>(We are ramping up to begin high-priority development of the new wdk
>>which will be user friendly and fully supported.  Till then you'r going
>>to need to bear with some of the difficulties of using the wdk-classic,
>>including that we aren't really supporting it so there isn't any
>>documentation, etc.)
>>
>>anyway, the first things you need to do are:
>>  1. learn how to read the log files
>>  2. make a minimal servlet-config file, say with only one query.  this
>>way you'll understand how all the elements of a query work
>>
>>i have attached my notes on the logs here at CBIL for the allgenes dev
>>site.   they will at least familiarize you with what logs exist.
>>
>>as far as the allgenes gif is concerned, to find out the answer to that
>>i looked in the browser at the page source for the allgenes home page,
>>and saw that the name of the gif is "allgenes.gif."    i then did a
>>search in the servlet-config file to find the line:
>>
>>allgenesImg.ImageURL=@IMAGE_DIR_URL@/allgenes.gif
>>
>>steve
>>
>>Sucheta Tripathy wrote:
>>
>>    
>>
>>>Thank you!!
>>>
>>>Here goes the first question. We have installed wdk, and I put some dummy
>>>data into the gene table for querying.
>>>
>>>>From the query page when I select the value of the transcript(the
>>>      
>>>
>>>>gene.name)
>>>>        
>>>>
>>>the query does not return any result.
>>>
>>>We have tested oracle thin client connectivity and it works fine with the
>>>JSPs.
>>>
>>>In order to customize our site we want the figure allgenes.org to
>>>disappear. Which value should I change/assign in the servlet-config file.
>>>
>>>Thanks
>>>
>>>Sucheta
>>>
>>>
>>>
>>>
>>>      
>>>
>>>>sure.
>>>>
>>>>steve
>>>>
>>>>Sucheta Tripathy wrote:
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>>Hello All,
>>>>>
>>>>>We are now trying to make use of the wdk. Can I put the issues related
>>>>>to
>>>>>wdk to this forum.
>>>>>
>>>>>Thanks
>>>>>
>>>>>Sucheta
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>
>>>
>>>      
>>>
>
>
>  
>

Re: [Fwd: [Gusdev-gusdev] dbest.pm plugin]

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

Hi Sucheta,

I use the dbEST plugin frequently. We have made a few changes in the
plugin lately so you may want to update it from cvs. The changes all 
relate to the option --taxon_id being changed to taxon_id_list which now 
takes a string (a comma delimited list of taxons) rather than an int (a 
single taxon_id). 

We maintain a mirrored dbEST database and this plugin was created to load 
data into GUS from our copy of the dbEST db. I didn't write the plugin and 
have never used the --update_file option, but I think it would be a list 
of id_est's that identify ests in the dbEST mirror that need to be updated 
but not a list of records that can be loaded directly into GUS.

One other point, I don't think you should use = between an option and a 
value. I believe that may be why it is hanging. 

                                                     Debbie






On Thu, 22 Apr 2004, Steve Fischer wrote:

> 
> 
> -------- Original Message --------
> Subject: 	[Gusdev-gusdev] dbest.pm plugin
> Date: 	Wed, 21 Apr 2004 18:48:32 -0400 (EDT)
> From: 	Sucheta Tripathy <su...@vb...>
> To: 	gus...@li...
> 
> 
> 
> Hi,
> 
> has anyone used dbest plugin. I have been trying to upload data with
> sequence files in genbank format using the following parameter, but it
> keeps hanging.
> 
> ga GUS::Common::Plugin::dbEST  --debug --fullupdate
> --log=/home/apps/oracle/data
> _load_dbest.log  --restart_number=1 --sqlVerbose --taxon_id=143371 
> --update_fil
> e=/usr/local/src/gus-related/dbest/tmp >& /home/apps/oracle/gusdev/dbest_err1
> 
> Any suggestion what file type I should be using etc..
> 
> Thanks
> 
> Sucheta
> 
> 

Re: [Gusdev-gusdev] Can I put wdk related questions to the forum

[Sucheta T. <su...@vb...>]

Steve,

Thanks, this will help.
Actually I have been playing around with the servlet-config file a bit,
and changed some of the images/values etc., but I think if I go to any
page like the news page where I think the image URL is embedded in the
java code(or may be not!!), I am unable to get rid of the logo.

However, I will try with simpler versions .

I have some old servlet-config files, can I have any other such files in
working condition.

Sucheta

> Sucheta-
>
> (We are ramping up to begin high-priority development of the new wdk
> which will be user friendly and fully supported.  Till then you'r going
> to need to bear with some of the difficulties of using the wdk-classic,
> including that we aren't really supporting it so there isn't any
> documentation, etc.)
>
> anyway, the first things you need to do are:
>   1. learn how to read the log files
>   2. make a minimal servlet-config file, say with only one query.  this
> way you'll understand how all the elements of a query work
>
> i have attached my notes on the logs here at CBIL for the allgenes dev
> site.   they will at least familiarize you with what logs exist.
>
> as far as the allgenes gif is concerned, to find out the answer to that
> i looked in the browser at the page source for the allgenes home page,
> and saw that the name of the gif is "allgenes.gif."    i then did a
> search in the servlet-config file to find the line:
>
> allgenesImg.ImageURL=@IMAGE_DIR_URL@/allgenes.gif
>
> steve
>
> Sucheta Tripathy wrote:
>
>>Thank you!!
>>
>>Here goes the first question. We have installed wdk, and I put some dummy
>>data into the gene table for querying.
>>
>>>From the query page when I select the value of the transcript(the
>>> gene.name)
>>the query does not return any result.
>>
>>We have tested oracle thin client connectivity and it works fine with the
>>JSPs.
>>
>>In order to customize our site we want the figure allgenes.org to
>>disappear. Which value should I change/assign in the servlet-config file.
>>
>>Thanks
>>
>>Sucheta
>>
>>
>>
>>
>>>sure.
>>>
>>>steve
>>>
>>>Sucheta Tripathy wrote:
>>>
>>>
>>>
>>>>Hello All,
>>>>
>>>>We are now trying to make use of the wdk. Can I put the issues related
>>>> to
>>>>wdk to this forum.
>>>>
>>>>Thanks
>>>>
>>>>Sucheta
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>GenToo technologies. Learn everything from fundamentals to system
>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>
>>
>>
>>
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

[Gusdev-gusdev] dbest.pm plugin

[Sucheta T. <su...@vb...>]

Hi,

has anyone used dbest plugin. I have been trying to upload data with
sequence files in genbank format using the following parameter, but it
keeps hanging.

ga GUS::Common::Plugin::dbEST  --debug --fullupdate
--log=/home/apps/oracle/data
_load_dbest.log  --restart_number=1 --sqlVerbose --taxon_id=143371 
--update_fil
e=/usr/local/src/gus-related/dbest/tmp >& /home/apps/oracle/gusdev/dbest_err1

Any suggestion what file type I should be using etc..

Thanks

Sucheta

-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] Can I put wdk related questions to the forum

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

sure.

steve

Sucheta Tripathy wrote:

>Hello All,
>
>We are now trying to make use of the wdk. Can I put the issues related to
>wdk to this forum.
>
>Thanks
>
>Sucheta
>
>  
>

[Gusdev-gusdev] Can I put wdk related questions to the forum

[Sucheta T. <su...@vb...>]

Hello All,

We are now trying to make use of the wdk. Can I put the issues related to
wdk to this forum.

Thanks

Sucheta

-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] uploading P. falciparum data

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

Hi,

I do not know, if that help's, but I had this line,
VLD     CBIL::Bio::GenBank::Origin      1
also like in an endless loop, when I transformed files to Genbank-files=20
with the bioperl-tool.

A part of this, the GBParser seems to need a lot of memory, because for=20
each feature it instance a new class, with a lot of childs, and not all=20
are closed.

Cheers,
Thomas

Steve Fischer wrote:

> i have never run the GBParser.    The plasmoDB folks have used it to=20
> load data.
>
> the funny thing is that P. falciparum is much smaller than human.
>
> unfortunately the guy who know this coded best, Angel, is in europe=20
> this week.
>
> maybe somebody else i'll pick this up.
>
> steve
>
> Fidel Salas wrote:
>
>> I tried uploding P. falciparum chromosome data using the GBParser and
>> ran out of memory in all cases.  setMaximumNumberOfObjects is set to
>> 4000000.  The verbose output files contain the line:
>> VLD     CBIL::Bio::GenBank::Origin      1
>> more than 20 million times before an =A8out of memory=A8 message is
>> output.
>>
>> Here are some of some of the numbers for some of the files:
>> bash-2.05$ grep VLD NC_004325.gbk-gbparser.out | grep -c Origin
>> 20479965
>> bash-2.05$ grep VLD NC_004314.gbk-gbparser.out | grep -c Origin
>> 20356504
>> bash-2.05$ grep VLD NC_004315.gbk-gbparser.out | grep -c Origin
>> 20335688
>>
>> Has anyone run into something similar before?  How did the people
>> working on P. falciparum upload the data into GUS?
>>
>> Thanks
>>
>> Fidel
>>
>>
>>
>>
>>
>> -------------------------------------------------------
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>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
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>>
>
>
>
> -------------------------------------------------------
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Re: [Gusdev-gusdev] Re: KEGG data (fwd)

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

Trish-

I thought another time over the stuff below.

Like I wrote before, I do not know how to enter the datasets, if there 
are involved more than two compounds in the reaction.

Apart of this, I think the classification-table (class) I send last week 
fit good with his schema. It will provide more information about the 
reaction, the compounds and the enzyme derived from kegg.

So just tell me how to solve the problem above, and I try to write a 
parse with the ga.

Cheers,
Thomas

Trish Whetzel wrote:

>Forwarding some mail regarding KEGG data that did not make it to the list.
>
>Trish
>
>---------- Forwarded message ----------
>Hi Thomas,
>
>Attached is the basic flow of data entry in order to represent the 
>reaction below. Let me know if/what questions you may have on this. 
>
>Sincerely,
>Trish
>
>========
>Attachment
>
>Mapping KEGG Data into GUS
>
>Case Study:
>Map the pathway C00103 <=> C00668 (alpha-D-glucose 1-phosphate =
>alpha-D-glucose 6-phosphate) which involves the enzyme 5.4.2.2
>(phosphoglucomutase)
>
>Information Needed:
>-GenBank Accession for the Enzymes in the Pathway of interest
>In order to be able to point to a row in DoTs.ExternalAASequence, the 
>following
>tables need to be loaded DoTS.ExternalNASequence <-na_sequence_id->
>DoTS.RNAFeature <-na_feature_id-> DoTS.TranslatedAAFeature, this can then 
>be
>joined to DoTS.ExternalAASequence using aa_sequence_id
>
>-Table that holds information on small molecules
>
>Tables Involved:
>Dots::Pathway
>DoTS::PathwayInteraction
>DoTS::Interaction
>DoTS::InteractionType
>DoTS::EffectorActionType
>DoTS::RowSet
>DoTS::RowSetMember
>SRes::ReviewStatus
>
>Flow of Data Entry:
>NOTE:  this pathway will need to be represented as 2 interactions
>NOTE:  Need to find/create tables to store compounds, look in EcoCyc 
>and/or
>BioComp, Adam Arkin, cheminformatics info
>
>-insert into dots.pathway (name, description) values ('RN00010' , 
>'Glycolysis /
>Gluconeogenesis');
>RESULT: $pathway_id
>
>-insert into dots.interactiontype (name, description) values ('term from
>controlled vocabulary' , 'definition of term');
>RESULT: $interaction_id
>
>-insert into dots.effectoractiontype (name, description,
>external_database_release_id, source_id) values ('phosphorylation' , 
>'residue
>modification' , 'ADD ext_db_rel_id for PSI Ontology' , 'MI:0170');
>RESULT: $effector_action_type_id
>
>For Interaction 1 and 2
>-insert into dots.rowset ();
>RESULT: $row_set_id1
>-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
>('$row_set_id1', 'table_id of DoTS.ExternalAASequence' , 'PK of row of
>interest'); --> this represents the enzyme (effector)
>
>For Interaction 1
>-insert into dots.rowset ();
>RESULT: $row_set_id2
>-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
>('$row_set_id2',  'table_id for table with small molecules/compounds' ,
>'Primary key of row of interest in the table with small 
>molecules/compounds');
>--> this represents the molecule (target)
>
>For interaction 2
>-insert into dots.rowset ();
>RESULT: $row_set_id3
>-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
>('$row_set_id' , 'table_id for table with small molecules/compounds' , 
>'Primary
>key of row of interest in the table with small molecules/compounds'); --> 
>this
>represents the molecule (target)
>
>-insert into dots.interaction (interaction_type_id, 
>effector_action_type_id,
>effector_row_set_id, target_row_set_id, has_direction, direction_is_known)
>values ($interaction_type_id, $effector_action_type_id, $row_set_id1,
>$row_set_id2, 'integer to represent direction', '1');
>RESULT: $interaction_id
>
>-insert into dots.pathwayinteraction (pathway_id, interaction_id) values
>($pathway_id, $interaction_id);
>========
>
>  
>
>>To understand the talbe, maybe it would be easier to do an example:
>>So how would you save in the table this reaction, of Pathway Map0010 
>>(http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=rn&mapno=00010):
>>
>>D-Glucose 1-phosphate (C00103) <--- reaction alpha-D-Glucose 1-phosphate 1,6-phosphomutase (envolving enzyme 5.4.2.2 <http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+5.4.2.2>         5.4.2.5 <http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+5.4.2.5>
>>
>>) --->  C00668 
>><http://www.genome.ad.jp/dbget-bin/get_linkdb?compound+C00668>  
>>alpha-D-Glucose 6-phosphate
>>
>>Maybe this helps me to understand the table.
>>
>>Thanks,
>>Thomas
>>    
>>
> 
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
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>  
>

Re: [Gusdev-gusdev] uploading P. falciparum data

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

i have never run the GBParser.    The plasmoDB folks have used it to=20
load data.

the funny thing is that P. falciparum is much smaller than human.

unfortunately the guy who know this coded best, Angel, is in europe this=20
week.

maybe somebody else i'll pick this up.

steve

Fidel Salas wrote:

>I tried uploding P. falciparum chromosome data using the GBParser and
>ran out of memory in all cases.  setMaximumNumberOfObjects is set to
>4000000.  The verbose output files contain the line:
>VLD     CBIL::Bio::GenBank::Origin      1
>more than 20 million times before an =A8out of memory=A8 message is
>output.
>
>Here are some of some of the numbers for some of the files:
>bash-2.05$ grep VLD NC_004325.gbk-gbparser.out | grep -c Origin
>20479965
>bash-2.05$ grep VLD NC_004314.gbk-gbparser.out | grep -c Origin
>20356504
>bash-2.05$ grep VLD NC_004315.gbk-gbparser.out | grep -c Origin
>20335688
>
>Has anyone run into something similar before?  How did the people
>working on P. falciparum upload the data into GUS?
>
>Thanks
>
>Fidel
>
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id638&op=CCk
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>