gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] Problem using LoadTaxon plugin

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

There is a bug in LoadNRDB.pm that has not been fixed yet.  If you run the
plugin without commit, the transaction closes after loading entries into
sres.taxon and a new one is opened to load sres.taxonname. That means that
all the inserts into taxon have been rolled back. Can you load with commit
on? The bug will be fixed soon.

                                                       Debbie


On Tue, 18 May 2004, 
Madhura Sharangpani wrote:

> Hi All
> 
> I am trying to use the LoadTaxon plugin to load NCBI taxonomy files, I downloaded the taxdump files from ncbi.nih.gov, I also created bootstrap rows using xml file input and that worked fine, but when I was running the LoadTaxon plugin to load the NCBI taxonomy files using command:
> 
> ga GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp
>  --names=names.dmp --gencode=gencode.dmp
> 
> I got following error:
> 
> Initially it went on for a while printing the tax_ids processed,
> 
> processed ncbi_tax_id : 40049
> processed ncbi_tax_id : 192122
> -------
> so on
> 
> and then it stopped with following error
> 
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into ("SRES"."TAXO NNAME"."TAXON_ID") (DBD ERROR: OCIStmtExecute) at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, 
> <NODES> line 217936. SQL ERROR!! involving INSERT INTO Res.TaxonName (  row_user_id, other_read,unique_name_variant,user_write, group_write, name_class, row_project_id, name, taxon_id,modification_date, ser_read, row_alg_invocation_id, group_read, other_write, row_group_id,   taxon_name_id  )  VALUES   (  ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? ) 
> Values: 1, 1, 1, 1, scientific name, 1, Influenza C virus (C/Miyagi/9/96), 1, 91, 1, 0, 1, 1 
> at/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHan dle.pm line 185 
> 
> Could someone explain what am I doing wrong?
> 
> Thanks!
> 
> 
> Madhura
> 
> 

[Gusdev-gusdev] Re:Error in Building ( in DbiTable.pm)

[jinal j. <jh...@us...>]

Hi,

I finally managed to solve the error. The problem was that I was not re-using the original build file which involves object creation. But now I have another problem as follows
 [exec] Global symbol "$query" requires explicit package name at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiTable.pm line 554.
     [exec] Compilation failed in require at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 21.
     [exec] BEGIN failed--compilation aborted at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 21.
     [exec] Compilation failed in require at /home/gus/gushome/bin/generateGusObjects line 5.
     [exec] BEGIN failed--compilation aborted at /home/gus/gushome/bin/generateGusObjects line 5.
 
BUILD FAILED
/home/gus/projects/install/build.xml:25: Following error occured while executing this line
/home/gus/projects/GUS/build.xml:194: exec returned: -1


----- Original Message -----
From: Dave Barkan <db...@pc...>
Date: Tuesday, May 18, 2004 10:09 am
Subject: Re: [Gusdev-gusdev] Error in Building

> Hey Jinal,
> 
> These are all 'hand edited' GUS objects; we add additional functionality 
> to them other than that provided by the default java object generator.
> 
> They should be in CVS right now; their location is 
> {Project_Home}/GUS/Model/src/java/org/gusdb/model/hand_edited.  Do you 
> have this directory checked out of CVS?  
> 
> In the hand_edited directory, there are subdirectories corresponding to 
> the GUS schemas.  Each hand edited object is within its appropriate 
> schema subdiretory (For example, Taxon.java.man is in SRes and 
> BLATAlignment.java.man is in DoTS.)  Make sure you have everything checked 
> out; if you can see the hand edited objects and the build is still 
> failing, let me know.
> 
> Dave
> 
> 
> On Tue, 18 May 2004, jinal jhaveri wrote:
> 
> > Hi,
> > 
> > I am getting following error while building GUS. It seems like 
> BLATAlignment_Row, and ... files are missing in the current CVS download. 
> Can anyone has an insight into why this could have happened?
> > 
> > Created dir: /home/gus/gushome/doc/GUS/Model
> >     [mkdir] Created dir: /home/gus/projects/GUS/Model/classes
> >     [javac] Compiling 3 source files to /home/gus/projects/GUS/Model/classes
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26: cannot resolve symbol
> >     [javac] symbol  : class BLATAlignment_Row 
> >     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> >     [javac] public class BLATAlignment extends BLATAlignment_Row {
> >     [javac]                                    ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:26: cannot resolve symbol
> >     [javac] symbol  : class NASequence_Row 
> >     [javac] location: class org.gusdb.model.DoTS.NASequence
> >     [javac] public class NASequence extends NASequence_Row {
> >     [javac]                                 ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:16: cannot resolve symbol
> >     [javac] symbol  : class Taxon_Row 
> >     [javac] location: class org.gusdb.model.SRes.Taxon
> >     [javac] public class Taxon extends Taxon_Row {
> >     [javac]                            ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:34: cannot resolve symbol
> >     [javac] symbol  : method getQstarts ()
> >     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> >     [javac]     String starts = getQstarts();
> >     [javac]                         ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:39: cannot resolve symbol
> >     [javac] symbol  : method getBlocksizes ()
> >     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> >     [javac]     String lengths = getBlocksizes();
> >     [javac]                          ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:44: cannot resolve symbol
> >     [javac] symbol  : method getTstarts ()
> >     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> >     [javac]     String tStarts = getTstarts();
> >     [javac]                          ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:42: cannot resolve symbol
> >     [javac] symbol  : method getSequenceLobLength ()
> >     [javac] location: class org.gusdb.model.DoTS.NASequence
> >     [javac]     return this.getSequenceAsSymbolList(1, 
> this.getSequenceLobLength().longValue());>     [javac]                     
>                           ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:53: cannot resolve symbol
> >     [javac] symbol  : method getSequence (long,long)
> >     [javac] location: class org.gusdb.model.DoTS.NASequence
> >     [javac]     char seqData[] = this.getSequence(start, end);
> >     [javac]                          ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:34: cannot resolve symbol
> >     [javac] symbol  : method getTaxonNameList (boolean)
> >     [javac] location: class org.gusdb.model.SRes.Taxon
> >     [javac]         Vector allTaxonNames = getTaxonNameList(false);
> >     [javac]                                    ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:57: cannot resolve symbol
> >     [javac] symbol  : method getTaxonNameList (boolean)
> >     [javac] location: class org.gusdb.model.SRes.Taxon
> >     [javac]         kids = this.getTaxonNameList(true);
> >     [javac]                    ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
> >     [javac] symbol  : class TaxonName 
> >     [javac] location: class org.gusdb.model.SRes.Taxon
> >     [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
> >     [javac]             ^
> >     [javac] 
> /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
> >     [javac] symbol  : class TaxonName 
> >     [javac] location: class org.gusdb.model.SRes.Taxon
> >     [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
> >     [javac]                             ^
> >     [javac] 12 errors
> > 
> > 
> > thanks
> > --Jinal
> > 
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: SourceForge.net Broadband
> > Sign-up now for SourceForge Broadband and get the fastest
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> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > 
> 
> 

[Gusdev-gusdev] Problem using LoadTaxon plugin

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

Hi All

I am trying to use the LoadTaxon plugin to load NCBI taxonomy files, I =
downloaded the taxdump files from ncbi.nih.gov, I also created bootstrap =
rows using xml file input and that worked fine, but when I was running =
the LoadTaxon plugin to load the NCBI taxonomy files using command:

ga GUS::Common::Plugin::LoadTaxon --nodes=3Dnodes.dmp
 --names=3Dnames.dmp --gencode=3Dgencode.dmp

I got following error:

Initially it went on for a while printing the tax_ids processed,

processed ncbi_tax_id : 40049
processed ncbi_tax_id : 192122
-------
so on

and then it stopped with following error

DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into =
("SRES"."TAXO NNAME"."TAXON_ID") (DBD ERROR: OCIStmtExecute) at =
/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm =
line 145,=20
<NODES> line 217936. SQL ERROR!! involving INSERT INTO Res.TaxonName (  =
row_user_id, other_read,unique_name_variant,user_write, group_write, =
name_class, row_project_id, name, taxon_id,modification_date, ser_read, =
row_alg_invocation_id, group_read, other_write, row_group_id,   =
taxon_name_id  )  VALUES   (  ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, =
?, ?, ?, ?, ? )=20
Values: 1, 1, 1, 1, scientific name, 1, Influenza C virus =
(C/Miyagi/9/96), 1, 91, 1, 0, 1, 1=20
at/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHan dle.pm =
line 185=20

Could someone explain what am I doing wrong?

Thanks!


Madhura

Re: [Gusdev-gusdev] Error in Building

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

Hey Jinal,

These are all 'hand edited' GUS objects; we add additional functionality 
to them other than that provided by the default java object generator.

They should be in CVS right now; their location is 
{Project_Home}/GUS/Model/src/java/org/gusdb/model/hand_edited.  Do you 
have this directory checked out of CVS?  

In the hand_edited directory, there are subdirectories corresponding to 
the GUS schemas.  Each hand edited object is within its appropriate 
schema subdiretory (For example, Taxon.java.man is in SRes and 
BLATAlignment.java.man is in DoTS.)  Make sure you have everything checked 
out; if you can see the hand edited objects and the build is still 
failing, let me know.

Dave
 

On Tue, 18 May 2004, jinal jhaveri wrote:

> Hi,
> 
> I am getting following error while building GUS. It seems like BLATAlignment_Row, and ... files are missing in the current CVS download. Can anyone has an insight into why this could have happened?
> 
> Created dir: /home/gus/gushome/doc/GUS/Model
>     [mkdir] Created dir: /home/gus/projects/GUS/Model/classes
>     [javac] Compiling 3 source files to /home/gus/projects/GUS/Model/classes
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26: cannot resolve symbol
>     [javac] symbol  : class BLATAlignment_Row 
>     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
>     [javac] public class BLATAlignment extends BLATAlignment_Row {
>     [javac]                                    ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:26: cannot resolve symbol
>     [javac] symbol  : class NASequence_Row 
>     [javac] location: class org.gusdb.model.DoTS.NASequence
>     [javac] public class NASequence extends NASequence_Row {
>     [javac]                                 ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:16: cannot resolve symbol
>     [javac] symbol  : class Taxon_Row 
>     [javac] location: class org.gusdb.model.SRes.Taxon
>     [javac] public class Taxon extends Taxon_Row {
>     [javac]                            ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:34: cannot resolve symbol
>     [javac] symbol  : method getQstarts ()
>     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
>     [javac]     String starts = getQstarts();
>     [javac]                         ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:39: cannot resolve symbol
>     [javac] symbol  : method getBlocksizes ()
>     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
>     [javac]     String lengths = getBlocksizes();
>     [javac]                          ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:44: cannot resolve symbol
>     [javac] symbol  : method getTstarts ()
>     [javac] location: class org.gusdb.model.DoTS.BLATAlignment
>     [javac]     String tStarts = getTstarts();
>     [javac]                          ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:42: cannot resolve symbol
>     [javac] symbol  : method getSequenceLobLength ()
>     [javac] location: class org.gusdb.model.DoTS.NASequence
>     [javac]     return this.getSequenceAsSymbolList(1, this.getSequenceLobLength().longValue());
>     [javac]                                                ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:53: cannot resolve symbol
>     [javac] symbol  : method getSequence (long,long)
>     [javac] location: class org.gusdb.model.DoTS.NASequence
>     [javac]     char seqData[] = this.getSequence(start, end);
>     [javac]                          ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:34: cannot resolve symbol
>     [javac] symbol  : method getTaxonNameList (boolean)
>     [javac] location: class org.gusdb.model.SRes.Taxon
>     [javac]         Vector allTaxonNames = getTaxonNameList(false);
>     [javac]                                    ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:57: cannot resolve symbol
>     [javac] symbol  : method getTaxonNameList (boolean)
>     [javac] location: class org.gusdb.model.SRes.Taxon
>     [javac]         kids = this.getTaxonNameList(true);
>     [javac]                    ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
>     [javac] symbol  : class TaxonName 
>     [javac] location: class org.gusdb.model.SRes.Taxon
>     [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
>     [javac]             ^
>     [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
>     [javac] symbol  : class TaxonName 
>     [javac] location: class org.gusdb.model.SRes.Taxon
>     [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
>     [javac]                             ^
>     [javac] 12 errors
> 
> 
> thanks
> --Jinal
> 
> 
> 
> 
> -------------------------------------------------------
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> 

[Gusdev-gusdev] Error in Building

[jinal j. <jh...@us...>]

Hi,

I am getting following error while building GUS. It seems like BLATAlignment_Row, and ... files are missing in the current CVS download. Can anyone has an insight into why this could have happened?

Created dir: /home/gus/gushome/doc/GUS/Model
    [mkdir] Created dir: /home/gus/projects/GUS/Model/classes
    [javac] Compiling 3 source files to /home/gus/projects/GUS/Model/classes
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26: cannot resolve symbol
    [javac] symbol  : class BLATAlignment_Row 
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac] public class BLATAlignment extends BLATAlignment_Row {
    [javac]                                    ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:26: cannot resolve symbol
    [javac] symbol  : class NASequence_Row 
    [javac] location: class org.gusdb.model.DoTS.NASequence
    [javac] public class NASequence extends NASequence_Row {
    [javac]                                 ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:16: cannot resolve symbol
    [javac] symbol  : class Taxon_Row 
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac] public class Taxon extends Taxon_Row {
    [javac]                            ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:34: cannot resolve symbol
    [javac] symbol  : method getQstarts ()
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac]     String starts = getQstarts();
    [javac]                         ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:39: cannot resolve symbol
    [javac] symbol  : method getBlocksizes ()
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac]     String lengths = getBlocksizes();
    [javac]                          ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:44: cannot resolve symbol
    [javac] symbol  : method getTstarts ()
    [javac] location: class org.gusdb.model.DoTS.BLATAlignment
    [javac]     String tStarts = getTstarts();
    [javac]                          ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:42: cannot resolve symbol
    [javac] symbol  : method getSequenceLobLength ()
    [javac] location: class org.gusdb.model.DoTS.NASequence
    [javac]     return this.getSequenceAsSymbolList(1, this.getSequenceLobLength().longValue());
    [javac]                                                ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:53: cannot resolve symbol
    [javac] symbol  : method getSequence (long,long)
    [javac] location: class org.gusdb.model.DoTS.NASequence
    [javac]     char seqData[] = this.getSequence(start, end);
    [javac]                          ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:34: cannot resolve symbol
    [javac] symbol  : method getTaxonNameList (boolean)
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         Vector allTaxonNames = getTaxonNameList(false);
    [javac]                                    ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:57: cannot resolve symbol
    [javac] symbol  : method getTaxonNameList (boolean)
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         kids = this.getTaxonNameList(true);
    [javac]                    ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
    [javac] symbol  : class TaxonName 
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
    [javac]             ^
    [javac] /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
    [javac] symbol  : class TaxonName 
    [javac] location: class org.gusdb.model.SRes.Taxon
    [javac]         TaxonName tn = (TaxonName)(kids.elementAt(i));
    [javac]                             ^
    [javac] 12 errors


thanks
--Jinal

Re: [Gusdev-gusdev] GBParser bug

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

Fidel Salas wrote:

>There is a bug in the parser that only becomes expressed if the DNA
>sequence goes over 99999999 nucleotides.  An error gets output like this:
>ERR     LINE=2575409    unparsed line   100000021 cggggcgggg agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt
>
>  
>
Fidel, I suspect that this error is coming from the support gbff parser 
CBIL::GenBank modules. J. Schug is the author and I'll ask him if he 
knows what causes this.

Angel

>The error happens because the parser assumes that there will be spaces
>before the number indicating the nucleotide number.  That is the case
>until the number of nucleotides goes over the threshold value
>indicated above.
>
>Fidel
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: SourceForge.net Broadband
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>  
>

[Gusdev-gusdev] amino acid data upload to GUS

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

Hello All,

Has anyone tried uploading amino acid related data to GUS(mainly to
aasequenceImp  and related tables). Is there a plugin for that? I have
lots of amino acid related data like the signalP output and other
annotations.

Any suggestions?

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] GBParser bug

[Fidel S. <fi...@vb...>]

Steve,

Sorry, I do not have a suggested patch at this moment.

Fidel


Steve Fischer <sfi...@pc...> writes:

     > Thanks Fidel.   Do you have a suggested patch?
>
     > steve
>
     > Fidel Salas wrote:
>
>>There is a bug in the parser that only becomes expressed if the DNA
>>sequence goes over 99999999 nucleotides.  An error gets output like this:
>>ERR     LINE=2575409    unparsed line   100000021 cggggcgggg agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt
>>
>>The error happens because the parser assumes that there will be spaces
>>before the number indicating the nucleotide number.  That is the case
>>until the number of nucleotides goes over the threshold value
>>indicated above.
>>
>>Fidel
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by: SourceForge.net Broadband
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Re: [Gusdev-gusdev] GBParser bug

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

Thanks Fidel.   Do you have a suggested patch?

steve

Fidel Salas wrote:

>There is a bug in the parser that only becomes expressed if the DNA
>sequence goes over 99999999 nucleotides.  An error gets output like this:
>ERR     LINE=2575409    unparsed line   100000021 cggggcgggg agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt
>
>The error happens because the parser assumes that there will be spaces
>before the number indicating the nucleotide number.  That is the case
>until the number of nucleotides goes over the threshold value
>indicated above.
>
>Fidel
>
>
>
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[Gusdev-gusdev] GBParser bug

[Fidel S. <fi...@vb...>]

There is a bug in the parser that only becomes expressed if the DNA
sequence goes over 99999999 nucleotides.  An error gets output like this:
ERR     LINE=2575409    unparsed line   100000021 cggggcgggg agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt

The error happens because the parser assumes that there will be spaces
before the number indicating the nucleotide number.  That is the case
until the number of nucleotides goes over the threshold value
indicated above.

Fidel

[Gusdev-gusdev] Re: Problem Loading pfam data into Gus

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

madhura, paul-

looking at paul's fix, it is not clear to me why it should work.   my 
understanding of the nameForDb hash is that it maps incoming names to 
ones in the database in order to locate the proper external database 
with which to make the relationship.

i suspect that those records that are not in the hash will not have the 
external links written.   while this might not be essential data, if 
that is so, then it subverts the design of the plugin. 

if i understand the situation correctly, it is not simple.   it is a 
problem of data integration.    the heart of the problem is that this 
part of the plugin was not written in a portable way.

we are loading data that links to entries in a set of external 
databases.   we want to make sure that we correctly capture that 
information so that we can query on it later.
 
to do so, we need to know:
  - all the databases referred to in the file, using the file's naming 
structure
  - for all those names, what is the GUS external database that it 
refers to in the actual instance of GUS that the plugin is running under.

for a proper solution what we need is:
  - a configuration file (instead of a hard-coded hash) that maps the 
Pfam names to names in the DB
  - a pre-process run of the plugin which:
          - confirms that all GUS names in the config file are actually 
in the database
          - confirms that all names in the Pfam file are in the config file
          - puts out proper error messages so that the config file 
and/or database can be corrected.

we could provide with the code a sample config file which holds the 
mapping used by CBIL. 

if you want to hack a solution, i think you should do what i described 
to madhura in a separate mail:
   - use UNIX's grep and sort -u to find all the names in the pfam file.
   - discover which of them are not in the hash
   - add entries in the db for them, and also, put them in the hash.
 
steve

Madhura Sharangpani wrote:

>Hi Steve
>
>I was also coordinating with Paul Mooney and he found out a bug in
>LoadPfam.pm which was causing the problem, he has fixed the bug and today he
>also checked in the revised version of LoadPfam.pm into cvs repository. I
>used that version and was able to successfully load Pfam-A.full file into
>GUS.
>
>Thanks for your help!
>
>Best
>
>Madhura
>
>----- Original Message ----- 
>From: "Steve Fischer" <sfi...@pc...>
>To: "Madhura Sharangpani" <sma...@st...>
>Sent: Wednesday, May 12, 2004 10:15 AM
>Subject: Re: Problem Loading pfam data into Gus
>
>
>  
>
>>madhura-
>>
>>i think i have an idea why this is happening.  on line 97 there is a
>>hash mapping from names found in the file to names found in our db.
>>probably the name in the file (on or near line 14034 in the pfam file)
>>is not in that hash.
>>
>>the use of that hash is not robust code.   the mapping should be
>>provided in a config file.
>>
>>i think the thing to do is discover all the DBs that your pfam file
>>references.   do that by using unix grep on the file, then pipe the
>>output to unix's 'sort -u' which will make the list unique.   compare
>>that list to the hash.   let me know what is not there.
>>
>>steve
>>
>>Madhura Sharangpani wrote:
>>
>>    
>>
>>>Hi Steve
>>>
>>>Thanks for your reply! On observing ExternalDatabase.xml and
>>>ExternalDatabaseRelease.xml files I
>>>observed that ExternalDatabase.xml file has entries for id 3001,3002 and
>>>3003 vs ExternalDatabaseRelease.xml file does not have them
>>>I inserted those entries and then ran the command to lead pfam-A.full
>>>      
>>>
>file
>  
>
>>>again, it made progress as compared to before, the previous error
>>>didnot occur
>>>But it is still giving following error:
>>>
>>>***********************************************************
>>>elaine7:~/RA/pfam> ga
>>>GUS::Common::Plugin::LoadPfam --verbose --parse_only
>>>--flat_file=Pfam-A.full
>>>.gz --release=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
>>>In readExternalDbReleases()
>>>0: PF00244.7
>>>1: PF00389.14
>>>2: PF02826.5
>>>3: PF00198.10
>>>4: PF04029.4
>>>5: PF02834.4
>>>6: PF03171.7
>>>7: PF03475.3
>>>8: PF06983.1
>>>9: PF06052.1
>>>10: PF01612.10
>>>11: PF00803.8
>>>12: PF01073.7
>>>13: PF06725.1
>>>14: PF02829.4
>>>15: PF00725.10
>>>16: PF02737.5
>>>17: PF05902.1
>>>18: PF02446.5
>>>19: PF04419.3
>>>20: PF03061.8
>>>21: PF01812.9
>>>22: PF06189.1
>>>23: PF01367.9
>>>24: PF02739.5
>>>25: PF05761.3
>>>26: PF02872.7
>>>27: PF03491.3
>>>28: PF02096.8
>>>Unable to find most recent ExternalDatabaseRelease for
>>>ExternalDatabase:****
>>>and Id:**** at
>>>/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm
>>>line 420, <PFAM> line 14034.
>>>
>>>gunzip: stdout: Broken pipe
>>>elaine7:~/RA/pfam>
>>>***********************************************************
>>>
>>>Note that I had put the **before and after $name field and $relId field
>>>      
>>>
>at
>  
>
>>>line 420 in LoadPfam.pm  to be able to read the name more clearly ( code
>>>line: die "Unable to find most recent ExternalDatabaseRelease for
>>>ExternalDatabase :**$name** and Id:**$relId**" if (not
>>>      
>>>
>defined($relId)); )
>  
>
>>>and I see that for this error there is no name, $name field is
>>>      
>>>
>null/empty
>  
>
>>>and hence $relId is also empty
>>>
>>>Can you suggetst any reason why this is happening?
>>>
>>>Thanks!
>>>
>>>Madhura
>>>
>>>      
>>>

[Gusdev-gusdev] GUS build system change; skipJavaCompiling

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

Hey all,

Last week I changed the GUS build system so that java compiling is turned 
on by default.  Since then, things seem to have gone smoothly, but on 
occasion, for various reasons (classpath problems, non-compiling java code 
in cvs, etc.) 
java compiling doesn't work, which breaks the rest of the build.

I just checked in a small change that allows the user to optionally add 
the flag:

-skipJavaCompiling

to the normal build command.  Thus if you wanted to build GUS, but 
something with the java code you have in hand is not working, simply run 
the command 

%build GUS install -append -skipJavaCompiling.

Note that java compiling should still be the default and this flag should 
be 
used only when something goes wrong with the build.  There may be certain 
times when you are trying to build, you get the compiling problems, and no 
one is around to do tech support, leaving you stuck with your work because 
of problems in another location.  That's what this flag is for.  

When you do use the flag, please copy the error message that you were 
getting and send it to me and the rest of the lab to let them know 
something is wrong.  I'll take a look, and when I (hopefully) fix it, you 
can re-build without the flag.

To get these changes, do a cvs update on ${Project_Home}/GUS/build.xml and 
also do a cvs update in the ${Project_Home}/install directory.

Please let me know if there are any issues with this change.  Thanks!

Dave

Re: [Gusdev-gusdev] GBParser failing to insert features

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

fidel-

can you send us a test file which is the smallest possible file that 
reproduces the problem?

thanks,
steve

Angel Pizarro wrote:

> Fidel,
> In looking at the code and quickly refreshing myself on what is there, 
> I have come to the following conclusions:
>
> Loading of Features are independent. For instance the "gene" and "CDS" 
> features have nothing to do with each other as far as GBParser is 
> concerned.
>
> Both of these entries should be able to be instered, since they have 
> valid attributes or a db_xref .
>
> In short, I do not knopw what the problem is from a cursury look into 
> the inner working of the code. I will need to try to re-create the 
> error here and look at the log output.
>
> Will update you when I have done this.
> Angel
> Fidel Salas wrote:
>
>> I used the GBParser plugin to upload some GenBank entry which contains
>> thousands of features.  However, only 33 features are found in the
>> database.
>>
>> The features found in the database are exemplified by the following
>> two features from the GenBank file:
>>     gene            complement(142270..143373)
>>                     /gene="lys9"
>>                     /locus_tag="APE0193m"
>>                     /db_xref="GeneID:1445541"
>>     CDS             complement(142270..143373)
>>                     /gene="lys9"
>>                     /locus_tag="APE0193m"
>>                     /codon_start=1
>>                     /transl_table=11
>>                     /product="saccharopine dehydrogenase"
>>                     /protein_id="NP_147035.1"
>>                     /db_xref="GI:14602185"
>>                     /db_xref="GeneID:1445541"
>>                     
>> /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
>>                     
>> LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
>>                     
>> DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
>>                     
>> RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
>>                     
>> GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
>>                     
>> DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
>>                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"
>>
>>
>> The ones that did not make it in look like this:
>>     gene            complement(213..938)
>>                     /locus_tag="APE0001"
>>                     /db_xref="GeneID:1445602"
>>     CDS             complement(213..938)
>>                     /locus_tag="APE0001"
>>                     /codon_start=1
>>                     /transl_table=11
>>                     /product="hypothetical protein"
>>                     /protein_id="NP_146894.1"
>>                     /db_xref="GI:14600380"
>>                     /db_xref="GeneID:1445602"
>>                     
>> /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
>>                     
>> VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
>>                     
>> SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
>>                     
>> ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
>>                     LLAGVTTLFVVTMLIMINKEGKY"
>>     gene            complement(938..1276)
>>                     /locus_tag="APE0002"
>>                     /db_xref="GeneID:1445577"
>>
>> The one element that is present in the features that are uploaded but
>> absent in those that do not is the gene qualifier.
>>
>> Looking at the schema it is not obvious to me why the gene qualifier
>> needs to be present in a feature in order to be uploaded.  Am I
>> missing something more obvious?
>>
>> Thanks
>>
>> Fidel
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by Sleepycat Software
>> Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to 
>> deliver
>> higher performing products faster, at low TCO.
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>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>  
>>
>
>
>
> -------------------------------------------------------
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> higher performing products faster, at low TCO.
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Re: [Gusdev-gusdev] GBParser failing to insert features

[Fidel S. <fi...@vb...>]

Angel,

Thanks.  A day or two works for me.

Fidel


Angel Pizarro <an...@pc...> writes:

     > Fidel,
     > I'll look into this problem. It may take me a bit of time to do so
     > (like a day or two) and get back to you with a full answer.
     > Angel
>
     > Fidel Salas wrote:
>
>>I used the GBParser plugin to upload some GenBank entry which contains
>>thousands of features.  However, only 33 features are found in the
>>database.
>>
>>The features found in the database are exemplified by the following
>>two features from the GenBank file:
>>     gene            complement(142270..143373)
>>                     /gene="lys9"
>>                     /locus_tag="APE0193m"
>>                     /db_xref="GeneID:1445541"
>>     CDS             complement(142270..143373)
>>                     /gene="lys9"
>>                     /locus_tag="APE0193m"
>>                     /codon_start=1
>>                     /transl_table=11
>>                     /product="saccharopine dehydrogenase"
>>                     /protein_id="NP_147035.1"
>>                     /db_xref="GI:14602185"
>>                     /db_xref="GeneID:1445541"
>>                     /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
>>                     LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
>>                     DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
>>                     RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
>>                     GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
>>                     DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
>>                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"
>>
>>
>>The ones that did not make it in look like this:
>>     gene            complement(213..938)
>>                     /locus_tag="APE0001"
>>                     /db_xref="GeneID:1445602"
>>     CDS             complement(213..938)
>>                     /locus_tag="APE0001"
>>                     /codon_start=1
>>                     /transl_table=11
>>                     /product="hypothetical protein"
>>                     /protein_id="NP_146894.1"
>>                     /db_xref="GI:14600380"
>>                     /db_xref="GeneID:1445602"
>>                     /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
>>                     VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
>>                     SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
>>                     ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
>>                     LLAGVTTLFVVTMLIMINKEGKY"
>>     gene            complement(938..1276)
>>                     /locus_tag="APE0002"
>>                     /db_xref="GeneID:1445577"
>>
>>The one element that is present in the features that are uploaded but
>>absent in those that do not is the gene qualifier.
>>
>>Looking at the schema it is not obvious to me why the gene qualifier
>>needs to be present in a feature in order to be uploaded.  Am I
>>missing something more obvious?
>>
>>Thanks
>>
>>Fidel
>>
>>
>>

Re: [Gusdev-gusdev] GBParser failing to insert features

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

Fidel,
In looking at the code and quickly refreshing myself on what is there, I 
have come to the following conclusions:

Loading of Features are independent. For instance the "gene" and "CDS" 
features have nothing to do with each other as far as GBParser is 
concerned.

Both of these entries should be able to be instered, since they have 
valid attributes or a db_xref .

In short, I do not knopw what the problem is from a cursury look into 
the inner working of the code. I will need to try to re-create the error 
here and look at the log output.

Will update you when I have done this.
Angel
Fidel Salas wrote:

>I used the GBParser plugin to upload some GenBank entry which contains
>thousands of features.  However, only 33 features are found in the
>database.
>
>The features found in the database are exemplified by the following
>two features from the GenBank file:
>     gene            complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /db_xref="GeneID:1445541"
>     CDS             complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="saccharopine dehydrogenase"
>                     /protein_id="NP_147035.1"
>                     /db_xref="GI:14602185"
>                     /db_xref="GeneID:1445541"
>                     /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
>                     LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
>                     DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
>                     RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
>                     GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
>                     DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
>                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"
>
>
>The ones that did not make it in look like this:
>     gene            complement(213..938)
>                     /locus_tag="APE0001"
>                     /db_xref="GeneID:1445602"
>     CDS             complement(213..938)
>                     /locus_tag="APE0001"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="hypothetical protein"
>                     /protein_id="NP_146894.1"
>                     /db_xref="GI:14600380"
>                     /db_xref="GeneID:1445602"
>                     /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
>                     VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
>                     SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
>                     ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
>                     LLAGVTTLFVVTMLIMINKEGKY"
>     gene            complement(938..1276)
>                     /locus_tag="APE0002"
>                     /db_xref="GeneID:1445577"
>
>The one element that is present in the features that are uploaded but
>absent in those that do not is the gene qualifier.
>
>Looking at the schema it is not obvious to me why the gene qualifier
>needs to be present in a feature in order to be uploaded.  Am I
>missing something more obvious?
>
>Thanks
>
>Fidel
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by Sleepycat Software
>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver
>higher performing products faster, at low TCO.
>http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] GBParser failing to insert features

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

Fidel,
I'll look into this problem. It may take me a bit of time to do so (like 
a day or two) and get back to you with a full answer.
Angel

Fidel Salas wrote:

>I used the GBParser plugin to upload some GenBank entry which contains
>thousands of features.  However, only 33 features are found in the
>database.
>
>The features found in the database are exemplified by the following
>two features from the GenBank file:
>     gene            complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /db_xref="GeneID:1445541"
>     CDS             complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="saccharopine dehydrogenase"
>                     /protein_id="NP_147035.1"
>                     /db_xref="GI:14602185"
>                     /db_xref="GeneID:1445541"
>                     /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
>                     LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
>                     DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
>                     RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
>                     GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
>                     DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
>                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"
>
>
>The ones that did not make it in look like this:
>     gene            complement(213..938)
>                     /locus_tag="APE0001"
>                     /db_xref="GeneID:1445602"
>     CDS             complement(213..938)
>                     /locus_tag="APE0001"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="hypothetical protein"
>                     /protein_id="NP_146894.1"
>                     /db_xref="GI:14600380"
>                     /db_xref="GeneID:1445602"
>                     /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
>                     VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
>                     SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
>                     ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
>                     LLAGVTTLFVVTMLIMINKEGKY"
>     gene            complement(938..1276)
>                     /locus_tag="APE0002"
>                     /db_xref="GeneID:1445577"
>
>The one element that is present in the features that are uploaded but
>absent in those that do not is the gene qualifier.
>
>Looking at the schema it is not obvious to me why the gene qualifier
>needs to be present in a feature in order to be uploaded.  Am I
>missing something more obvious?
>
>Thanks
>
>Fidel
>
>
>  
>

Re: [Gusdev-gusdev] GBParser failing to insert features

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

Hi,

I had the same problems. So I just put new columns to the tables...

Normaly the xref - column is saved apart...

Cheers,
Thomas

Fidel Salas wrote:

>I used the GBParser plugin to upload some GenBank entry which contains
>thousands of features.  However, only 33 features are found in the
>database.
>
>The features found in the database are exemplified by the following
>two features from the GenBank file:
>     gene            complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /db_xref="GeneID:1445541"
>     CDS             complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="saccharopine dehydrogenase"
>                     /protein_id="NP_147035.1"
>                     /db_xref="GI:14602185"
>                     /db_xref="GeneID:1445541"
>                     /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
>                     LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
>                     DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
>                     RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
>                     GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
>                     DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
>                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"
>
>
>The ones that did not make it in look like this:
>     gene            complement(213..938)
>                     /locus_tag="APE0001"
>                     /db_xref="GeneID:1445602"
>     CDS             complement(213..938)
>                     /locus_tag="APE0001"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="hypothetical protein"
>                     /protein_id="NP_146894.1"
>                     /db_xref="GI:14600380"
>                     /db_xref="GeneID:1445602"
>                     /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
>                     VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
>                     SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
>                     ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
>                     LLAGVTTLFVVTMLIMINKEGKY"
>     gene            complement(938..1276)
>                     /locus_tag="APE0002"
>                     /db_xref="GeneID:1445577"
>
>The one element that is present in the features that are uploaded but
>absent in those that do not is the gene qualifier.
>
>Looking at the schema it is not obvious to me why the gene qualifier
>needs to be present in a feature in order to be uploaded.  Am I
>missing something more obvious?
>
>Thanks
>
>Fidel
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by Sleepycat Software
>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver
>higher performing products faster, at low TCO.
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>
>  
>

[Gusdev-gusdev] GBParser failing to insert features

[Fidel S. <fi...@vb...>]

I used the GBParser plugin to upload some GenBank entry which contains
thousands of features.  However, only 33 features are found in the
database.

The features found in the database are exemplified by the following
two features from the GenBank file:
     gene            complement(142270..143373)
                     /gene="lys9"
                     /locus_tag="APE0193m"
                     /db_xref="GeneID:1445541"
     CDS             complement(142270..143373)
                     /gene="lys9"
                     /locus_tag="APE0193m"
                     /codon_start=1
                     /transl_table=11
                     /product="saccharopine dehydrogenase"
                     /protein_id="NP_147035.1"
                     /db_xref="GI:14602185"
                     /db_xref="GeneID:1445541"
                     /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
                     LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
                     DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
                     RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
                     GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
                     DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"


The ones that did not make it in look like this:
     gene            complement(213..938)
                     /locus_tag="APE0001"
                     /db_xref="GeneID:1445602"
     CDS             complement(213..938)
                     /locus_tag="APE0001"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_146894.1"
                     /db_xref="GI:14600380"
                     /db_xref="GeneID:1445602"
                     /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
                     VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
                     SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
                     ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
                     LLAGVTTLFVVTMLIMINKEGKY"
     gene            complement(938..1276)
                     /locus_tag="APE0002"
                     /db_xref="GeneID:1445577"

The one element that is present in the features that are uploaded but
absent in those that do not is the gene qualifier.

Looking at the schema it is not obvious to me why the gene qualifier
needs to be present in a feature in order to be uploaded.  Am I
missing something more obvious?

Thanks

Fidel

[Gusdev-gusdev] new SAM column

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

Users of RAD,
SAM added a new result column "fold_change". The attached file is the 
new view defnition for it.

Angel

[Gusdev-gusdev] table change

[Trish W. <wh...@pc...>]

Hi Mike, 

I would like to be able to point to the person who has provided EC number 
assignments to plasmodb genes so I would like to add an attribute 
named something like "ec_assignment_contact_id" with type "number (10)" to 
dots.aasequenceenzymeclass with as a foreign key to sres.contact.  Also, 
can you add this attribute to the view of this table in the plasmodb 
namespace?

Thanks,
Trish

[Gusdev-gusdev] Re: Plasmodium data upload

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

fidel-

just talked to bindu.   jessie is in africa.

plasmodb loaded the data directly from the sequencing centers, sanger 
and tigr, and recieved the data in tigr xml format.  bindu will be 
sending you contact info for folks there.  there is a plugin for that.

the DoTS project uses the GBParser to load smaller files than you are 
trying.  The most recent time we ran it, on only a small amount of 
update data, it struggled because of the memory leak.   In past times we 
were using the earlier version of DBD so therre was no leak.

so, you have two options:
  - try GBParser again, after reverting DBD
  - try to get the xml data and go that route.

hope this helps,
steve


Fidel Salas wrote:

>Steve,
>
>I never heard back from either Jessica or Bindu about how the CBIL
>Plasmodium data got uploaded.
>
>Given your report on the memory leakiness of the Oracle::DBD module,
>should I assume that the CBIL data was uploaded with a DBD module that
>did not leak memory?
>
>Thanks
>
>Fidel
>  
>

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

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

ok, we can look into this.   it might be that we ask for a volunteer.   
i don't yet know what is involved.

steve

MICHAEL LUCHTAN wrote:

>Hello-
>Such a thing--an XML from CBIL with all of the ExternalDatabase table
>entries and matching ExternalDatabaseRelease rows would probably be useful
>to almost everyone running or with plans to run GUS.  So much of the perl
>plugin codebase already has ties to this.  I think making it available as
>an option in the install would help solve MANY issues that arise in
>installing/populating/retrieving data from GUS using the perl object layer
>and the WDK.  Are there any issues with having people standardized on an
>ExternalDatabaseID?  Everyone is probably using some subset of a standard
>set of external databases, and it is easy to add another one.
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Thu, 6 May 2004 pj...@sa... wrote:
>
>  
>
>>If I remember correctly I got an XML dump from CBIL with
>>all of the ExternalDatabase table entries with the matching
>>ExternalDatabaseRelease rows. I added a few entries that GeneDB needed.
>>
>>Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema
>>is created?
>>
>>I have a copy of those files that I can send to you but I can't access it right now.
>>
>>
>>Quoting Madhura Sharangpani <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=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
>>>
>>>      
>>>
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by Sleepycat Software
>>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver
>>higher performing products faster, at low TCO.
>>http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by Sleepycat Software
>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver
>higher performing products faster, at low TCO.
>http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

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

[MICHAEL L. <lu...@cs...>]

Hello-
Such a thing--an XML from CBIL with all of the ExternalDatabase table
entries and matching ExternalDatabaseRelease rows would probably be useful
to almost everyone running or with plans to run GUS.  So much of the perl
plugin codebase already has ties to this.  I think making it available as
an option in the install would help solve MANY issues that arise in
installing/populating/retrieving data from GUS using the perl object layer
and the WDK.  Are there any issues with having people standardized on an
ExternalDatabaseID?  Everyone is probably using some subset of a standard
set of external databases, and it is easy to add another one.

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Thu, 6 May 2004 pj...@sa... wrote:

>
> If I remember correctly I got an XML dump from CBIL with
> all of the ExternalDatabase table entries with the matching
> ExternalDatabaseRelease rows. I added a few entries that GeneDB needed.
>
> Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema
> is created?
>
> I have a copy of those files that I can send to you but I can't access it right now.
>
>
> Quoting Madhura Sharangpani <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=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
> >
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by Sleepycat Software
> Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver
> higher performing products faster, at low TCO.
> http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

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

[<pj...@sa...>]

If I remember correctly I got an XML dump from CBIL with 
all of the ExternalDatabase table entries with the matching
ExternalDatabaseRelease rows. I added a few entries that GeneDB needed.

Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema
is created?

I have a copy of those files that I can send to you but I can't access it right now.


Quoting Madhura Sharangpani <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=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
> 

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

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

Hi Madhura,

The error you're seeing is due to there not being an external_database_id
and external_database_release_id for medline in your database's
sres.externaladatabase and sres.externaladatabaserelease tables.

You will have to insert those rows with the appropriate information. I 
generally use UpdateGusFromXML to enter rows into the db but I think you 
can use SubmitRow also. 

sres.externaladatabase is pretty minimal with only the name (MEDLINE) and 
lowercasename (medline) 

Entries in sres.externaladatabaserelease only require an 
external_database_id and version but the other fields are useful to track 
your data source properly.


                                                      Debbie  




On Thu, 6 May 2004, 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
>