gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] GBParser error

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

dear Jeetendra -

it looks like the genbank parser does force a new external database 
called taxon into the ExternalDatabase table, as it doesn't seem to have 
a facility to map 'taxon' to an alternative name for that db.

it looks like its failing because it may be having trouble with the 
sequence (db sequence, not bio sequence) which generates the next key.

did you send the complete error output?   I am not sure i understand why 
i am not seeing a primary key value in the insert statement.

steve


Jeetendra Soneja wrote:

>I am trying to upload a genbank flat file, and I am getting the error
>listed below.
>    When I looked at the source code of GbParser.pm, I figured out that
>the plugin is getting the database name as 'taxon' from the db_xref
>qualifier (e.g. db_xref='taxon:4932') and is trying to retrieve the
>external_database_id and external_database_release_id for the 'taxon'
>database. Now, even though I have an entry for 'Taxonomy' database in
>my Sres.ExternalDatabase table, it is unable to match that since it is
>looking for 'taxon' as the database name. Finally, it tries to insert
>new entry for 'taxon' database in the Sres.ExternalDatabase and
>Sres.ExternalDatabaseRelease tables, and the insert statement fails ..
>don't know why ?
>
>I would greatly appreciate if someone could help me on this.
>
>Thanks,
>Jeetendra.
>
>
>
>allNonNullsSet: db_ref_na_feature_id not set... = ''
>allNonNullsSet: external_database_id not set... = ''
>GUS::Model::SRes::ExternalDatabase->retrieveFromDB($doNotRetrieveAtts=,)
>Submitting GUS::Model::SRes::ExternalDatabase:
> Table: ExternalDatabase
>        lowercase_name: [taxon]
>        name: [taxon]
>
>HasChangedAttributes='0'
>Setting all foreign keys
>GUS::Model::SRes::ExternalDatabase->Submit: All foreign keys are
>set...proceeding
>allNonNullsSet: external_database_id not set... = ''
>Inserting:
>Table: ExternalDatabase
>        group_write: [1]
>        other_read: [1]
>        group_read: [1]
>        lowercase_name: [taxon]
>        name: [taxon]
>        user_read: [1]
>        row_user_id: [1]
>        modification_date: [SYSDATE]
>        other_write: [0]
>        row_alg_invocation_id: [171]
>        row_project_id: [1]
>        row_group_id: [1]
>        user_write: [1]
>DBD::Oracle::st execute failed: ORA-00001: unique constraint
>(SRES.PK_EXTERNALDATABASE) violated (DBD ERROR: OCIStmtExecute)$
>    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
>group_read, lowercase_name, name, user_read, row_user_id, $
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
>ParamValues: :p5='taxon', :p12='1', :p8='7', :p10='1$
>Wed Aug 18 17:44:50 2004        Genbank entries inserted= 0;  updated= 0;
>total #(inserted::updated::deleted)=16::::
>
>Wed Aug 18 17:44:50 2004        FAILURES        Unable to process 2
>entries. See gbparserFailures/
>Wed Aug 18 17:44:50 2004        RESULT  Genbank entries inserted= 0; 
>updated= 0;  failed= 2
>
>
>
>
>  
>

[Gusdev-gusdev] GBParser error

[Jeetendra S. <so...@vb...>]

I am trying to upload a genbank flat file, and I am getting the error
listed below.
    When I looked at the source code of GbParser.pm, I figured out that
the plugin is getting the database name as 'taxon' from the db_xref
qualifier (e.g. db_xref='taxon:4932') and is trying to retrieve the
external_database_id and external_database_release_id for the 'taxon'
database. Now, even though I have an entry for 'Taxonomy' database in
my Sres.ExternalDatabase table, it is unable to match that since it is
looking for 'taxon' as the database name. Finally, it tries to insert
new entry for 'taxon' database in the Sres.ExternalDatabase and
Sres.ExternalDatabaseRelease tables, and the insert statement fails ..
don't know why ?

I would greatly appreciate if someone could help me on this.

Thanks,
Jeetendra.



allNonNullsSet: db_ref_na_feature_id not set... = ''
allNonNullsSet: external_database_id not set... = ''
GUS::Model::SRes::ExternalDatabase->retrieveFromDB($doNotRetrieveAtts=,)
Submitting GUS::Model::SRes::ExternalDatabase:
 Table: ExternalDatabase
        lowercase_name: [taxon]
        name: [taxon]

HasChangedAttributes='0'
Setting all foreign keys
GUS::Model::SRes::ExternalDatabase->Submit: All foreign keys are
set...proceeding
allNonNullsSet: external_database_id not set... = ''
Inserting:
Table: ExternalDatabase
        group_write: [1]
        other_read: [1]
        group_read: [1]
        lowercase_name: [taxon]
        name: [taxon]
        user_read: [1]
        row_user_id: [1]
        modification_date: [SYSDATE]
        other_write: [0]
        row_alg_invocation_id: [171]
        row_project_id: [1]
        row_group_id: [1]
        user_write: [1]
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SRES.PK_EXTERNALDATABASE) violated (DBD ERROR: OCIStmtExecute)$
    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
group_read, lowercase_name, name, user_read, row_user_id, $
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
ParamValues: :p5='taxon', :p12='1', :p8='7', :p10='1$
Wed Aug 18 17:44:50 2004        Genbank entries inserted= 0;  updated= 0;
total #(inserted::updated::deleted)=16::::

Wed Aug 18 17:44:50 2004        FAILURES        Unable to process 2
entries. See gbparserFailures/
Wed Aug 18 17:44:50 2004        RESULT  Genbank entries inserted= 0; 
updated= 0;  failed= 2




-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

Re: [Gusdev-gusdev] Questions about LoadBlastSimFast.pm

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

The subject_id and query_id are the ones you are talking about
On Friday 06 August 2004 12:51 pm, Jeetendra Soneja wrote:
> Hi,
>
> 1. Does anyone know how do I link the Similarity tables (Dots.similarity
> and Dots.similarityspan) with the ExternalAASequence (or
> ExternalNASequence) table ?
>      Let's assume that we already have the query and subject sequences in
> ExternalAASequence, and the BLAST results in the similarity tables.
> Now, using the similarity tables, I can only get query_table_id and
> subject_table_id, and not the actual sequence_id. However, I want to
> access the actual query and subject sequences. After accessing the
> Similarity.min_query_start and Similarity.max_query_end values, how
> do I access the actual query sequence, since there might be a large
> number of sequences in the table referred by query_table_id?
>
> 2. Since the Similarity.algorithm_id value is not a part of the parsed
> Blast output generated by generateBlastSimilarity.pl, what is the best way
> to incorporate algorithm information in Dots.Similarity ?
>
> Thanks,
> Jeetendra.

[Gusdev-gusdev] Doubts about Gus Schema

[thnascimento <thn...@uo...>]

Hi,

My name is Thiago Nascimento. I`m a student from NCE-
Universidade Federal Do Rio de Janeiro.

I`m making a study about GUS Schema and I`m trying to find 
some models of representation in this.

Actually, i`m trying to map the sequence variation 
representation in GUS Schema. Until now, i have fouded the 
following components: Allele, AllelePhenotype, 
AllelePhenotypeClass, AlleleInstance, AlleleComplementation, 
AlleleFeature and SeqVariation.

How can I represent SNPs, InDel, Deletion, Replacement and 
Disruption in this model.

I hope for answers.

Thank you

Thiago Nascimento
NCE-UFRJ-Brazil.=0A =0A__________________________________________________=
________________________=0AAcabe com aquelas janelinhas que pulam na sua =
tela.=0AAntiPop-up UOL - =C9 gr=E1tis!=0Ahttp://antipopup.uol.com.br/=0A

Re: [Gusdev-gusdev] PostgreSQL Version

[Michael S. <msa...@pc...>]

Hello Jeetendra,

We're actively working on the PostgreSQL version of GUS, and I hope to 
release late next week.

We have a proof of concept version in place, and we're just now working 
to integrate this with our installation and configuration framework.

Thanks,

Mike

On Aug 11, 2004, at 4:57 PM, Jeetendra Soneja wrote:

> Any idea on when the PostgreSQL version of GUS is expected to be 
> released?
>
> ~Jeetendra.
>
>
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[Gusdev-gusdev] PostgreSQL Version

[Jeetendra S. <so...@vb...>]

Any idea on when the PostgreSQL version of GUS is expected to be released?

~Jeetendra.

Re: [Gusdev-gusdev] BlastAnal.pm and LoadBlastSimFast.pm

[Arnaud K. <ax...@sa...>]

Hi

Steve Fischer wrote:

> arnaud-
>
> i will make the change to BlastAnal and release a new .tar for the 
> CBIL code.
>
> go ahead and commit your fix to LoadBlastSimFast.pm
>
I have commited an updated version of LoadBlastSimFast plugin. It can 
also parse the real subject and query identifiers and get the primary 
keys associated with them.
It shouldn't affect the parsing if the primary keys are already in the 
BLAST formated output. If not let me know.

cheers
Arnaud

> steve
>
> Arnaud Kerhornou wrote:
>
>> Hi
>>
>> I've got a script from Pablo Mendes called 
>> parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal 
>> module part of the CBIL distribution. To make the blast parsing work 
>> for me (to parse the score), I had to do a minor modification, line 131:
>>    if (/... \s(\d+) .../) {
>> by
>>    if (/... \s+(\d+) .../) {
>>
>> ie match at least one space before parsing the score value, instead 
>> of matching one and only one space.
>>
>> Also, in the BLAST output, the query and subject ids are meant to be 
>> GUS Primary keys, I have instead the real subject and query identifiers.
>> In LoadBlastSimFast.pm, could we make the parsing more generic so it 
>> can accept both ? I have made the changes locally, I can commit an 
>> update if nobody minds.
>>
>> Shall I make sourceforge entries to log them ?
>>
>> cheers
>> Arnaud
>>

Re: [Gusdev-gusdev] BlastAnal.pm and LoadBlastSimFast.pm

[Arnaud K. <ax...@sa...>]

Hi Steve

Steve Fischer wrote:

> i have updated the cbil .tar with the change below.   it is in v1-6-0.
>
thanks

> steve
>
> Arnaud Kerhornou wrote:
>
>> Hi
>>
>> I've got a script from Pablo Mendes called 
>> parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal 
>> module part of the CBIL distribution. To make the blast parsing work 
>> for me (to parse the score), I had to do a minor modification, line 131:
>>    if (/... \s(\d+) .../) {
>> by
>>    if (/... \s+(\d+) .../) {
>>
>> ie match at least one space before parsing the score value, instead 
>> of matching one and only one space.
>>
>> Also, in the BLAST output, the query and subject ids are meant to be 
>> GUS Primary keys, I have instead the real subject and query identifiers.
>> In LoadBlastSimFast.pm, could we make the parsing more generic so it 
>> can accept both ? I have made the changes locally, I can commit an 
>> update if nobody minds.
>>
will commit my update

>> Shall I make sourceforge entries to log them ?
>>
>> cheers
>> Arnaud
>>
cheers
Arnaud

Re: [Gusdev-gusdev] BlastAnal.pm and LoadBlastSimFast.pm

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

i have updated the cbil .tar with the change below.   it is in v1-6-0.

steve

Arnaud Kerhornou wrote:

> Hi
>
> I've got a script from Pablo Mendes called 
> parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal 
> module part of the CBIL distribution. To make the blast parsing work 
> for me (to parse the score), I had to do a minor modification, line 131:
>    if (/... \s(\d+) .../) {
> by
>    if (/... \s+(\d+) .../) {
>
> ie match at least one space before parsing the score value, instead of 
> matching one and only one space.
>
> Also, in the BLAST output, the query and subject ids are meant to be 
> GUS Primary keys, I have instead the real subject and query identifiers.
> In LoadBlastSimFast.pm, could we make the parsing more generic so it 
> can accept both ? I have made the changes locally, I can commit an 
> update if nobody minds.
>
> Shall I make sourceforge entries to log them ?
>
> cheers
> Arnaud
>
>
> -------------------------------------------------------
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Re: [Gusdev-gusdev] BlastAnal.pm and LoadBlastSimFast.pm

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

arnaud-

i will make the change to BlastAnal and release a new .tar for the CBIL 
code.

go ahead and commit your fix to LoadBlastSimFast.pm

steve

Arnaud Kerhornou wrote:

> Hi
>
> I've got a script from Pablo Mendes called 
> parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal 
> module part of the CBIL distribution. To make the blast parsing work 
> for me (to parse the score), I had to do a minor modification, line 131:
>    if (/... \s(\d+) .../) {
> by
>    if (/... \s+(\d+) .../) {
>
> ie match at least one space before parsing the score value, instead of 
> matching one and only one space.
>
> Also, in the BLAST output, the query and subject ids are meant to be 
> GUS Primary keys, I have instead the real subject and query identifiers.
> In LoadBlastSimFast.pm, could we make the parsing more generic so it 
> can accept both ? I have made the changes locally, I can commit an 
> update if nobody minds.
>
> Shall I make sourceforge entries to log them ?
>
> cheers
> Arnaud
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by OSTG. Have you noticed the changes on
> Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now,
> one more big change to announce. We are now OSTG- Open Source Technology
> Group. Come see the changes on the new OSTG site. www.ostg.com
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] BlastAnal.pm and LoadBlastSimFast.pm

[Arnaud K. <ax...@sa...>]

Hi

I've got a script from Pablo Mendes called 
parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal 
module part of the CBIL distribution. To make the blast parsing work for 
me (to parse the score), I had to do a minor modification, line 131:
    if (/... \s(\d+) .../) {
by
    if (/... \s+(\d+) .../) {

ie match at least one space before parsing the score value, instead of 
matching one and only one space.

Also, in the BLAST output, the query and subject ids are meant to be GUS 
Primary keys, I have instead the real subject and query identifiers.
In LoadBlastSimFast.pm, could we make the parsing more generic so it can 
accept both ? I have made the changes locally, I can commit an update if 
nobody minds.

Shall I make sourceforge entries to log them ?

cheers
Arnaud

Re: [Gusdev-gusdev] Similarity Links

[Arnaud K. <ax...@sa...>]

Hi

Can't we make the plugin LoadBlastSimFast.pm parse directly the Blast 
output, so it doesn't require running generateBlastSimilarity.pl as an 
extra step ?

Arnaud

Jonathan Schug wrote:

> Jeetendra:
>
> 1: Note that the DoTS.Similarity table contains the columns 
> subject_id  and query_id which contain aa_sequence_id or 
> na_sequence_id values.   Since we want to be able to link any two 
> kinds of sequences we can't  make these ordinary foreign keys.
>
> 2: Sounds like an omission to me.  I can't find  
> generateBlastSimilarity.pl, but setting the algorithm_id should be  
> trivial.
>
> Jonathan
>
>
>
>
> ------------------------------------------------------------------------ 
> ---
> Jonathan Schug            Center for Bioinformatics
> js...@pc...     Computational Biology and Informatics Lab
> (215) 573-3113 voice      University of Pennsylvania,
> (215) 573-3111 fax        1413 Blockley Hall, Philadelphia, PA  
> 19014-6021
>
>

Re: [Gusdev-gusdev] Loading BLAST results

[Arnaud K. <ax...@sa...>]

Pablo N. Mendes wrote:

>Hi Arnaud,
>I don't know if I'll be able to answer all your questions, but I'll try
>some to the extent of my knowledge on GUS up to now.
>
>  
>
>>I have the sequences in FASTA, what regexp shall I need?
>>Is only --regex_name parameter required?
>>Does it matter if I don't give taxon_id parameter ?
>>    
>>
>
>I've run the plugin with these parameters:
>
>[pablo@mkiwi mcl]$ ga GUS::Common::Plugin::InsertNewExternalSequences
>--external_database_release_id=38
>--regex_source_id=(.*)
>--table_name=DoTS::ExternalAASequence
>--sequencefile=tbrucei –commit
>
>The regex_*, as you probably noted, are the regular expressions to
>extract the referred info from the FASTA header (name, source_id,
>secondary_id, etc.). I've only used the regex_source_id. Also, it seems
>not to matter if you don't give the taxon_id parameter. But you
>obviously won't make the associations in DoTS::AASequenceTaxon between
>sequences and taxa.
>
>  
>
it still doesn't work...

>>Does LoadBlastSimFast module require generateBlastSimilarity.pl
>>    
>>
>script? Where can I get this script ?
>
>This module reads similarity results in an especific format like:
>
>  
>
>>479679 (3 subjects)
>>    
>>
>  Sum: 479680:1871:1.2e-194:1:353:1:353:1:353:353:353:0:
>   HSP1: 479680:353:353:353:1871:1.2e-194:1:353:1:353:0:
>  Sum: 488460:1826:7.0e-190:1:353:1:353:1:353:342:348:0:
>   HSP1: 488460:342:348:353:1826:7.0e-190:1:353:1:353:0:
>  
>
>>479680 (3 subjects)
>>    
>>
>  Sum: 479679:1871:1.2e-194:1:353:1:353:1:353:353:353:0:
>   HSP1: 479679:353:353:353:1871:1.2e-194:1:353:1:353:0:
>
>The script parseBlastFilesForSimilarity.pl (attached) will do the trick.
>I don't know if there are multiple versions of this script traveling
>around the list.
>
>[jdai@headnode mclorth]$ ls /scratch/jdai/Cpgus_vs_Pfgus/ | perl
>parseBlastFilesForSimilarity.pl
>--regex='(\S+)'
>--outputFile=Lm_vs_Lm_parsed 
>--dir=/scratch/jdai/Cpgus_vs_Pfgus/
>
>  
>
Thanks, it works fine.

Arnaud

>Hope this is useful,
>Pablo
>
>On Thu, 2004-08-05 at 08:49, Arnaud Kerhornou wrote:
>  
>
>>Hi
>>
>>I want to load BLAST results in GUS.
>>Before running LoadBlastSimFast module, I want to load Uniprot and EMBL 
>>databases in DoTS::ExternalAASequence and DoTS::ExternalNASequence., 
>>just the Ids not the sequences themselves.
>>
>>I need some help to use GUS::Common::Plugin::InsertNewExternalSequences 
>>plugin.
>>
>>I have the sequences in FASTA, what regexp shall I need  ? Is only  
>>--regex_name parameter required ? I don't know the taxon attached to the 
>>sequence entries. Does it matter if I don't give taxon_id parameter ?
>>
>>Re. LoadBlastSimFast module, It seems to parse the output in a specific 
>>format. Does it require generateBlastSimilarity.pl script ? Where can I 
>>get this script ?
>>
>>cheers
>>Arnaud
>>    
>>

-- 
Arnaud Kerhornou

The Wellcome Trust Sanger Institute
The Pathogen Sequencing Unit
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Work: +44 (0) 1223 494955
Fax:  +44 (0) 1223 494919

[Gusdev-gusdev] Similarity Links

[Jonathan S. <js...@pc...>]

Jeetendra:

1: Note that the DoTS.Similarity table contains the columns subject_id  
and query_id which contain aa_sequence_id or na_sequence_id values.   
Since we want to be able to link any two kinds of sequences we can't  
make these ordinary foreign keys.

2: Sounds like an omission to me.  I can't find  
generateBlastSimilarity.pl, but setting the algorithm_id should be  
trivial.

Jonathan




------------------------------------------------------------------------ 
---
Jonathan Schug            Center for Bioinformatics
js...@pc...     Computational Biology and Informatics Lab
(215) 573-3113 voice      University of Pennsylvania,
(215) 573-3111 fax        1413 Blockley Hall, Philadelphia, PA  
19014-6021

[Gusdev-gusdev] Questions about LoadBlastSimFast.pm

[Jeetendra S. <so...@vb...>]

Hi,

1. Does anyone know how do I link the Similarity tables (Dots.similarity
and Dots.similarityspan) with the ExternalAASequence (or
ExternalNASequence) table ?
     Let's assume that we already have the query and subject sequences in
ExternalAASequence, and the BLAST results in the similarity tables.
Now, using the similarity tables, I can only get query_table_id and
subject_table_id, and not the actual sequence_id. However, I want to
access the actual query and subject sequences. After accessing the
Similarity.min_query_start and Similarity.max_query_end values, how
do I access the actual query sequence, since there might be a large
number of sequences in the table referred by query_table_id?

2. Since the Similarity.algorithm_id value is not a part of the parsed
Blast output generated by generateBlastSimilarity.pl, what is the best way
to incorporate algorithm information in Dots.Similarity ?

Thanks,
Jeetendra.

-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

Re: [Gusdev-gusdev] source_id error with LoadNRDB - add

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

Hi,

It slipped my mind but the last time I ran this, when I had a problem with 
an entry, I added an eval statement that should print to a log rather than 
failing when it encounters an error. It is rather unorthodox but the 
sequence is also printed. The error I encountered in the nr record 
prevented the plugin from "knowing" the source_id and the gi so I had no 
identifiers to use. Entry into the GUS db occurs only when there is a 
sequence so that I was confident that would be known and a substring could 
be used to search for the record in the file.

Try to update your LoadNRDB.pm from cvs and try it again.

                                                           Debbie

On Thu, 5 Aug 2004, Pablo N. Mendes wrote:

> Hello all,
> I've been "playing" with the loadNRDB module in the previous weeks, but
> it is still crashing. I got this "cannot insert NULL into source_id
> (DoTS.NRDBEntry)" error when reading line 8298021 of my NR file.
>
> That line is:
>> gi|45549465|gb|AAS67649.1| spike glycoprotein S1 subunit precursor
> [Avian infectious bronchitis virus]
>
> I cannot see why this would crash. I'm looking into the code, but maybe
> someone who already knows the module can help me with guesses.
>
> Here part of the dump:
>
> [pablo@mkiwi loadNRDB]$ ga GUS::Common::Plugin::LoadNRDB
> --comment="loading NRDB data from July" --extDbRelId=48
> --gitax="/home/luchtan/GUS/loadNRDB/June232004/gi_taxid_prot.dmp"
> --nrdb="/scratch/pablo/nr"
> --SourceDB="84:tpe,76:pdb,77:dbj,78:prf,79:emb,81:sp,82:pir,80:gb,83:ref,80:tpg,151:genpept,153:tpd" --plugin --temp_login='pablo' --temp_password='pablo123' --dbi_str='dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD' --commit | tee loadnrdb.log
> (...)
> Submitted set number:1462975
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("DOTS"."NRDBENTRY"."SOURCE_ID") (DBD ERROR: OCIStmtExecute) at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, <NRDB>
> line 8298021.
>
> SQL ERROR!! involving
>
>    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
> group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
> external_database_release_id, group_read, aa_sequence_id, row_group_id,
> other_read, gid, source_id, modification_date, user_read,
> row_alg_invocation_id, other_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, '', SYSDATE,
> ?, ?, ? )
> Values: Luminal binding protein 3 (BiP 3) (78 kDa glucose-regulated
> protein homolog 3) (GRP 78-3), 8, 1, 1, 5063019, 1, 2, 169692, 81, 1,
> 2943307, 2, 1, 729619, 1, 30713, 0 at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NRDBEntry (  desc...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x450007d8)', 'ARRAY(0x40a8ffd0)', '^J    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, use...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', 'HASH(0x11e51efc)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>
> GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>
> GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>
> GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)', 'GUS::Model::DoTS::NRDBEntry') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
>
> GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
> GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 335
>
> GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x85a26cc)', 'HASH(0x85a23cc)', 48) called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
>
> GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x8811950)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
>        eval {...} called at
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
>
> Thanks,
> Pablo
>
>
> --
> -----------------------------
> Pablo Nascimento Mendes
> Research Scholar
> Kissinger Lab
> Department of Genetics
> University of Georgia
> C210 Life Sciences Bldg.
> Athens, Georgia 30602
> Phone:706 542-1447
> E-mail: pa...@ug...
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by OSTG. Have you noticed the changes on
> Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now,
> one more big change to announce. We are now OSTG- Open Source Technology
> Group. Come see the changes on the new OSTG site. www.ostg.com
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] source_id error with LoadNRDB

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

Hi,

I've had some hard to track down problems with entries in the nr protein 
db. Several of these were due to new undocumented source databases - I 
don't think NCBI supports this database as far as documentation goes (they 
don't keep it up to date) although they do update the files very 
frequently, I think nightly. The last time I loaded, they had violated the 
format by neglecting to put the ^A before a subsequent entry in the 
defline, something I could see by opening the file using vi. I think I 
got the error you are getting.

I can't really check this entry in the files I have because I don't think 
the line you sent is the one in question, based on the description. (spike 
glycoprotein S1 subunit precursor... vs Luminal binding protein 3...).


If you encountered this error after successfully loading many others than 
I would suspect some problem with the entry itself.

                                                       Debbie


On Thu, 5 Aug 2004, Pablo N. Mendes wrote:

> Hello all,
> I've been "playing" with the loadNRDB module in the previous weeks, but
> it is still crashing. I got this "cannot insert NULL into source_id
> (DoTS.NRDBEntry)" error when reading line 8298021 of my NR file.
>
> That line is:
>> gi|45549465|gb|AAS67649.1| spike glycoprotein S1 subunit precursor
> [Avian infectious bronchitis virus]
>
> I cannot see why this would crash. I'm looking into the code, but maybe
> someone who already knows the module can help me with guesses.
>
> Here part of the dump:
>
> [pablo@mkiwi loadNRDB]$ ga GUS::Common::Plugin::LoadNRDB
> --comment="loading NRDB data from July" --extDbRelId=48
> --gitax="/home/luchtan/GUS/loadNRDB/June232004/gi_taxid_prot.dmp"
> --nrdb="/scratch/pablo/nr"
> --SourceDB="84:tpe,76:pdb,77:dbj,78:prf,79:emb,81:sp,82:pir,80:gb,83:ref,80:tpg,151:genpept,153:tpd" --plugin --temp_login='pablo' --temp_password='pablo123' --dbi_str='dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD' --commit | tee loadnrdb.log
> (...)
> Submitted set number:1462975
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("DOTS"."NRDBENTRY"."SOURCE_ID") (DBD ERROR: OCIStmtExecute) at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, <NRDB>
> line 8298021.
>
> SQL ERROR!! involving
>
>    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
> group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
> external_database_release_id, group_read, aa_sequence_id, row_group_id,
> other_read, gid, source_id, modification_date, user_read,
> row_alg_invocation_id, other_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, '', SYSDATE,
> ?, ?, ? )
> Values: Luminal binding protein 3 (BiP 3) (78 kDa glucose-regulated
> protein homolog 3) (GRP 78-3), 8, 1, 1, 5063019, 1, 2, 169692, 81, 1,
> 2943307, 2, 1, 729619, 1, 30713, 0 at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NRDBEntry (  desc...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x450007d8)', 'ARRAY(0x40a8ffd0)', '^J    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, use...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', 'HASH(0x11e51efc)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>
> GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>
> GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>
> GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)', 'GUS::Model::DoTS::NRDBEntry') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
>
> GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
> GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 335
>
> GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x85a26cc)', 'HASH(0x85a23cc)', 48) called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
>
> GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x8811950)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
>        eval {...} called at
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
>
> Thanks,
> Pablo
>
>
> --
> -----------------------------
> Pablo Nascimento Mendes
> Research Scholar
> Kissinger Lab
> Department of Genetics
> University of Georgia
> C210 Life Sciences Bldg.
> Athens, Georgia 30602
> Phone:706 542-1447
> E-mail: pa...@ug...
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by OSTG. Have you noticed the changes on
> Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now,
> one more big change to announce. We are now OSTG- Open Source Technology
> Group. Come see the changes on the new OSTG site. www.ostg.com
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] source_id error with LoadNRDB

[Pablo N. M. <pa...@pa...>]

Hello all,
I've been "playing" with the loadNRDB module in the previous weeks, but
it is still crashing. I got this "cannot insert NULL into source_id
(DoTS.NRDBEntry)" error when reading line 8298021 of my NR file.

That line is:
>gi|45549465|gb|AAS67649.1| spike glycoprotein S1 subunit precursor
[Avian infectious bronchitis virus]

I cannot see why this would crash. I'm looking into the code, but maybe
someone who already knows the module can help me with guesses.

Here part of the dump:

[pablo@mkiwi loadNRDB]$ ga GUS::Common::Plugin::LoadNRDB
--comment="loading NRDB data from July" --extDbRelId=48
--gitax="/home/luchtan/GUS/loadNRDB/June232004/gi_taxid_prot.dmp"
--nrdb="/scratch/pablo/nr"
--SourceDB="84:tpe,76:pdb,77:dbj,78:prf,79:emb,81:sp,82:pir,80:gb,83:ref,80:tpg,151:genpept,153:tpd" --plugin --temp_login='pablo' --temp_password='pablo123' --dbi_str='dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD' --commit | tee loadnrdb.log
(...)
Submitted set number:1462975
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("DOTS"."NRDBENTRY"."SOURCE_ID") (DBD ERROR: OCIStmtExecute) at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, <NRDB>
line 8298021.
 
 SQL ERROR!! involving
  
    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
external_database_release_id, group_read, aa_sequence_id, row_group_id,
other_read, gid, source_id, modification_date, user_read,
row_alg_invocation_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, '', SYSDATE,
?, ?, ? )
 Values: Luminal binding protein 3 (BiP 3) (78 kDa glucose-regulated
protein homolog 3) (GRP 78-3), 8, 1, 1, 5063019, 1, 2, 169692, 81, 1,
2943307, 2, 1, 729619, 1, 30713, 0 at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
       
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NRDBEntry (  desc...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
       
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x450007d8)', 'ARRAY(0x40a8ffd0)', '^J    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, use...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
       
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', 'HASH(0x11e51efc)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
       
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
       
GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
       
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)', 'GUS::Model::DoTS::NRDBEntry') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
       
GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
       
GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 335
       
GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x85a26cc)', 'HASH(0x85a23cc)', 48) called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
       
GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x8811950)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
        eval {...} called at
/var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
       
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
       
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
       
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
 
Thanks,
Pablo


-- 
-----------------------------
Pablo Nascimento Mendes
Research Scholar
Kissinger Lab
Department of Genetics
University of Georgia
C210 Life Sciences Bldg.
Athens, Georgia 30602
Phone:706 542-1447
E-mail: pa...@ug...

Re: [Gusdev-gusdev] Loading BLAST results

[Pablo N. M. <pa...@pa...>]

Hi Arnaud,
I don't know if I'll be able to answer all your questions, but I'll try
some to the extent of my knowledge on GUS up to now.

> I have the sequences in FASTA, what regexp shall I need?
> Is only --regex_name parameter required?
> Does it matter if I don't give taxon_id parameter ?

I've run the plugin with these parameters:

[pablo@mkiwi mcl]$ ga GUS::Common::Plugin::InsertNewExternalSequences
--external_database_release_id=3D38
--regex_source_id=3D(.*)
--table_name=3DDoTS::ExternalAASequence
--sequencefile=3Dtbrucei =96commit

The regex_*, as you probably noted, are the regular expressions to
extract the referred info from the FASTA header (name, source_id,
secondary_id, etc.). I've only used the regex_source_id. Also, it seems
not to matter if you don't give the taxon_id parameter. But you
obviously won't make the associations in DoTS::AASequenceTaxon between
sequences and taxa.

> Does LoadBlastSimFast module require generateBlastSimilarity.pl
script? Where can I get this script ?

This module reads similarity results in an especific format like:

>479679 (3 subjects)
  Sum: 479680:1871:1.2e-194:1:353:1:353:1:353:353:353:0:
   HSP1: 479680:353:353:353:1871:1.2e-194:1:353:1:353:0:
  Sum: 488460:1826:7.0e-190:1:353:1:353:1:353:342:348:0:
   HSP1: 488460:342:348:353:1826:7.0e-190:1:353:1:353:0:
>479680 (3 subjects)
  Sum: 479679:1871:1.2e-194:1:353:1:353:1:353:353:353:0:
   HSP1: 479679:353:353:353:1871:1.2e-194:1:353:1:353:0:

The script parseBlastFilesForSimilarity.pl (attached) will do the trick.
I don't know if there are multiple versions of this script traveling
around the list.

[jdai@headnode mclorth]$ ls /scratch/jdai/Cpgus_vs_Pfgus/ | perl
parseBlastFilesForSimilarity.pl
--regex=3D'(\S+)'
--outputFile=3DLm_vs_Lm_parsed=20
--dir=3D/scratch/jdai/Cpgus_vs_Pfgus/

Hope this is useful,
Pablo

On Thu, 2004-08-05 at 08:49, Arnaud Kerhornou wrote:
> Hi
>=20
> I want to load BLAST results in GUS.
> Before running LoadBlastSimFast module, I want to load Uniprot and EMBL=
=20
> databases in DoTS::ExternalAASequence and DoTS::ExternalNASequence.,=20
> just the Ids not the sequences themselves.
>=20
> I need some help to use GUS::Common::Plugin::InsertNewExternalSequences=
=20
> plugin.
>=20
> I have the sequences in FASTA, what regexp shall I need  ? Is only =20
> --regex_name parameter required ? I don't know the taxon attached to th=
e=20
> sequence entries. Does it matter if I don't give taxon_id parameter ?
>=20
> Re. LoadBlastSimFast module, It seems to parse the output in a specific=
=20
> format. Does it require generateBlastSimilarity.pl script ? Where can I=
=20
> get this script ?
>=20
> cheers
> Arnaud
--=20
-----------------------------
Pablo Nascimento Mendes
CTEGD EMF TIPS Fellow
Kissinger Lab
Department of Genetics
University of Georgia
C210 Life Sciences Bldg.
Athens, Georgia 30602
Phone:706 542-1447
E-mail: pa...@ug...

[Gusdev-gusdev] Error in LoadBlastSimFast plugin

[Jeetendra S. <so...@vb...>]

Hi,
I want to upload BLAST data into GUS. I have the parsed output but, I am
getting an error. When I run the LoadBlastSimFast plugin, it lists the
columns containing values of all the options (parameters) and then gives
the following error.


DBD::Oracle::db prepare failed: ORA-02289: sequence does not exist (DBD
ERROR: error possibly near <*> indicator at char 12 in 'select
dots.<*>similarity_SQ.NEXTVAL from DUAL') [for Statement "select
dots.similarity_SQ.NEXTVAL from DUAL"] at
/home/soneja.local/GUS/dev/gushome/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm
line 346, <GEN0> line 11.
Can't call method "execute" on an undefined value at
/home/soneja.local/GUS/dev/gushome/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm
line 443, <GEN0> line 11.


Could someone help me out on this ?

Thanks,
Jeetendra Soneja.




-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

[Gusdev-gusdev] Error in LoadBlastSimFast plugin

[Jeetendra S. <so...@vb...>]

Hi,
I want to upload BLAST data into GUS. I have the parsed output but, I am
getting an error. When I run the LoadBlastSimFast plugin, it lists the
columns containing values of all the options (parameters) and then gives
the following error.


DBD::Oracle::db prepare failed: ORA-02289: sequence does not exist (DBD
ERROR: error possibly near <*> indicator at char 12 in 'select
dots.<*>similarity_SQ.NEXTVAL from DUAL') [for Statement "select
dots.similarity_SQ.NEXTVAL from DUAL"] at
/home/soneja.local/GUS/dev/gushome/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm
line 346, <GEN0> line 11.
Can't call method "execute" on an undefined value at
/home/soneja.local/GUS/dev/gushome/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm
line 443, <GEN0> line 11.


Could someone help me out on this ?

Thanks,
Jeetendra Soneja.




-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

[Gusdev-gusdev] Loading BLAST results

[Arnaud K. <ax...@sa...>]

Hi

I want to load BLAST results in GUS.
Before running LoadBlastSimFast module, I want to load Uniprot and EMBL 
databases in DoTS::ExternalAASequence and DoTS::ExternalNASequence., 
just the Ids not the sequences themselves.

I need some help to use GUS::Common::Plugin::InsertNewExternalSequences 
plugin.

I have the sequences in FASTA, what regexp shall I need  ? Is only  
--regex_name parameter required ? I don't know the taxon attached to the 
sequence entries. Does it matter if I don't give taxon_id parameter ?

Re. LoadBlastSimFast module, It seems to parse the output in a specific 
format. Does it require generateBlastSimilarity.pl script ? Where can I 
get this script ?

cheers
Arnaud

-- 
Arnaud Kerhornou

The Wellcome Trust Sanger Institute
The Pathogen Sequencing Unit
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Work: +44 (0) 1223 494955
Fax: +44 (0) 1223 494919

[Gusdev-gusdev] Registering ga - problem fixed

[Zen <zen...@re...>]

Dear Developers,=0A=0A    I was able to fix the problem.=0A=0A=0A =A0> --Th=
is is to grant permission to the users=0A > =0A > GRANT CREATE SESSION TO G=
USrw;=0A > GRANT CREATE TABLE TO GUSrw;=0A > GRANT CREATE VIEW TO GUSrw;=0A=
 > GRANT CREATE SEQUENCE TO GUSrw;=0A > GRANT CREATE TRIGGER TO GUSrw;=0A >=
 GRANT CREATE SYNONYM TO GUSrw;=0A > GRANT SELECT ANY TABLE TO GUSrw;=0A > =
GRANT INSERT ANY TABLE TO GUSrw;=0A > GRANT UPDATE ANY TABLE TO GUSrw;=0A >=
 GRANT DELETE ANY TABLE TO GUSrw;=0A > GRANT CREATE SESSION TO GUSdevReadOn=
ly;=0A > GRANT SELECT ANY TABLE TO GUSdevReadOnly;=0A > GRANT SELECT ANY TA=
BLE TO GUSdevReadOnly;=0A > -----------------------------------------------=
---=0A =0A To the above list, we had to add the line:=0A =0A GRANT SELECT A=
NY SEQUENCE TO GUSrw;=0A =0A After doing this, the "ga +meta --commit" comm=
and worked properly.=0A =0AFor more details you can Juan Perin's mail dated=
 2004-07-16 in the archive.=0A=0A=0AThanks,=0ASenthil =0A=0A=0A

[Gusdev-gusdev] Registering ga

[Zen <zen...@re...>]

 Dear GUS Developers,=0A=0A I am trying to register ga but have run into th=
e following block.=0A When I run "ga +meta --commit" I get a DBD::Oracle::d=
b prepare failed=0A (see below) due to apparently insufficient privileges w=
hen running the=0A statement "select Core.Algorithm_SQ.NEXTVAL from DUAL." =
 However,=0A as, also shown below, gus or core can run that command without=
 any=0A problems within sqlplus.=0A =0A Any ideas what might be the problem=
?=0A =0A Thanks=0A Senthil=0A=0Aamrit % ga +meta=0A  <Core::Algorithm>=0A  =
  <name>GA-Plugin</name>=0A    <description>GUS application framework for p=
lugins</description>=0A    <Core::AlgorithmImplementation>=0A      <cvs_rev=
ision>1.53</cvs_revision>=0A      <cvs_tag> </cvs_tag>=0A      <executable>=
GUS::PluginMgr::GusApplication</executable>=0A      <executable_md5>5a2d7e8=
36b14d54027e90f4e8f174fec</executable_md5>=0A      <description>update for =
GUS 3.0</description>=0A      <Core::AlgorithmInvocation>=0A        <start_=
time>SYSDATE</start_time>=0A        <end_time>SYSDATE</end_time>=0A        =
<machine_id>0</machine_id>=0A        <cpus_used>1</cpus_used>=0A        <re=
sult>meta</result>=0A      </Core::AlgorithmInvocation>=0A    </Core::Algor=
ithmImplementation>=0A  </Core::Algorithm>=0ADBD::Oracle::db prepare failed=
: ORA-01031: insufficient privileges (DBD ERROR: error possibly near <*> in=
dicator at char 12 in 'select Core.<*>Algorithm_SQ.NEXTVAL from DUAL') [for=
 Statement "select Core.Algorithm_SQ.NEXTVAL from DUAL"] at /farm/gus2/gush=
ome/lib/perl/GUS/ObjRelP/DbiTable.pm line 550.=0AFailed preparing sql 'sele=
ct Core.Algorithm_SQ.NEXTVAL from DUAL' with error: ORA-01031: insufficient=
 privileges (DBD ERROR: error possibly near <*> indicator at char 12 in 'se=
lect Core.<*>Algorithm_SQ.NEXTVAL from DUAL') at /farm/gus2/gushome/lib/per=
l/GUS/ObjRelP/DbiTable.pm line 548=0A        GUS::ObjRelP::DbiTable::getNex=
tID('GUS::Model::Core::Algorithm_Table=3DHASH(0x86c4474)', 'undef') called =
at /farm/gus2/gushome/lib/perl/GUS/ObjRelP/DbiRow.pm line 535=0A        GUS=
::ObjRelP::DbiRow::getNextID('GUS::Model::Core::Algorithm=3DHASH(0x866ec18)=
') called at /farm/gus2/gushome/lib/perl/GUS/ObjRelP/DbiRow.pm line 606=0A =
       GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::Algorithm=3DHASH(0x8=
66ec18)') called at /farm/gus2/gushome/lib/perl/GUS/Model/GusRow.pm line 16=
77=0A        GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=3DHASH=
(0x866ec18)') called at /farm/gus2/gushome/lib/perl/GUS/PluginMgr/GusApplic=
ation.pm line 361=0A        GUS::PluginMgr::GusApplication::doMajorMode_Met=
a('GUS::PluginMgr::GusApplication=3DHASH(0x811f180)', 'undef') called at /f=
arm/gus2/gushome/lib/perl/GUS/PluginMgr/GusApplication.pm line 289=0A      =
  GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x811f180)', 'undef') called at /farm/gus2/gushome/lib/perl/GUS/P=
luginMgr/GusApplication.pm line 198=0A        GUS::PluginMgr::GusApplicatio=
n::parseAndRun('GUS::PluginMgr::GusApplication=3DHASH(0x811f180)', 'ARRAY(0=
x8129ecc)') called at /farm/gus2/gushome/bin/ga line 11=0Aamrit % =0A=0A=0A=
=0Aamrit % sqlplus sys@"gus2 as sysdba"=0A=0ASQL*Plus: Release 9.2.0.4.0 - =
Production on Wed Aug 4 17:55:44 2004=0A=0ACopyright (c) 1982, 2002, Oracle=
 Corporation.  All rights reserved.=0A=0AEnter password: =0A=0AConnected to=
:=0AOracle9i Enterprise Edition Release 9.2.0.4.0 - Production=0AWith the P=
artitioning, OLAP and Oracle Data Mining options=0AJServer Release 9.2.0.4.=
0 - Production=0A=0ASQL> select core.algorithminvocation_sq.nextval from du=
al;=0A=0A   NEXTVAL=0A----------=0A        21=0A=0ASQL> select core.algorit=
hmimplementation_sq.nextval from dual;=0A=0A   NEXTVAL=0A----------=0A     =
   21=0A=0A=0A=0Aamrit % cat .gus.properties =0AdatabaseLogin=3DGUSrw=0Adat=
abasePassword=3D*******=0AreadOnlyDatabaseLogin=3DGUSdevReadOnly=0AreadOnly=
DatabasePassword=3D*******=0AcoreSchemaName=3DCore=0AuserName=3Ddba=0Agroup=
=3Ddba=0Aproject=3DDatabase administration=0AdbiDsn=3Ddbi:Oracle:host=3Damr=
it;sid=3Dgus2=0A=0A=0A=0A

[Gusdev-gusdev] Problems GBParser

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

Hello,

since the last update of GUS, my GBParser doesn't work anymore properly. 
Used it like before.

Who might help me?

Thanks,
Thomas


errors:

##############################

********GEtting loc below1188486

DBD::Oracle::st execute failed: ORA-00913: too many values (DBD ERROR: 
OCIStmtExecute) at 
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, 
<GEN0> line 33579.
Fri Jul 30 14:51:50 2004        Genbank entries inserted= 0;  updated= 
0; total #(inserted::updated::deleted)=16::::59

Fri Jul 30 14:51:50 2004        FAILURES        Unable to process 1 
entries. See gbparserFailures/

errorlog:
------------------ entry number 1 -----------------

 SQL ERROR!! involving
 
 Values: 93444 at 
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
        
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33f5c)','\x{a} 
SQL ERROR!! involving\x{a}  \x{a} Values: 93444')
called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
        
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33f5c)','GUS::ObjRelP::DbiDbHandle::st=HASH(0xbd9cd90)','ARRAY(
0xbd9ccf4)') called at 
/home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 1798
        
GUS::Model::GusRow::version('GUS::Model::DoTS::Repeats=HASH(0xb9ae250)') 
called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1628
        
GUS::Model::GusRow::submit('GUS::Model::DoTS::Repeats=HASH(0xb9ae250)') 
called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBP
arser.pm line 1113
        
GUS::Common::Plugin::GBParser::processChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0xafaf33c)','ARRAY(0x8ba0d44)','ARRAY(0x8ba0
d5c)') called at 
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 272
        
GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8599870)','CBIL::Bio::GenBank::ArrayStream=HASH(0x90
4fec8)') called at 
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
        eval {...} called at 
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
        
GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8599870)','HASH(0x8e6c154)') 
called at /home/oracle/gus_home/
lib/perl/GUS/PluginMgr/GusApplication.pm line 453
        eval {...} called at 
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
        
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParse
r',1) called at 
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
        
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser') 
call
ed at /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
line 289
        
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser') 
called a
t /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
        
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060684)') 
called at /home/oracl
e/gus_home/bin/ga line 11


##############################3
DBD::Oracle::st execute failed: ORA-00001: unique constraint 
(DOTS.PK_NAGENE) violated (DBD ERROR: OCIStmtExecute) at 
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, 
<GEN0> line 1039.
Fri Jul 30 14:46:27 2004        Genbank entries inserted= 0;  updated= 
0; total #(inserted::updated::deleted)=16::::

Fri Jul 30 14:46:27 2004        FAILURES        Unable to process 2 
entries. See gbparserFailures/
Fri Jul 30 14:46:27 2004        RESULT  Genbank entries inserted= 0;  
updated= 0;  failed= 2


//the next sequence of na_gene is 43 or so...

 SQL ERROR!! involving
 
    INSERT INTO DoTS.NAGene (  group_write, other_read, group_read, 
name, user_read, row_user_id, is_verified, other_write, modification_date,
 row_alg_invocation_id, row_project_id, na_gene_id, row_group_id, 
user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
 Values: 1, 1, 1, F49E11.11, 1, 1, 0, 0, 50250, 1, 21, 1, 1 at 
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
        
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33e4c)','\x{a} 
SQL ERROR!! involving\x{a} \x{a}    INSERT INTO Do
TS.NAGene (  grou...') called at 
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
        
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33e4c)','GUS::ObjRelP::DbiDbHandle::st=HASH(0x9121740)','ARRAY(
0x9121788)','\x{a}    INSERT INTO DoTS.NAGene (  group_write, 
other_read, grou...') called at 
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiRo
w.pm line 681
        
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAGene=HASH(0x9104bcc)','HASH(0x9111424)') 
called at /home/oracle/gus_home/l
ib/perl/GUS/ObjRelP/DbiRow.pm line 628
        
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAGene=HASH(0x9104bcc)') 
called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1677
        
GUS::Model::GusRow::submit('GUS::Model::DoTS::NAGene=HASH(0x9104bcc)') 
called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBPa
rser.pm line 727
        GUS::Common::Plugin::GBParser::getNAGeneId('F49E11.11') called 
at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 71
4
        
GUS::Common::Plugin::GBParser::buildGene('CBIL::Bio::GenBank::Qualifier=HASH(0x8f7de60)','CBIL::Bio::GenBank::Feature=HASH(0x8f7ad48)'
) called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm 
line 503
        
GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBParser=HASH(0x8599604)','CBIL::Bio::GenBank::Entry=HASH(0x8ef2790
)','GUS::Model::DoTS::ExternalNASequence=HASH(0x8ffa638)') called at 
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 251
        
GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8599604)','CBIL::Bio::GenBank::ArrayStream=HASH(0x8e
ff678)') called at 
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
        eval {...} called at 
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
        
GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8599604)','HASH(0x8e6bdc4)') 
called at /home/oracle/gus_home/
lib/perl/GUS/PluginMgr/GusApplication.pm line 453
        eval {...} called at 
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
        
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParse
r',1) called at 
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
        
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser') 
call
ed at /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm 
line 289
        
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser') 
called a
t /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
        
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060684)') 
called at /home/oracl
e/gus_home/bin/ga line 11


#############################################

VLD     CBIL::Bio::GenBank::Origin      1
ERR     LINE=33578      unparsed line

ERR     LINE=33579      unparsed line

Fri Jul 30 14:45:13 2004        STATUS  N=1 ACC=NC_005063        
TOTAL_OBJECTS=16
Fri Jul 30 14:45:13 2004        Genbank entries inserted= 0;  updated= 
0; total #(inserted::updated::deleted)=16::::

Fri Jul 30 14:45:13 2004        RESULT  Genbank entries inserted= 0;  
updated= 0;  failed= 0