gusdev-gusdev — Topics concerning GUS development

Re: [GUSDEV] InsertSequenceFeature Issue in GUS3.5

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

sanjeev-

take a look at the bioperl unflattener.  read the docs there.   we may 
have it configured to ignore introns, as they are implied by exons.  if 
you figure out how to re-configure the unflattener, and, think that ISF 
should support alternative unflattener configurations, we may need to 
add a command line option to ISF specifying how to configure the unflattener

steve

Kumar, Sanjeev wrote:

> Hi Group,
>    I am having little problem with InsertSequenceFeature in our 
> environment.
>    It is loading all features from the genBank file except "intron" 
> feature. I tried to look into the code and found that it is all 
> together skipping the "intron" feature from genBank file. Is that the 
> issue with "BioPerl"?
>
> Did any one face this issue earlier?
>
> The version of bioperl in our environment is :1.5.0
> And I am using very first version of GUS3.5. Do we have any subsequent 
> release like GUS3.5.X?
> And the file I am trying to load is related to MICROSPORIDIA organism 
> (NC_003238.gbf).
> ------
> *The genBank2gus.xml has entry for the intron like this*:
> <feature name="intron" table="DoTS::IntronFeature" so="intron">
>     <qualifier name="allele" lost="true"/>
>     <qualifier name="citation"/>
>     <qualifier name="cons_splice"/>
>     <qualifier name="evidence"/>
>     <qualifier name="function"/>
>     <qualifier name="gene" specialcase="gene"/>
>     <qualifier name="label"/>
>     <qualifier name="locus_tag" column="source_id"/>
>     <qualifier name="map"/>
>     <qualifier name="note" specialcase="note"/>
>     <qualifier name="number" column="num"/>
>     <qualifier name="old_locus_tag" lost="true"/>
>     <qualifier name="standard_name"/>
>     <qualifier name="usedin"/>
>     <qualifier name="db_xref" specialcase="dbxref"/>
>   </feature>
>
> *And the intron entry in genBank file looks like this:*
> gene            complement(52254..52444)
>                      /db_xref="GeneID:860376"
>                      /locus_tag="ECU09_0395"
>      CDS             
> join(complement(52254..52409),complement(52442..52444))
>                      /db_xref="GI:19173160"
>                      /db_xref="GeneID:860376"
>                      /locus_tag="ECU09_0395"
>                      /codon_start=1
>                      /protein_id="NP_596963.1"
>                      
> /translation="MGSRKTALVKTRLMRALKRNREIPAWKRMMKEHKGEYNRARRHW
>                      RSKKLKIY"
>                      /product="60S RIBOSOMAL PROTEIN L39"
>      misc_feature    
> join(complement(52260..52409),complement(52442..52444))
>                      /db_xref="CDD:11875"
>                      /locus_tag="ECU09_0395"
>                      /note="RPL39; Region: Ribosomal protein L39E
>                      [Translation, ribosomal structure and biogenesis]"
>      intron          complement(52410..52441)
>                      /locus_tag="ECU09_0395"
>                      /note="intron L39"
>
> Any help will be appreciated.
>
> Thanks
> Sanjeev Kumar
> Northrop Grumman
>

[GUSDEV] InsertSequenceFeature Issue in GUS3.5

[Kumar, S. <San...@ng...>]

Hi Group,
   I am having little problem with InsertSequenceFeature in our
environment.
   It is loading all features from the genBank file except "intron"
feature. I tried to look into the code and found that it is all together
skipping the "intron" feature from genBank file. Is that the issue with
"BioPerl"?
Did any one face this issue earlier?

The version of bioperl in our environment is :1.5.0
And I am using very first version of GUS3.5. Do we have any subsequent
release like GUS3.5.X?=20
And the file I am trying to load is related to MICROSPORIDIA organism
(NC_003238.gbf).
------
The genBank2gus.xml has entry for the intron like this:
<feature name=3D"intron" table=3D"DoTS::IntronFeature" so=3D"intron">
    <qualifier name=3D"allele" lost=3D"true"/>
    <qualifier name=3D"citation"/>
    <qualifier name=3D"cons_splice"/>
    <qualifier name=3D"evidence"/>
    <qualifier name=3D"function"/>
    <qualifier name=3D"gene" specialcase=3D"gene"/>
    <qualifier name=3D"label"/>
    <qualifier name=3D"locus_tag" column=3D"source_id"/>
    <qualifier name=3D"map"/>
    <qualifier name=3D"note" specialcase=3D"note"/>
    <qualifier name=3D"number" column=3D"num"/>
    <qualifier name=3D"old_locus_tag" lost=3D"true"/>
    <qualifier name=3D"standard_name"/>
    <qualifier name=3D"usedin"/>
    <qualifier name=3D"db_xref" specialcase=3D"dbxref"/>
  </feature>

And the intron entry in genBank file looks like this:
gene            complement(52254..52444)
                     /db_xref=3D"GeneID:860376"
                     /locus_tag=3D"ECU09_0395"
     CDS
join(complement(52254..52409),complement(52442..52444))
                     /db_xref=3D"GI:19173160"
                     /db_xref=3D"GeneID:860376"
                     /locus_tag=3D"ECU09_0395"
                     /codon_start=3D1
                     /protein_id=3D"NP_596963.1"
=20
/translation=3D"MGSRKTALVKTRLMRALKRNREIPAWKRMMKEHKGEYNRARRHW
                     RSKKLKIY"
                     /product=3D"60S RIBOSOMAL PROTEIN L39"
     misc_feature
join(complement(52260..52409),complement(52442..52444))
                     /db_xref=3D"CDD:11875"
                     /locus_tag=3D"ECU09_0395"
                     /note=3D"RPL39; Region: Ribosomal protein L39E
                     [Translation, ribosomal structure and biogenesis]"
     intron          complement(52410..52441)
                     /locus_tag=3D"ECU09_0395"
                     /note=3D"intron L39"

Any help will be appreciated.

Thanks
Sanjeev Kumar
Northrop Grumman

Re: [GUSDEV] Build issue

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

john-

as you might know gus provides a perl and a java object layer.   each 
gus table is represented by a perl object and by a java object.

part of the intall process is a code-generation step that generates 3 
perl files and 3 java files per gus table.

then, after that, the install compiles the generated java files.

this compile error is during that compile.

it means that the code generation step didn't work right.   in 
particular, what happened is that the code generator did not 
successfully get info from postgresql on what the type of the 
Core.Algorithm column is.

i'm not certain, but, i think this is brought about when you have a 
correct list of all the gus tables and views is core.tableinfo (which is 
where the code-generator looks to find out what tables exist), but, that 
the actual tables are not accessible to the code generator.   this 
sometimes happens because of permissions.   so, you need to make sure 
that Core.Algorithm is defined and accessible.

steve

John F Flynn III wrote:

> Hiya folks! This is John Flynn from the Florida International 
> University School of Computer Science. We are trying to build GUSdb 
> and are running into issues.
>
> Apologies if anyone sees this twice, but I opened a bugzilla bug and 
> no one has responded, so I'm assuming no one is listening over there. 
> Hopefully someone here can help us.
>
> I read the list through archives, so if anyone responds, please CC me 
> as well as the list so I see the message sooner. Thanks!
>
> Basically, the GUS build process fails with numerous compilation errors.
>
>
> I ensured all the requirements were met, set up the database, and set 
> up the configuration file as follows:
>
> ==begin configuration file snippet==
> dbVendor=Postgres
> dbiDsn=dbi:Pg:dbname=gusdb;host=localhost
> jdbcDsn=jdbc:postgresql://localhost/gusdb
>
> # Login and Password to the RDBMS
>
> databaseLogin=gusdb
> databasePassword=<password here>
>
> # Username, group, and project info from the relevant Core tables
>
> userName=dba
> group=dba
> project=Database administration
>
> tablespace=GUS
> ==End configuration file snippet==
>
> Relevant software versions follow:
>
> CentOS 4.3
> J2SE 1.5
> Ant 1.6.5
> Postgresql 7.4
> Perl 5.8.5 with required modules
>
> Error output follows:
>
>
>      [echo] Installing GUS/Model
>     [javac] Compiling 1260 source files to
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/classes
>     [javac]
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:78: 
>
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.Core.Algorithm_Row
>     [javac]     public void setModificationDate (notdefyet value)
>     [javac]                                      ^
>     [javac]
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:83: 
>
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.Core.Algorithm_Row
>     [javac]     public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
>     [javac]            ^
>     [javac]
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:78: 
>
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
>     [javac]     public void setModificationDate (notdefyet value)
>     [javac]                                      ^
>     [javac]
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:83: 
>
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
>     [javac]     public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
>     [javac]            ^
>     [javac]
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:54: 
>
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
>     [javac]     public void setStartTime (notdefyet value)
>     [javac]                               ^
>     [javac]
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:59: 
>
> cannot find symbol
>     [javac] symbol  : class notdefyet
>     [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
>     [javac]     public notdefyet getStartTime () { return
> (notdefyet)get_Attribute("start_time"); }
>     [javac]            ^
> ....snipped; this goes on with similar errors for many pages...
>     [javac]            ^
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 100 errors
>
> BUILD FAILED
> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:28: The 
> following
> error occurred while executing this line:
> /home/acrl-storage-1/gusdb/GUS/project_home/GUS/build.xml:99: The 
> following
> error occurred while executing this line:
> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:259: The
> following error occurred while executing this line:
> /home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:278: 
> Compile
> failed; see the compiler error output for details.
>
> Total time: 18 seconds
>

[GUSDEV] Build issue

[John F F. I. <fl...@cs...>]

Hiya folks! This is John Flynn from the Florida International University 
School of Computer Science. We are trying to build GUSdb and are running 
into issues.

Apologies if anyone sees this twice, but I opened a bugzilla bug and no 
one has responded, so I'm assuming no one is listening over there. 
Hopefully someone here can help us.

I read the list through archives, so if anyone responds, please CC me as 
well as the list so I see the message sooner. Thanks!

Basically, the GUS build process fails with numerous compilation errors.


I ensured all the requirements were met, set up the database, and set up 
the configuration file as follows:

==begin configuration file snippet==
dbVendor=Postgres
dbiDsn=dbi:Pg:dbname=gusdb;host=localhost
jdbcDsn=jdbc:postgresql://localhost/gusdb

# Login and Password to the RDBMS

databaseLogin=gusdb
databasePassword=<password here>

# Username, group, and project info from the relevant Core tables

userName=dba
group=dba
project=Database administration

tablespace=GUS
==End configuration file snippet==

Relevant software versions follow:

CentOS 4.3
J2SE 1.5
Ant 1.6.5
Postgresql 7.4
Perl 5.8.5 with required modules

Error output follows:


      [echo] Installing GUS/Model
     [javac] Compiling 1260 source files to
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/classes
     [javac]
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:78:
cannot find symbol
     [javac] symbol  : class notdefyet
     [javac] location: class org.gusdb.model.Core.Algorithm_Row
     [javac]     public void setModificationDate (notdefyet value)
     [javac]                                      ^
     [javac]
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/Algorithm_Row.java:83:
cannot find symbol
     [javac] symbol  : class notdefyet
     [javac] location: class org.gusdb.model.Core.Algorithm_Row
     [javac]     public notdefyet getModificationDate () { return
(notdefyet)get_Attribute("modification_date"); }
     [javac]            ^
     [javac]
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:78:
cannot find symbol
     [javac] symbol  : class notdefyet
     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
     [javac]     public void setModificationDate (notdefyet value)
     [javac]                                      ^
     [javac]
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:83:
cannot find symbol
     [javac] symbol  : class notdefyet
     [javac] location: class org.gusdb.model.Core.ProjectInfo_Row
     [javac]     public notdefyet getModificationDate () { return
(notdefyet)get_Attribute("modification_date"); }
     [javac]            ^
     [javac]
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:54:
cannot find symbol
     [javac] symbol  : class notdefyet
     [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
     [javac]     public void setStartTime (notdefyet value)
     [javac]                               ^
     [javac]
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:59:
cannot find symbol
     [javac] symbol  : class notdefyet
     [javac] location: class org.gusdb.model.Core.AlgorithmInvocation_Row
     [javac]     public notdefyet getStartTime () { return
(notdefyet)get_Attribute("start_time"); }
     [javac]            ^
....snipped; this goes on with similar errors for many pages...
     [javac]            ^
     [javac] Note: Some input files use unchecked or unsafe operations.
     [javac] Note: Recompile with -Xlint:unchecked for details.
     [javac] 100 errors

BUILD FAILED
/home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:28: The 
following
error occurred while executing this line:
/home/acrl-storage-1/gusdb/GUS/project_home/GUS/build.xml:99: The following
error occurred while executing this line:
/home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:259: The
following error occurred while executing this line:
/home/acrl-storage-1/gusdb/GUS/project_home/install/build.xml:278: Compile
failed; see the compiler error output for details.

Total time: 18 seconds

-- 
John Flynn                              fl...@cs...
=========================================================
Systems and Network Administration             /\_/\
School of Computer Science                    ( O.O )
Florida International University               >   <

Re: [GUSDEV] Error in running GUS Plugin "DeleteFromTable"

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

sanjeev-

the error you're getting is produced in the file 
$PROJECT_HOME/GUS/Model/lib/perl/GusRow.pm, in the method 
checkReadPermission().   GusRow is the superclass for all GUS objects.

its not a very good error message.   it seems to be saying that you 
don't have read permission for one of the NAFeatureImp children of the 
sequence you are trying to delete.   take a look at that method to see 
what the logic there is.

if, for example, a row in NAFeatureImp doesn't have other_read set to 1, 
then you might have permission problems.

steve

Kumar, Sanjeev wrote:

>Hi,
> I am trying to run "DeleteFromTable" plugin and getting following error
>:
>
>"Insufficient permission to retrieve GUS::Model::DoTS::NAFeatureImp
>Child of GUS::Model::DoTS::NASequenceImp
>Table: Source
>"
>The requirement is to delete a old sequence record from the database.
>I am using GUS3.5
>
>
>Any help to resolve this will be appreciated. 
>
>Thanks
>Sanjeev
>Northrop Grumman
>
>
>-------------------------------------------------------
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job easier
>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>http://sel.as-us.falkag.net/sel?cmd_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[GUSDEV] Error in running GUS Plugin "DeleteFromTable"

[Kumar, S. <San...@ng...>]

Hi,
 I am trying to run "DeleteFromTable" plugin and getting following error
:

"Insufficient permission to retrieve GUS::Model::DoTS::NAFeatureImp
Child of GUS::Model::DoTS::NASequenceImp
Table: Source
"
The requirement is to delete a old sequence record from the database.
I am using GUS3.5


Any help to resolve this will be appreciated.=20

Thanks
Sanjeev
Northrop Grumman

Re: [GUSDEV] LoadTaxon: null value in "taxon_id" violates not-null constraint

[Fernan A. <fe...@ii...>]

+----[ Deborah Pinney <pi...@pc...> (23.Apr.2006 11:22):
|
| Are you running this without commit on? 

Yes.

| We did have a problem that the taxon_ids were loaded in a
| separate transaction and so the taxon_ids were not
| available for the taxonname insertions when the plugin was
| run with commit off. I thought this was fixed but perhaps
| the fix was bogus (either didn't work or is a figment of
| my imagination) or you don't have the most up to date
| version.

I've just got LoadTaxon.pm again from the repository and
it is identical to my local copy:
https://www.cbil.upenn.edu/svn/gus/
=> GusAppFramework/ => trunk => Supported

| 
| Can you try running it with commit on?
|
| Deborah
|
+----]

I'm running it now again with commit on, I'll let
you know how it goes.

Thanks for the suggestion!

Fernan

Re: [GUSDEV] LoadTaxon: null value in "taxon_id" violates not-null constraint

[<pi...@pc...>]

Are you running this without commit on? We did have a problem that the 
taxon_ids
were loaded in a separate transaction and so the taxon_ids were not available
for the taxonname insertions when the plugin was run with commit off. I 
thought
this was fixed but perhaps the fix was bogus (either didn't work or is a
figment of my imagination) or you don't have the most up to date version.

Can you try running it with commit on?

Deborah



Quoting Fernan Aguero <fe...@ii...>:

> Hi,
>
> I've came across this error while trying to load the ncbi
> taxonomy dumps using LoadTaxon. Any idea if this is due to a
> bad input file or a software bug?
>
> This is a fresh db instance, and this was the first run
> (non-commit mode). Seems like taxon_id is clearly empty for
> ncbi_tax_id=127219
>
> Thanks in advance for any suggestion,
>
> Fernan
>
> LoadTaxon (supported) plugin rev: 4488
> GUS 3.5.1 (SVN snapshot of 11.Apr.2006)
> PostgreSQL 8.1.3 (FreeBSD, i386)
> NCBI taxonomy files from 17.Apr.2006
>
>
> [fernan@omega] ga GUS::Supported::Plugin::LoadTaxon --names names.dmp \
> --nodes nodes.dmp --gencode gencode.dmp --merged merged.dmp --verbose \
> --debug --sqlVerbose
>
>
> Merging taxons: OK
> Updating and inserting SRes.GeneticCode: OK
> Process ncbi_tax_id: OK
> Fails at the first ocurrence of 'Inserting and updating TaxonName'
>
> [ ..... ]
>
> sqlExec:
>    INSERT INTO SRes.Taxon (  group_write, other_read, group_read, 
> taxon_id, ncbi_tax_id, user_read, genetic_code_id, row_user_id, 
> modification_date, other_write, row_project_id, 
> row_alg_invocation_id, row_group_id, mitochondrial_genetic_code_id, 
> rank, user_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
>  bindValues (1, 1, 1, 607974, 188885, 1, 20, 1, 0, 1, 6, 1, 19, no rank, 1)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> Fri Apr 21 21:32:40 2006	Processed ncbi_tax_id : 188885
>
> Fri Apr 21 21:32:40 2006	Inserting and updating TaxonName
>
>
> prepareAndExecute: select t.taxon_id from sres.taxon t where 
> t.ncbi_tax_id = 127219
> allNonNullsSet: taxon_name_id not set... = ''
> GUS::Model::SRes::TaxonName->retrieveFromDB($doNotRetrieveAtts=,)
>
> RetrieveFromDB: select * from SRes.TaxonName where  
> unique_name_variant is NULL and  name_class = ? and  name = ? and  
> taxon_id is NULL
>  bindValues (scientific name, Tellervini)
> Submitting GUS::Model::SRes::TaxonName:
> Table: TaxonName
> 	unique_name_variant: []
> 	name_class: [scientific name]
> 	name: [Tellervini]
> 	taxon_id: []
>
> HasChangedAttributes='0'
> Setting all foreign keys
> GUS::Model::SRes::TaxonName->Submit: All foreign keys are set...proceeding
> allNonNullsSet: taxon_name_id not set... = ''
> Inserting:
> Table: TaxonName
> 	unique_name_variant: []
> 	group_write: [1]
> 	other_read: [1]
> 	group_read: [1]
> 	name: [Tellervini]
> 	taxon_id: []
> 	user_read: [1]
> 	row_user_id: [1]
> 	modification_date: [now()]
> 	name_class: [scientific name]
> 	other_write: [0]
> 	row_alg_invocation_id: [6]
> 	row_project_id: [1]
> 	row_group_id: [1]
> 	user_write: [1]
>
>
> sqlExec:
>    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write, 
> other_read, group_read, name, taxon_id, user_read, row_user_id, 
> modification_date, name_class, other_write, row_alg_invocation_id, 
> row_project_id, taxon_name_id, row_group_id, user_write )
>    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
>  bindValues (1, 1, 1, Tellervini, 1, 1, scientific name, 0, 6, 1, 2, 1, 1)
> DBD::Pg::st execute failed: ERROR:  null value in column "taxon_id" 
> violates not-null constraint
> Submitting GUS::Model::Core::AlgorithmInvocation:
> Table: AlgorithmInvocation
> 	group_read: [1]
> 	comment_string: []
> 	user_read: [1]
> 	algorithm_implementation_id: [5]
> 	other_write: [0]
> 	end_time: [now()]
> 	modification_date: [now()]
> 	cpu_time: [0]
> 	row_group_id: [1]
> 	user_write: [1]
> 	other_read: [1]
> 	cpus_used: [1]
> 	group_write: [1]
> 	start_time: [now()]
> 	row_user_id: [1]
> 	row_alg_invocation_id: [1]
> 	row_project_id: [1]
> 	algorithm_invocation_id: [6]
> 	result: [pending]
>
> HasChangedAttributes='1'
> Setting all foreign keys
> GUS::Model::Core::AlgorithmInvocation->Submit: All foreign keys are 
> set...proceeding
> Updating GUS::Model::Core::AlgorithmInvocation=HASH(0x86bcc54)
> Am updateable and have changed atts
> Table: AlgorithmInvocation
> 	group_read: [1]
> 	comment_string: []
> 	user_read: [1]
> 	algorithm_implementation_id: [5]
> 	other_write: [0]
> 	end_time: [now()]
> 	modification_date: [now()]
> 	cpu_time: [0]
> 	row_group_id: [1]
> 	user_write: [1]
> 	other_read: [1]
> 	cpus_used: [1]
> 	group_write: [1]
> 	start_time: [now()]
> 	row_user_id: [1]
> 	row_alg_invocation_id: [6]
> 	row_project_id: [1]
> 	algorithm_invocation_id: [6]
> 	result: [pending]
>
>
> sqlExec:
>    UPDATE  Core.AlgorithmInvocation
>    SET
> 	modification_date = ?,
> 	end_time = ?,
> 	row_alg_invocation_id = ?
>    WHERE   algorithm_invocation_id = ?
>  bindValues (now(), now(), 6, 6)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
>
> ERROR:
>
> SQL ERROR!! involving
>
>    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write, 
> other_read, group_read, name, taxon_id, user_read, row_user_id, 
> modification_date, name_class, other_write, row_alg_invocation_id, 
> row_project_id, taxon_name_id, row_group_id, user_write )
>    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
> Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 6, 1, 2, 1, 1 
> at 
> /scratch/shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm 
> line 166
> 	GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8627670)', '\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO SRes.TaxonName (  u...') called at /scratch/shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 
> 150
>
>
>
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] LoadTaxon: null value in "taxon_id" violates not-null constraint

[Fernan A. <fe...@ii...>]

Hi,

I've came across this error while trying to load the ncbi
taxonomy dumps using LoadTaxon. Any idea if this is due to a
bad input file or a software bug?

This is a fresh db instance, and this was the first run
(non-commit mode). Seems like taxon_id is clearly empty for
ncbi_tax_id=127219

Thanks in advance for any suggestion,

Fernan

LoadTaxon (supported) plugin rev: 4488
GUS 3.5.1 (SVN snapshot of 11.Apr.2006)
PostgreSQL 8.1.3 (FreeBSD, i386)
NCBI taxonomy files from 17.Apr.2006


[fernan@omega] ga GUS::Supported::Plugin::LoadTaxon --names names.dmp \
--nodes nodes.dmp --gencode gencode.dmp --merged merged.dmp --verbose \
--debug --sqlVerbose


Merging taxons: OK
Updating and inserting SRes.GeneticCode: OK
Process ncbi_tax_id: OK
Fails at the first ocurrence of 'Inserting and updating TaxonName'

[ ..... ]

sqlExec: 
    INSERT INTO SRes.Taxon (  group_write, other_read, group_read, taxon_id, ncbi_tax_id, user_read, genetic_code_id, row_user_id, modification_date, other_write, row_project_id, row_alg_invocation_id, row_group_id, mitochondrial_genetic_code_id, rank, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (1, 1, 1, 607974, 188885, 1, 20, 1, 0, 1, 6, 1, 19, no rank, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Fri Apr 21 21:32:40 2006	Processed ncbi_tax_id : 188885

Fri Apr 21 21:32:40 2006	Inserting and updating TaxonName


prepareAndExecute: select t.taxon_id from sres.taxon t where t.ncbi_tax_id = 127219 
allNonNullsSet: taxon_name_id not set... = ''
GUS::Model::SRes::TaxonName->retrieveFromDB($doNotRetrieveAtts=,)

RetrieveFromDB: select * from SRes.TaxonName where  unique_name_variant is NULL and  name_class = ? and  name = ? and  taxon_id is NULL
  bindValues (scientific name, Tellervini)
Submitting GUS::Model::SRes::TaxonName:
 Table: TaxonName
	unique_name_variant: []
	name_class: [scientific name]
	name: [Tellervini]
	taxon_id: []

HasChangedAttributes='0'
Setting all foreign keys
GUS::Model::SRes::TaxonName->Submit: All foreign keys are set...proceeding
allNonNullsSet: taxon_name_id not set... = ''
Inserting:
Table: TaxonName
	unique_name_variant: []
	group_write: [1]
	other_read: [1]
	group_read: [1]
	name: [Tellervini]
	taxon_id: []
	user_read: [1]
	row_user_id: [1]
	modification_date: [now()]
	name_class: [scientific name]
	other_write: [0]
	row_alg_invocation_id: [6]
	row_project_id: [1]
	row_group_id: [1]
	user_write: [1]


sqlExec: 
    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write, other_read, group_read, name, taxon_id, user_read, row_user_id, modification_date, name_class, other_write, row_alg_invocation_id, row_project_id, taxon_name_id, row_group_id, user_write )
    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (1, 1, 1, Tellervini, 1, 1, scientific name, 0, 6, 1, 2, 1, 1)
DBD::Pg::st execute failed: ERROR:  null value in column "taxon_id" violates not-null constraint
Submitting GUS::Model::Core::AlgorithmInvocation:
 Table: AlgorithmInvocation
	group_read: [1]
	comment_string: []
	user_read: [1]
	algorithm_implementation_id: [5]
	other_write: [0]
	end_time: [now()]
	modification_date: [now()]
	cpu_time: [0]
	row_group_id: [1]
	user_write: [1]
	other_read: [1]
	cpus_used: [1]
	group_write: [1]
	start_time: [now()]
	row_user_id: [1]
	row_alg_invocation_id: [1]
	row_project_id: [1]
	algorithm_invocation_id: [6]
	result: [pending]

HasChangedAttributes='1'
Setting all foreign keys
GUS::Model::Core::AlgorithmInvocation->Submit: All foreign keys are set...proceeding
Updating GUS::Model::Core::AlgorithmInvocation=HASH(0x86bcc54)
Am updateable and have changed atts
Table: AlgorithmInvocation
	group_read: [1]
	comment_string: []
	user_read: [1]
	algorithm_implementation_id: [5]
	other_write: [0]
	end_time: [now()]
	modification_date: [now()]
	cpu_time: [0]
	row_group_id: [1]
	user_write: [1]
	other_read: [1]
	cpus_used: [1]
	group_write: [1]
	start_time: [now()]
	row_user_id: [1]
	row_alg_invocation_id: [6]
	row_project_id: [1]
	algorithm_invocation_id: [6]
	result: [pending]


sqlExec: 
    UPDATE  Core.AlgorithmInvocation
    SET     
	modification_date = ?,
	end_time = ?,
	row_alg_invocation_id = ?
    WHERE   algorithm_invocation_id = ?
  bindValues (now(), now(), 6, 6)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

ERROR:

 SQL ERROR!! involving
 
    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write, other_read, group_read, name, taxon_id, user_read, row_user_id, modification_date, name_class, other_write, row_alg_invocation_id, row_project_id, taxon_name_id, row_group_id, user_write )
    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )  
 Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 6, 1, 2, 1, 1 at /scratch/shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
	GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8627670)', '\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO SRes.TaxonName (  u...') called at /scratch/shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150

[GUSDEV] Re: GUS on postgres: DB version number

[Fernan A. <fe...@ii...>]

Hi again,

now replying to myself since I got no answer before

| [InstallSchema] SEVERE: Null version, skipping.  Note:  You will need to manually add a version number to the DB
 
| What do I have to do now? Is this (manually adding a version
| number) documented somewhere?

I also see this when I try to use it:

[fernan@omega] ga +meta

Database version does not match required version for Plugin.
Database Version:     Plugin Version: 3.5


I'm guessing that maybe '3.5' or '3.5.1' need to be entered
in Core.DatabaseVersion (as per GusApplication.pm, line
1210)

database_version_id	=> 1
version			=> 3.5

and, AFAICS, from reading gus_schema.xml there's no other
table referencing DATABASE_VERSION_ID ... so is it safe to
go on and insert these values here?

What would be a sensible value for version, given that I'm
working with a GUS snapshot obtained from the repository on
11.Apr.2006? 

3.5.1 is what upgrade.txt suggests ... but this file is
dated Oct 2005 ... moreover, given that 'version' only
accepts a float, this shoule be '3.51' instead which may
cause problems if GUS ever reaches 3.51.0 AND I'm still
using the same db instance :) 

BTW, in other tables, GUS stores versions, including cvs
revisions as 'string' ... 

Thanks,

Fernan

+----[ To GUS-Dev <fe...@ii...> (12.Apr.2006 13:34):
|
| Hi!
| 
| I've just checked out GUS using SVN 
| (svn checkout https://www.cbil.upenn.edu/svn/gus/gusTrunk GUS)
| and I'm building it against a local postgres-8.1.3 database.
| 
| Everything seems to go fine up to this point:
| 
| [InstallSchema] INFO: Writing Database 
| [InstallSchema] Apr 12, 2006 1:20:10 PM org.gusdb.dbadmin.util.InstallSchemaTask
| conditionalWriteVersion
| [InstallSchema] SEVERE: Null version, skipping.  Note:  You will need to manually add a version number to the DB
| [InstallSchema] Apr 12, 2006 1:20:31 PM org.gusdb.dbadmin.util.InstallSchemaTask
| conditionalWriteVersion
| [InstallSchema] SEVERE: Null version, skipping.  Note:  You will need to manually add a version number to the DB
 
| What do I have to do now? Is this (manually adding a version
| number) documented somewhere?
| 
| Thanks in advance,
| 
| Fernan
|
+----]

Re: [GUSDEV] dbiDsn weirdness

[Chris S. <sto...@pc...>]

Hi Fernan,
Not doing much here on the postgres side of things so can't offer  
much help. Hopefully one of the other groups using postgres will  
reply. Certainly file a bug report and if no one says anything I  
would certainly welcome your contributing to software.
Cheers,
Chris

Chris Stoeckert, Ph.D.
Research Associate Professor, Dept. of Genetics
1415 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Ph: 215-573-4409 FAX: 215-573-3111

On Apr 12, 2006, at 5:12 PM, Fernan Aguero wrote:

> Hello, again,
>
> I'm having a problem with my gus.config file, and more
> specifically with the dbiDsn string.
>
> I have a test database (testdb) and I can connect to this
> database either using perl or java (using minimal programs
> that just connect to the DB) or in a terminal using psql.
>
> However, the dbiDsn that I use succesfully in my scripts
> (dbi:Pg:dbname=testdb) doesn't work when used in the
> gus.config file.
>
> The details are below. Should I file a bug report?
>
> Fernan
>
> ======================================================================
> Details
> ======================================================================
> perl: 5.8.8
> DBI: 1.5.0
> DBD-Pg: 1.43
> GUS: SVN snapshot from 11.Apr.2006
>
> dbiDsn in gus.config:
> dbiDsn=dbi:Pg:dbname=testdb
>
> output of 'build GUS install -append':
> [exec] Can't connect to data source "dbi:Pg:dbname=testdb", no  
> database driver specified and DBI_DSN env var not set at /scratch/ 
> shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm  
> line 173
>
> Just to test, I tried the following dbiDsn, which I found
> mentioned in one bug report
> dbiDsn=dbi:Pg:dbname=testdb;port=5432
>
> and now 'build GUS install -append' went through without
> errors. 5432 is the default port for postgres, so it
> shouldn't need to be set explicitly. This made me think that
> the problem was the missing ';' and so I tried the following:
> dbiDsn=dbi:Pg:dbname=testdb;
>
> which also worked quite nicely. Which brings us to the question:
> is this a documentation bug? Or a software bug?
>
> I can file a bug report and either fix it (documentation) or
> help as much as I can (software).
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting  
> language
> that extends applications into web and mobile media. Attend the  
> live webcast
> and join the prime developer group breaking into this new coding  
> territory!
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=110944&bid=241720&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] dbiDsn weirdness

[Fernan A. <fe...@ii...>]

Hello, again,

I'm having a problem with my gus.config file, and more
specifically with the dbiDsn string.

I have a test database (testdb) and I can connect to this
database either using perl or java (using minimal programs
that just connect to the DB) or in a terminal using psql.

However, the dbiDsn that I use succesfully in my scripts
(dbi:Pg:dbname=testdb) doesn't work when used in the
gus.config file.

The details are below. Should I file a bug report?

Fernan

======================================================================
Details
======================================================================
perl: 5.8.8
DBI: 1.5.0
DBD-Pg: 1.43
GUS: SVN snapshot from 11.Apr.2006

dbiDsn in gus.config:
dbiDsn=dbi:Pg:dbname=testdb

output of 'build GUS install -append':
[exec] Can't connect to data source "dbi:Pg:dbname=testdb", no database driver specified and DBI_DSN env var not set at /scratch/shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 173

Just to test, I tried the following dbiDsn, which I found
mentioned in one bug report 
dbiDsn=dbi:Pg:dbname=testdb;port=5432

and now 'build GUS install -append' went through without
errors. 5432 is the default port for postgres, so it
shouldn't need to be set explicitly. This made me think that
the problem was the missing ';' and so I tried the following:
dbiDsn=dbi:Pg:dbname=testdb;

which also worked quite nicely. Which brings us to the question:
is this a documentation bug? Or a software bug? 

I can file a bug report and either fix it (documentation) or
help as much as I can (software).

[GUSDEV] GUS on postgres: DB version number

[Fernan A. <fe...@ii...>]

Hi!

I've just checked out GUS using SVN 
(svn checkout https://www.cbil.upenn.edu/svn/gus/gusTrunk GUS)
and I'm building it against a local postgres-8.1.3 database.

Everything seems to go fine up to this point:

[InstallSchema] INFO: Writing Database 
[InstallSchema] Apr 12, 2006 1:20:10 PM org.gusdb.dbadmin.util.InstallSchemaTask
conditionalWriteVersion
[InstallSchema] SEVERE: Null version, skipping.  Note:  You will need to manually add a version number to the DB
[InstallSchema] Apr 12, 2006 1:20:31 PM org.gusdb.dbadmin.util.InstallSchemaTask
conditionalWriteVersion
[InstallSchema] SEVERE: Null version, skipping.  Note:  You will need to manually add a version number to the DB

What do I have to do now? Is this (manually adding a version
number) documented somewhere?

Thanks in advance,

Fernan

Re: [GUSDEV] GUS schema to support Genbank features

[Chris S. <sto...@pc...>]

Ed,
Thanks for addressing this. The semantics in GUS for capturing operon =20=

is to consider it as equivalent to a gene and thus an entry in the =20
Gene table. Multiple RNA entries can be associated with a Gene entry =20
and these can reflect the common transcript or processed transcripts =20
depending upon what occurs. Multiple Protein entries can be =20
associated with a RNA entry if there is one common transcript that is =20=

translated into different proteins.

In terms of loading a GenBank file, this would be loaded as a feature =20=

as you describe as is true for other GenBank features.

Hope this helps,
Chris

On Mar 15, 2006, at 2:35 PM, Ed Robinson wrote:

> First, let me beg an analyst or bilogist to correct me if any
> of this is wrong.
>
> Yes, the quick and dirty way would be to incorporate an operon
> attribute in your Gene feature and point it towards a
> convenient column using "column=3D".
>
> I also noticed that the genbank2gus.xml map does not have a
> table for an operon feature.  If you have operon features, in
> addition to operon attributes, you will need to find a
> suitable table to store these.  Modify the map as you need to.
>
> Unfortunately, GUS was designed primarily with Eukaryotic
> organisms in mind.  There is nothing in GUS that I know of (if
> I am wrong, some analyst please correct me) to support
> super-gene organizations. If you want to group your genes into
> their respective operons, the best way I can see doing that is
> to store each operon with it's source_id in some table, and
> then store the source_id for each genes operon in some
> attribute in your GeneFeature entry.  Then, you can simply
> select all of the GeneFeatures with the same source_id to
> recover all of the genes in one operon.  The operon itself, if
> you store it, will just be a big, long feature on your
> NASequence within which you will find many gene records.
> There will be no explicit ordering of genes in this operon via
> parent_ids.  You will need to use the gene locations to
> determine ordering within the span of an operon.
>
> Unfortunately, there isn't any way to record the order that
> genes appear in an operon other than to retrieve their
> individual locations.  There is also no hierarchical
> organization of super-gene structures in gus.
> InsertSequenceFeatures does support the hierarchy
>
>    gene->mRNA->Exon
>              ->CDS->TranslatedAASequence
>
> It does this via the BioPerl unflattener.  However, neither
> GUS nor the unflattener supports a hierarchy such as
>
>       ->promoter
> Operon->gene.....
>       ->gene.....
>
> Of course, GUS is expandable if someone were inclined to work
> on this.....
>
> Hope this is hepful.
>
> -ed
>
>
> ---- Original message ----
>> Date: Wed, 15 Mar 2006 14:10:27 -0500
>> From: Jian Lu <jl...@vb...>
>> Subject: Re: [GUSDEV] GUS schema to support Genbank features
>> To: Ed Robinson <ero...@ug...>
>> Cc: gus...@li...
>>
>> So if we want to incorporate a new qualifier "operon" into
> either
>> GeneFeature or Transcript, we have to add it to them. Will
> GUS consider
>> it for future new release?
>>
>>  <feature name=3D"gene" table=3D"DoTS::GeneFeature" so=3D"gene">
>>  <qualifier name=3D"allele" />
>>  <qualifier name=3D"citation" />
>>  <qualifier name=3D"evidence" />
>>  <qualifier name=3D"function" />
>>  <qualifier name=3D"gene" handler=3D"standard" method=3D"gene" />
>>  <qualifier name=3D"label" />
>>  <qualifier name=3D"locus_tag" column=3D"source_id" />
>>  <qualifier name=3D"map" />
>>  <qualifier name=3D"note" handler=3D"standard" method=3D"note" />
>>  <qualifier name=3D"old_locus_tag" ignore=3D"true" />
>>  <qualifier name=3D"operon" ignore=3D"true" />
>>  <qualifier name=3D"product" />
>>  <qualifier name=3D"pseudo" =0C />
>>  <qualifier name=3D"phenotype" />
>>  <qualifier name=3D"standard_name" />
>>  <qualifier name=3D"usedin" />
>>  <qualifier name=3D"db_xref" handler=3D"standard" method=3D"dbXRef" =
/>
>>  </feature>
>>
>> Ed Robinson wrote:
>>> The genbank2gus.xml was designed to match all GB features to
>>> tables in GUS.  You shouldn't find any GB feature which is not
>>> in the file.  You may find some feature attributes which are
>>> not in the file.  Feel free to add any attributes you may need.
>>>
>>> The mapping of genbank features to gus tables is not one to
>>> one.  GUS was not written to mirror GenBank.
>>>
>>> The genbank2gus.xml file was written as an idealized mapping
>>> for some of the datasets we have seen while working on
>>> ApiComplexan data sets.  As such, the file is a good
>>> suggesstion on how to map GenBank features into GUS.  However,
>>> it is not the final word on how to handle such a mapping.
>>> Features such as Gene, Exon, and CDS are central to the
>>> working of InsertSequenceFeatures.  Thus, you should probably
>>> leave those features pointing at their respective tables.  If
>>> you want to change one of the other features to point at a
>>> different table, you should feel free to do so.  You should
>>> design a map that allows you to make the best use of the GUS
>>> tables for your own data.
>>>
>>> I hope this helps.  If you have any more specific questions
>>> about using the map for your data, please post them.  Data
>>> modeling discussions are always lively.
>>>
>>> -ed
>>>
>>>
>>>
>>> ---- Original message ----
>>>
>>>> Date: Wed, 15 Mar 2006 13:24:11 -0500
>>>> From: Jian Lu <jl...@vb...>
>>>> Subject: [GUSDEV] GUS schema to support Genbank features
>>>> To: gus...@li...
>>>>
>>>> Hi GUS,
>>>>
>>>> The GUS 3.5 doesn't support all Genbank features such as
>>>>
>>> "operon". From
>>>
>>>> the mapping file "genbank2gus.xml", we could see "operon" has
>>>>
>>> been
>>>
>>>> included in several feature tables.
>>>> Questions:
>>>> 1. Does "genbank2gus.xml" contain all Genbank features or
> will?
>>>> 2. How soon GUS schema will support all Genbank features or
>>>>
>>> at least
>>>
>>>> features within genbank2gus.xml
>>>> 3. How will GUS plug-ins support the added Genbank features?
>>>>
>>>> Thanks,
>>>>
>>>> Jian Lu
>>>> VBI
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by xPML, a groundbreaking
>>>>
>>> scripting language
>>>
>>>> that extends applications into web and mobile media. Attend
>>>>
>>> the live webcast
>>>
>>>> and join the prime developer group breaking into this new
>>>>
>>> coding territory!
>>>
>>>>
> http://sel.as-us.falkag.net/sel?=20
> cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D121642
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>> -----------------
>>> Ed Robinson
>>> Center for Tropical and Emerging Global Diseases
>>> University of Georgia, Athens, GA 30602
>>> ero...@ug.../(706)542.1447/254.8883
>>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by xPML, a groundbreaking
> scripting language
>> that extends applications into web and mobile media. Attend
> the live webcast
>> and join the prime developer group breaking into this new
> coding territory!
>> http://sel.as-us.falkag.net/sel?=20
>> cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D121642
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting =20
> language
> that extends applications into web and mobile media. Attend the =20
> live webcast
> and join the prime developer group breaking into this new coding =20
> territory!
> http://sel.as-us.falkag.net/sel?=20
> cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GUS schema to support Genbank features

[Ed R. <ero...@ug...>]

First, let me beg an analyst or bilogist to correct me if any
of this is wrong.

Yes, the quick and dirty way would be to incorporate an operon
attribute in your Gene feature and point it towards a
convenient column using "column=".

I also noticed that the genbank2gus.xml map does not have a
table for an operon feature.  If you have operon features, in
addition to operon attributes, you will need to find a
suitable table to store these.  Modify the map as you need to.

Unfortunately, GUS was designed primarily with Eukaryotic
organisms in mind.  There is nothing in GUS that I know of (if
I am wrong, some analyst please correct me) to support
super-gene organizations. If you want to group your genes into
their respective operons, the best way I can see doing that is
to store each operon with it's source_id in some table, and
then store the source_id for each genes operon in some
attribute in your GeneFeature entry.  Then, you can simply
select all of the GeneFeatures with the same source_id to
recover all of the genes in one operon.  The operon itself, if
you store it, will just be a big, long feature on your
NASequence within which you will find many gene records. 
There will be no explicit ordering of genes in this operon via
parent_ids.  You will need to use the gene locations to
determine ordering within the span of an operon.

Unfortunately, there isn't any way to record the order that
genes appear in an operon other than to retrieve their
individual locations.  There is also no hierarchical
organization of super-gene structures in gus. 
InsertSequenceFeatures does support the hierarchy

   gene->mRNA->Exon
             ->CDS->TranslatedAASequence

It does this via the BioPerl unflattener.  However, neither
GUS nor the unflattener supports a hierarchy such as

      ->promoter
Operon->gene.....
      ->gene.....  

Of course, GUS is expandable if someone were inclined to work
on this.....

Hope this is hepful.

-ed


---- Original message ----
>Date: Wed, 15 Mar 2006 14:10:27 -0500
>From: Jian Lu <jl...@vb...>  
>Subject: Re: [GUSDEV] GUS schema to support Genbank features  
>To: Ed Robinson <ero...@ug...>
>Cc: gus...@li...
>
> So if we want to incorporate a new qualifier "operon" into
either 
>GeneFeature or Transcript, we have to add it to them. Will
GUS consider 
>it for future new release?
>
>  <feature name="gene" table="DoTS::GeneFeature" so="gene">
>  <qualifier name="allele" />
>  <qualifier name="citation" />
>  <qualifier name="evidence" />
>  <qualifier name="function" />
>  <qualifier name="gene" handler="standard" method="gene" />
>  <qualifier name="label" />
>  <qualifier name="locus_tag" column="source_id" />
>  <qualifier name="map" />
>  <qualifier name="note" handler="standard" method="note" />
>  <qualifier name="old_locus_tag" ignore="true" />
>  <qualifier name="operon" ignore="true" />
>  <qualifier name="product" />
>  <qualifier name="pseudo"  />
>  <qualifier name="phenotype" />
>  <qualifier name="standard_name" />
>  <qualifier name="usedin" />
>  <qualifier name="db_xref" handler="standard" method="dbXRef" />
>  </feature>
>
>Ed Robinson wrote:
>> The genbank2gus.xml was designed to match all GB features to
>> tables in GUS.  You shouldn't find any GB feature which is not
>> in the file.  You may find some feature attributes which are
>> not in the file.  Feel free to add any attributes you may need.
>>
>> The mapping of genbank features to gus tables is not one to
>> one.  GUS was not written to mirror GenBank.  
>>
>> The genbank2gus.xml file was written as an idealized mapping
>> for some of the datasets we have seen while working on
>> ApiComplexan data sets.  As such, the file is a good
>> suggesstion on how to map GenBank features into GUS.  However,
>> it is not the final word on how to handle such a mapping. 
>> Features such as Gene, Exon, and CDS are central to the
>> working of InsertSequenceFeatures.  Thus, you should probably
>> leave those features pointing at their respective tables.  If
>> you want to change one of the other features to point at a
>> different table, you should feel free to do so.  You should
>> design a map that allows you to make the best use of the GUS
>> tables for your own data.
>>
>> I hope this helps.  If you have any more specific questions
>> about using the map for your data, please post them.  Data
>> modeling discussions are always lively.
>>
>> -ed
>>
>>
>>
>> ---- Original message ----
>>   
>>> Date: Wed, 15 Mar 2006 13:24:11 -0500
>>> From: Jian Lu <jl...@vb...>  
>>> Subject: [GUSDEV] GUS schema to support Genbank features  
>>> To: gus...@li...
>>>
>>> Hi GUS,
>>>
>>> The GUS 3.5 doesn't support all Genbank features such as
>>>     
>> "operon". From 
>>   
>>> the mapping file "genbank2gus.xml", we could see "operon" has
>>>     
>> been 
>>   
>>> included in several feature tables.
>>> Questions:
>>> 1. Does "genbank2gus.xml" contain all Genbank features or
will?
>>> 2. How soon GUS schema will support all Genbank features or
>>>     
>> at least 
>>   
>>> features within genbank2gus.xml
>>> 3. How will GUS plug-ins support the added Genbank features?
>>>
>>> Thanks,
>>>
>>> Jian Lu
>>> VBI
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by xPML, a groundbreaking
>>>     
>> scripting language
>>   
>>> that extends applications into web and mobile media. Attend
>>>     
>> the live webcast
>>   
>>> and join the prime developer group breaking into this new
>>>     
>> coding territory!
>>   
>>>
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>     
>> -----------------
>> Ed Robinson
>> Center for Tropical and Emerging Global Diseases
>> University of Georgia, Athens, GA 30602
>> ero...@ug.../(706)542.1447/254.8883
>>   
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by xPML, a groundbreaking
scripting language
>that extends applications into web and mobile media. Attend
the live webcast
>and join the prime developer group breaking into this new
coding territory!
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

Re: [GUSDEV] GUS schema to support Genbank features

[Jian Lu <jl...@vb...>]

 So if we want to incorporate a new qualifier "operon" into either 
GeneFeature or Transcript, we have to add it to them. Will GUS consider 
it for future new release?

  <feature name="gene" table="DoTS::GeneFeature" so="gene">
  <qualifier name="allele" />
  <qualifier name="citation" />
  <qualifier name="evidence" />
  <qualifier name="function" />
  <qualifier name="gene" handler="standard" method="gene" />
  <qualifier name="label" />
  <qualifier name="locus_tag" column="source_id" />
  <qualifier name="map" />
  <qualifier name="note" handler="standard" method="note" />
  <qualifier name="old_locus_tag" ignore="true" />
  <qualifier name="operon" ignore="true" />
  <qualifier name="product" />
  <qualifier name="pseudo" column="is_pseudo" />
  <qualifier name="phenotype" />
  <qualifier name="standard_name" />
  <qualifier name="usedin" />
  <qualifier name="db_xref" handler="standard" method="dbXRef" />
  </feature>

Ed Robinson wrote:
> The genbank2gus.xml was designed to match all GB features to
> tables in GUS.  You shouldn't find any GB feature which is not
> in the file.  You may find some feature attributes which are
> not in the file.  Feel free to add any attributes you may need.
>
> The mapping of genbank features to gus tables is not one to
> one.  GUS was not written to mirror GenBank.  
>
> The genbank2gus.xml file was written as an idealized mapping
> for some of the datasets we have seen while working on
> ApiComplexan data sets.  As such, the file is a good
> suggesstion on how to map GenBank features into GUS.  However,
> it is not the final word on how to handle such a mapping. 
> Features such as Gene, Exon, and CDS are central to the
> working of InsertSequenceFeatures.  Thus, you should probably
> leave those features pointing at their respective tables.  If
> you want to change one of the other features to point at a
> different table, you should feel free to do so.  You should
> design a map that allows you to make the best use of the GUS
> tables for your own data.
>
> I hope this helps.  If you have any more specific questions
> about using the map for your data, please post them.  Data
> modeling discussions are always lively.
>
> -ed
>
>
>
> ---- Original message ----
>   
>> Date: Wed, 15 Mar 2006 13:24:11 -0500
>> From: Jian Lu <jl...@vb...>  
>> Subject: [GUSDEV] GUS schema to support Genbank features  
>> To: gus...@li...
>>
>> Hi GUS,
>>
>> The GUS 3.5 doesn't support all Genbank features such as
>>     
> "operon". From 
>   
>> the mapping file "genbank2gus.xml", we could see "operon" has
>>     
> been 
>   
>> included in several feature tables.
>> Questions:
>> 1. Does "genbank2gus.xml" contain all Genbank features or will?
>> 2. How soon GUS schema will support all Genbank features or
>>     
> at least 
>   
>> features within genbank2gus.xml
>> 3. How will GUS plug-ins support the added Genbank features?
>>
>> Thanks,
>>
>> Jian Lu
>> VBI
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by xPML, a groundbreaking
>>     
> scripting language
>   
>> that extends applications into web and mobile media. Attend
>>     
> the live webcast
>   
>> and join the prime developer group breaking into this new
>>     
> coding territory!
>   
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>     
> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883
>   

Re: [GUSDEV] GUS schema to support Genbank features

[Ed R. <ero...@ug...>]

The genbank2gus.xml was designed to match all GB features to
tables in GUS.  You shouldn't find any GB feature which is not
in the file.  You may find some feature attributes which are
not in the file.  Feel free to add any attributes you may need.

The mapping of genbank features to gus tables is not one to
one.  GUS was not written to mirror GenBank.  

The genbank2gus.xml file was written as an idealized mapping
for some of the datasets we have seen while working on
ApiComplexan data sets.  As such, the file is a good
suggesstion on how to map GenBank features into GUS.  However,
it is not the final word on how to handle such a mapping. 
Features such as Gene, Exon, and CDS are central to the
working of InsertSequenceFeatures.  Thus, you should probably
leave those features pointing at their respective tables.  If
you want to change one of the other features to point at a
different table, you should feel free to do so.  You should
design a map that allows you to make the best use of the GUS
tables for your own data.

I hope this helps.  If you have any more specific questions
about using the map for your data, please post them.  Data
modeling discussions are always lively.

-ed



---- Original message ----
>Date: Wed, 15 Mar 2006 13:24:11 -0500
>From: Jian Lu <jl...@vb...>  
>Subject: [GUSDEV] GUS schema to support Genbank features  
>To: gus...@li...
>
>Hi GUS,
>
>The GUS 3.5 doesn't support all Genbank features such as
"operon". From 
>the mapping file "genbank2gus.xml", we could see "operon" has
been 
>included in several feature tables.
>Questions:
>1. Does "genbank2gus.xml" contain all Genbank features or will?
>2. How soon GUS schema will support all Genbank features or
at least 
>features within genbank2gus.xml
>3. How will GUS plug-ins support the added Genbank features?
>
>Thanks,
>
>Jian Lu
>VBI
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by xPML, a groundbreaking
scripting language
>that extends applications into web and mobile media. Attend
the live webcast
>and join the prime developer group breaking into this new
coding territory!
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

[GUSDEV] GUS schema to support Genbank features

[Jian Lu <jl...@vb...>]

Hi GUS,

The GUS 3.5 doesn't support all Genbank features such as "operon". From 
the mapping file "genbank2gus.xml", we could see "operon" has been 
included in several feature tables.
Questions:
1. Does "genbank2gus.xml" contain all Genbank features or will?
2. How soon GUS schema will support all Genbank features or at least 
features within genbank2gus.xml
3. How will GUS plug-ins support the added Genbank features?

Thanks,

Jian Lu
VBI

[GUSDEV] blastSimilarity: broken coordinates when using TBLASTN

[Aaron J. M. <am...@pc...>]

FYI, the subject start/end coordinates of the SUM line seem to be  
fubar'ed in the short-form output (and the HSP lines are also  
suspect).  For instance:

   Sum: 995361:1777:2.1e-193:506993:506973:2:696:2:734:369:514:0:
    HSP1: 995361:336:463:645:1777:2.1e-193:508907:506973:2:639:0:
    HSP2: 995361:33:51:89:148:2.1e-193:506993:506727:610:696:0:

I believe this should instead look something like:

   Sum: 995361:1777:2.1e-193:506727:508907:2:696:2:734:369:514:1:
    HSP1: 995361:336:463:645:1777:2.1e-193:506973:508907:2:639:1:
    HSP2: 995361:33:51:89:148:2.1e-193:506727:506993:610:696:1:

I've only seen this in TBLASTN output, but there may be other  
algorithms that also behave poorly.

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
         215-746-7018 (PCBI, 1428 Blockley Hall)
fax:    215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

Re: [GUSDEV] [Slightly-OT] ASM with Oracle10G

[<ju...@cs...>]

Michael; thank you for your insight!

As we will be integrating another Oracle
installation that is still using 9i, I think I will
just go with the standard file system for now 
and upgrade to ASM when both our Oracle installations
have been upgraded to 10g.  I may as well take one
complication at a time.

Thanks again;

Josef


Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 702-9559
fax:   (773) 702-6648

Re: [GUSDEV] [Slightly-OT] ASM with Oracle10G

[Michael S. <m...@sa...>]

Hi Josef,

CBIL has been using ASM for about a year now.  It's a new technology, 
and it's not without its pains, so you should be comfortable working 
with the bleeding edge and of course ensure that you have valid backups. 
  Release 2 is much better than Release 1, so make sure you use that 
(i.e. 10gR2).

Having said all of that, ASM is a very cool technology and has a lot of 
appealing promises.  Among those are automatic balancing to address IO 
load, simplified management of files, etc.  As the number of disks and 
nodes you have in your database system increase, the value of ASM increases.

See below for specifics.


Josef Jurek wrote:
> Up to now, we at the Preuss lab have installed and used
> GUS under Oracle9i only.  As we are beginning to install
> Oracle on a new machine (RHEL ES release 4/Linux 2.6.9-22.ELsmp),
> we decided to go with version 10g here.  So far, the only issue
> with this installation has been installing the Automatic Storage
> System or ASM, a new feature to Oracle10g.
> 
> Some questions:
> 
>    Is it worth going to ASM instead of just using the 9i
>    method of managing tablespaces, what the manual calls the
>    "File System" approach?  I suppose I could just
>    start with the File System approach and upgrade to ASM
>    later.

True on this latter point.  Whether it is worth it is highly dependent 
on your setup-- how many nodes and disks?

> 
>    ASM Support Library; the manual calls it "optional" yet
>    "recommended".  Do people find this worth having?
>    As far as I can tell, using the ASMLib means that you cannot
>    run SELinux (Security-Enhanced Linux).  Is this what
>    other people are finding?
> 

As far as I know, ASMLib is required under Linux.  I can't imagine it 
not being there.  CBIL is/was exploring SELinux, but didn't have any 
machines that had it activated.  Migrating to SELinux poses some 
challenges on existing machines since a large number of items can 
potentially break in mysterious ways.

>    Our Linux box already has RAID disks, therefore the manual
>    seems to indicate that the "external redundancy" option for
>    ASM is a way to go as opposed to the "normal redundancy"
>    or "high redundancy" options.  Do people agree?
> 

Yes, this is how CBIL does it-- external redundancy handled by the RAID 
controller.  If you're not using RAID, or don't want to, normal 
redundancy seems like a nice option, but note that it's equivalent to 
RAID 1-- there's no equivalence to RAID 5.

>    Does anyone have any suggestions for other things to
>    watch out for?
> 

Oh, too many to list here :)  If you do do ASM, just watch for 
permissions on the asmdisks under /dev-- oracle:oinstall needs write 
access or you'll get very strange errors.

--Mike

> Thanks; Josef
> 
> 
> 
> Josef Jurek
> 
> Daphne Preuss Laboratory
> Molecular Genetics and Cell Biology
> The University of Chicago
> ju...@cs...
> 
> voice: (773) 702-9559
> fax:   (773) 702-6648
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting language
> that extends applications into web and mobile media. Attend the live webcast
> and join the prime developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] Re: ISF errors list

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

ricardo-

no we don't have any immediate plans to improve ISF in this direction. 

what i think you should do is write a pre-processor which searches for 
known issues.   (we pre-process our data all the time.)  for example, 
you could write a program that passes each genbank record separately to 
bioperl/unflattener for parsing (steal that code from ISF).   if there 
is an exception, catch it, (use perl's eval statement), write the broken 
accession to a log file, and keep going.  now you have a list of 
accessions to inspect and/or programmatically remove.

steve

Ricardo Balbi wrote:

> Steve,
>
>   We have a GenBank file with 1.5GB and to fix all issues that we find 
> manually becomes a very cost task, because we do not have as much 
> time.  Do you have plans to improve the ISF in this direction?
>
> Ricardo
>
> On 3/7/06, *Steve Fischer* <sfi...@pc... 
> <mailto:sfi...@pc...>> wrote:
>
>     ISF does not now support any way to ignore a GI.
>
>     so, for now, copy the genbank to file to a .fixed version, and fix the
>     problem, either by removing the GI or by tweeking the feaatures
>
>     steve
>
>     Ricardo Balbi wrote:
>
>     > Ok Aaron, but what we have to do ? edit the GenBank file? ignore
>     this
>     > GI? if yes, how to ignore?
>     >
>     > On 2/16/06, *Aaron J. Mackey* < am...@pc...
>     <mailto:am...@pc...>
>     > <mailto:am...@pc... <mailto:am...@pc...>>>
>     wrote:
>     >
>     >
>     >
>     >     On Feb 17, 2006, at 6:58 PM, davila wrote:
>     >
>     >     > 3. 102829.txt - Apparently a BioPerl error
>     >     > A 102829.gb <http://102829.gb> <http://102829.gb> file is
>     an example
>     >
>     >     Read the error message, it tells you exactly what is wrong:
>     >
>     >     ------------- EXCEPTION  -------------
>     >     MSG: 1 there is a conflict with exons; there was an
>     explicitly stated
>     >     exon with location 12..21, yet I cannot generate this e
>     >     xon from the supplied mRNA locations
>     >     1 There are some inferred exons that are not in the explicit
>     exon
>     >     list; they are the exons at locations:
>     >     25..447
>     >
>     >     STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
>     /usr/lib/
>     >     perl5/site_perl/5.8.6/Bio/SeqFeature/Tools/Unflattener.pm:1
>     >     606
>     >     ...
>     >
>     >
>     >     Then look at the GenBank file:
>     >
>     >           gene            1..447
>     >                           /gene="ESAG1"
>     >           primer_bind     1..11
>     >                           /gene="ESAG1"
>     >           exon            <12..21
>     >                           /gene="ESAG1"
>     >                           /note="min-exon"
>     >           CDS             25..>447
>     >                           /gene="ESAG1"
>     >
>     >     I have to agree with the Unflattener, this doesn't make any
>     sense at
>     >     all.
>     >
>     >     Garbage in, garbage out.
>     >
>     >     -Aaron
>     >
>     >
>     >     --
>     >     Aaron J. Mackey, Ph.D.
>     >     Project Manager, ApiDB Bioinformatics Resource Center
>     >     Penn Genomics Institute, University of Pennsylvania
>     >     email:   am...@pc...
>     <mailto:am...@pc...> <mailto:am...@pc...
>     <mailto:am...@pc...>>
>     >     office: 215-898-1205 (Biology, 212 Goddard Labs)
>     >              215-746-7018 (PCBI, 1428 Blockley Hall)
>     >     fax:    215-746-6697 (Penn Genomics Institute)
>     >     postal: Penn Genomics Institute
>     >              Goddard Labs 212
>     >              415 S. University Avenue
>     >              Philadelphia, PA  19104-6017
>     >
>     >
>     >
>     >
>     >     -------------------------------------------------------
>     >     This SF.net email is sponsored by: Splunk Inc. Do you grep
>     through
>     >     log files
>     >     for problems?  Stop!  Download the new AJAX search engine
>     that makes
>     >     searching your log files as easy as surfing the  web.  DOWNLOAD
>     >     SPLUNK!
>     >    
>     http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642
>     <http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642>
>     >    
>     <http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642
>     <http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642>>
>     >     _______________________________________________
>     >     Gusdev-gusdev mailing list
>     >     Gus...@li...
>     <mailto:Gus...@li...>
>     >     <mailto: Gus...@li...
>     <mailto:Gus...@li...>>
>     >     https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>     >
>     >
>
>

Re: [GUSDEV] Sugestion for the ISF plugin

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

the problem with deploying the increased error threshold as a solution 
in this case is that you have just pushed the problem to the downstream 
processes. 

steve

Ricardo Balbi wrote:

> Ok Chris,
>
>   We'll see this.
>
> thanks,
> Ricardo
>
> On 3/7/06, *chris mungall* <cj...@fr... 
> <mailto:cj...@fr...>> wrote:
>
>
>     You can increase the threshold at which the severity of a problem
>     causes the unflattener to throw an error.
>
>     $unf->error_threshold(2);  # do not throw for problems of severity <2
>
>     see the docs for more details
>
>     The policy here is up to you. As we discovered the last time this came
>     up, this particular genbank record has an inconsistency. It's up
>     to you
>     whether you want to load the exons from this file, or if you would
>     prefer to reject the entire record
>
>
>
>     On Mar 7, 2006, at 10:36 AM, Steve Fischer wrote:
>
>     > in this case, i am not sure this is possible.  the problem is during
>     > the bioperl parsing.   if you would like to do the work to
>     investigate
>     > whether the bioperl parser (and the unflattener) have options for
>     > this, that would be a first step.
>     >
>     > steve
>     >
>     > Ricardo Balbi wrote:
>     >
>     >> Hi all,
>     >>
>     >>   Ahead of all the problems that we are facing to load a
>     GenBank file
>     >> using the InsertSequenceFeatures (we thougth in coming back to use
>     >> the GBParser), we have one sugestion:
>     >>   Maybe modify the ISF to separate the GIs that present problems in
>     >> separate files, as GBParser does, not interrupting the
>     execution.  We
>     >> believe that this could help solve many of the problems that we are
>     >> finding (and I believe that other groups too) and would very
>     easy to
>     >> correct these problems without interrupting the work that we are
>     >> carrying at the moment.   We believe that with this
>     modification, the
>     >> ISF would become much more flexible and easy to work.
>     >>
>     >> thanks in advance,
>     >> Ricardo
>     >
>
>

Re: [GUSDEV] Sugestion for the ISF plugin

[Ricardo B. <rb...@gm...>]

Ok Chris,

  We'll see this.

thanks,
Ricardo

On 3/7/06, chris mungall <cj...@fr...> wrote:
>
>
> You can increase the threshold at which the severity of a problem
> causes the unflattener to throw an error.
>
> $unf->error_threshold(2);  # do not throw for problems of severity <2
>
> see the docs for more details
>
> The policy here is up to you. As we discovered the last time this came
> up, this particular genbank record has an inconsistency. It's up to you
> whether you want to load the exons from this file, or if you would
> prefer to reject the entire record
>
>
>
> On Mar 7, 2006, at 10:36 AM, Steve Fischer wrote:
>
> > in this case, i am not sure this is possible.  the problem is during
> > the bioperl parsing.   if you would like to do the work to investigate
> > whether the bioperl parser (and the unflattener) have options for
> > this, that would be a first step.
> >
> > steve
> >
> > Ricardo Balbi wrote:
> >
> >> Hi all,
> >>
> >>   Ahead of all the problems that we are facing to load a GenBank file
> >> using the InsertSequenceFeatures (we thougth in coming back to use
> >> the GBParser), we have one sugestion:
> >>   Maybe modify the ISF to separate the GIs that present problems in
> >> separate files, as GBParser does, not interrupting the execution.  We
> >> believe that this could help solve many of the problems that we are
> >> finding (and I believe that other groups too) and would very easy to
> >> correct these problems without interrupting the work that we are
> >> carrying at the moment.   We believe that with this modification, the
> >> ISF would become much more flexible and easy to work.
> >>
> >> thanks in advance,
> >> Ricardo
> >
>
>

Re: [GUSDEV] Re: ISF errors list

[Ricardo B. <rb...@gm...>]

Steve,

  We have a GenBank file with 1.5GB and to fix all issues that we find
manually becomes a very cost task, because we do not have as much time.  Do
you have plans to improve the ISF in this direction?

Ricardo

On 3/7/06, Steve Fischer <sfi...@pc...> wrote:
>
> ISF does not now support any way to ignore a GI.
>
> so, for now, copy the genbank to file to a .fixed version, and fix the
> problem, either by removing the GI or by tweeking the feaatures
>
> steve
>
> Ricardo Balbi wrote:
>
> > Ok Aaron, but what we have to do ? edit the GenBank file? ignore this
> > GI? if yes, how to ignore?
> >
> > On 2/16/06, *Aaron J. Mackey* < am...@pc...
> > <mailto:am...@pc...>> wrote:
> >
> >
> >
> >     On Feb 17, 2006, at 6:58 PM, davila wrote:
> >
> >     > 3. 102829.txt - Apparently a BioPerl error
> >     > A 102829.gb <http://102829.gb> file is an example
> >
> >     Read the error message, it tells you exactly what is wrong:
> >
> >     ------------- EXCEPTION  -------------
> >     MSG: 1 there is a conflict with exons; there was an explicitly
> stated
> >     exon with location 12..21, yet I cannot generate this e
> >     xon from the supplied mRNA locations
> >     1 There are some inferred exons that are not in the explicit exon
> >     list; they are the exons at locations:
> >     25..447
> >
> >     STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/lib/
> >     perl5/site_perl/5.8.6/Bio/SeqFeature/Tools/Unflattener.pm:1
> >     606
> >     ...
> >
> >
> >     Then look at the GenBank file:
> >
> >           gene            1..447
> >                           /gene=3D"ESAG1"
> >           primer_bind     1..11
> >                           /gene=3D"ESAG1"
> >           exon            <12..21
> >                           /gene=3D"ESAG1"
> >                           /note=3D"min-exon"
> >           CDS             25..>447
> >                           /gene=3D"ESAG1"
> >
> >     I have to agree with the Unflattener, this doesn't make any sense a=
t
> >     all.
> >
> >     Garbage in, garbage out.
> >
> >     -Aaron
> >
> >
> >     --
> >     Aaron J. Mackey, Ph.D.
> >     Project Manager, ApiDB Bioinformatics Resource Center
> >     Penn Genomics Institute, University of Pennsylvania
> >     email:   am...@pc... <mailto:am...@pc...>
> >     office: 215-898-1205 (Biology, 212 Goddard Labs)
> >              215-746-7018 (PCBI, 1428 Blockley Hall)
> >     fax:    215-746-6697 (Penn Genomics Institute)
> >     postal: Penn Genomics Institute
> >              Goddard Labs 212
> >              415 S. University Avenue
> >              Philadelphia, PA  19104-6017
> >
> >
> >
> >
> >     -------------------------------------------------------
> >     This SF.net email is sponsored by: Splunk Inc. Do you grep through
> >     log files
> >     for problems?  Stop!  Download the new AJAX search engine that make=
s
> >     searching your log files as easy as surfing the  web.  DOWNLOAD
> >     SPLUNK!
> >
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=
=3D121642
> >     <
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=
=3D121642>
> >     _______________________________________________
> >     Gusdev-gusdev mailing list
> >     Gus...@li...
> >     <mailto:Gus...@li...>
> >     https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>