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From: Deborah P. <pi...@pc...> - 2005-09-09 12:37:56
|
I would like to propose another table(s) to hold synonym information but
I'm uncertain what to propose. Therefore, I would like to solicit opinions.
Immediate motivation:
Genetic markers often have aliases and, as in many cases, there could be
more than one alias per marker. Storing multiple aliases as a string
list in a single attribute of a view or table is clumsy and results in
inefficient queries. The obvious solution is a separate table for
aliases which I've called synonyms.
There are several possible tables that could be proposed:
1) The proposed view to hold Genetic Markers is a view of NAFeatureImp
so we could have a NAFeatureSynonym table with hard links to NAFeature.
2) We could have a GeneticMarkerSynonym table dedicated to a
GeneticMarker view, which would also have hard links to NAFeature.
3) We could have a Synonym table with linking tables - e.g.
SynonymNAFeature - and the linking table could have hard links to
Synonym and NAFeature.
There are others but these capture the general idea. I am partial to the
third as this Synonym table could be multi-purpose while the linking
tables could have only hard links.
Let me add, there are synonym tables in GUS -
AAGeneSyynonym,GeneSynonym,ProteinSynonym,MoietySynonym,GOSynonym - but
none that can be used for nafeatures.
Debbie
|
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From: Junmin L. <ju...@pc...> - 2005-09-08 18:58:25
|
Hi, there, Is there a SVN task in ant? Can someone tell me how to access svn in ant? I think I saw some emails in this list describe it. Thanks, --junmin |
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From: Kumar, S. \(Contr\) <San...@ng...> - 2005-09-08 16:23:56
|
Hi Jonathan, Very Very clear explanation!!!. I appreciate your help in this regard. If any further questions come then I may try to reach you for help. Thanks Sanjeev=20 -----Original Message----- From: Jonathan Schug [mailto:js...@pc...]=20 Sent: Thursday, September 08, 2005 8:11 AM To: Chris Stoeckert Cc: Kumar, Sanjeev (Contr); Deborah Pinney; gus...@li... Subject: Re: [GUSDEV] Gene Association data load (GFUS 3.0) Sanjeev: The table dots.GoAssociationInstanceLoe is a 'controlled' vocabulary of that indicate the different lines of evidence one might use when assigning a GO term to an entity. We developed it because we load GO term associations from multiple sources. For example, the PlasmoDB project got GO annotations from the sequencing centers and we also made our own GO function term predictions. The link in dots.GoAssociationInstance to this table allows us to distinguish the two. I would use GUS::Common::Plugin::UpdateGusFromXML to load dots.GoAssociationInstanceLoe. Here's an example of the XML you might use as input to that plugin: <DoTS.GOAssociationInstanceLOE> <name>Human Annotators</name> <description>Members of a team of experts look at the gene name and think up a GO term.</description> </DoTS.GOAssociationInstanceLOE> <DoTS.GOAssociationInstanceLOE> <name>Automatic Annotation</name> <description>A very smart programs looks at the DNA sequence and thinks up a GO term.</description> </DoTS.GOAssociationInstanceLOE> This bit of XML defines two source of annotation; you can define more by running the plugin again or by putting more in the file. Note that dots.GoAssociationInstance also has an external_database_release_id column which can pin-point the source of the data very precisely. The goal of dots.GoAssociationInstanceLoe is a broad classification of sources. Remember there is also the =20 evidence code which also indicates how the association was formed. =20 If you don't think you'll care about categorizing sources in this way, just enter a single 'some method' in dots.GoAssociationInstanceLoe and use that for all association sources. Hope that helped. Jonathan Jonathan Schug, Ph.D. Center for Bioinformatics Computational Biology and Informatics Lab University of Pennsylvania js...@pc... (215) 573-3113 voice (215) 573-3111 fax 1413 Blockley Hall, Philadelphia, PA 19014-6021 On Sep 7, 2005, at 10:51 PM, Chris Stoeckert wrote: > Hi Sanjeev, > These tables were created for our GO prediction pipeline (see=20 > http://www.cbil.upenn.edu/GO/). You might want to check if this is=20 > really appropriate to what you want to do. > The person responsible for this (Dave Barkan) has left the group. =20 > Jonathan, Debbie any insights to provide? > Thanks, > Chris > > On Sep 6, 2005, at 10:22 AM, Kumar, Sanjeev (Contr) wrote: > > >> Hi, >> I am trying to load GOAssociation data by usingga=20 >> GUS::GOPredict::Plugin::LoadGoAssoc >> plug in in GUS3.0 . >> I am getting an error at the initial stage of data load. It is=20 >> looking for data in >> table called "Dots.GOASSOCIATIONINSTANCELOE" , because=20 >> "Dots.GOASSOCIATIONINSTANCE" has >> foreign key relationship with the first table. >> I don't know how I am going to get data in the=20 >> "Dots.GOASSOCIATIONINSTANCELOE" table. >> >> Can some one help me? >> >> Thanks >> Sanjeev >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO=20 >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 >> Practices Agile & Plan-Driven Development * Managing Projects & Teams >> * Testing & QA Security * Process Improvement & Measurement *=20 >> http://www.sqe.com/ bsce5sf=20 >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > |
|
From: Jonathan S. <js...@pc...> - 2005-09-08 14:57:25
|
Mark: If I recall correctly, the with/from annotation indicates another sequence or database entry of some kind that supports the association. It appears that this will still be the approach as there are no new tables or columns related to GO terms. I'm not sure that it's the best possible approach. Perhaps this needs to be revisited? Jonathan On Sep 8, 2005, at 9:56 AM, Mark Heiges wrote: > Thanks for the info, and for your wiki posting on the subject > ( http://www.gusdb.org/wiki/index.php/GusSchemaGoOntologies ). > > While we are on the subject... I want to store the 'with/from' > annotation file field for some of our annotations. Digging around > in the Bioperl2Gus module (thanks to the authors who included nice > documentation in the comments) it looks such links are made via > GOAssociationInstance-> Evidence-> ExternalDatabaseEntry. Is that > (still) the Right Way for GUS3.5? > > -Mark > > Mark Heiges > C210 Life Sciences Building > Center for Tropical and Emerging Global Diseases > University of Georgia, Athens, GA 30602 > TEL: (706) 542-1447 FAX: (706) 542-3582 > > On Sep 8, 2005, at 8:10 AM, Jonathan Schug wrote: > > >> Sanjeev: >> >> The table dots.GoAssociationInstanceLoe is a 'controlled' >> vocabulary of that indicate the different lines of evidence one >> might use when assigning a GO term to an entity. We developed it >> because we load GO term associations from multiple sources. For >> example, the PlasmoDB project got GO annotations from the >> sequencing centers and we also made our own GO function term >> predictions. The link in dots.GoAssociationInstance to this table >> allows us to distinguish the two. >> >> I would use GUS::Common::Plugin::UpdateGusFromXML to load >> dots.GoAssociationInstanceLoe. Here's an example of the XML you >> might use as input to that plugin: >> >> <DoTS.GOAssociationInstanceLOE> >> <name>Human Annotators</name> >> <description>Members of a team of experts look at the gene name >> and think up a GO term.</description> >> </DoTS.GOAssociationInstanceLOE> >> >> <DoTS.GOAssociationInstanceLOE> >> <name>Automatic Annotation</name> >> <description>A very smart programs looks at the DNA sequence and >> thinks up a GO term.</description> >> </DoTS.GOAssociationInstanceLOE> >> >> This bit of XML defines two source of annotation; you can define >> more by running the plugin again or by putting more in the file. >> Note that dots.GoAssociationInstance also has an >> external_database_release_id column which can pin-point the source >> of the data very precisely. The goal of >> dots.GoAssociationInstanceLoe is a broad classification of >> sources. Remember there is also the evidence code which also >> indicates how the association was formed. If you don't think >> you'll care about categorizing sources in this way, just enter a >> single 'some method' in dots.GoAssociationInstanceLoe and use that >> for all association sources. >> >> Hope that helped. >> >> Jonathan >> >> Jonathan Schug, Ph.D. >> >> Center for Bioinformatics >> Computational Biology and Informatics Lab >> University of Pennsylvania >> >> js...@pc... >> (215) 573-3113 voice >> (215) 573-3111 fax >> >> 1413 Blockley Hall, Philadelphia, PA 19014-6021 >> >> >> >> On Sep 7, 2005, at 10:51 PM, Chris Stoeckert wrote: >> >> >>> Hi Sanjeev, >>> These tables were created for our GO prediction pipeline (see >>> http://www.cbil.upenn.edu/GO/). You might want to check if this >>> is really appropriate to what you want to do. >>> The person responsible for this (Dave Barkan) has left the group. >>> Jonathan, Debbie any insights to provide? >>> Thanks, >>> Chris >>> >>> On Sep 6, 2005, at 10:22 AM, Kumar, Sanjeev (Contr) wrote: >>> >>> >>> >>>> Hi, >>>> I am trying to load GOAssociation data by usingga >>>> GUS::GOPredict::Plugin::LoadGoAssoc >>>> plug in in GUS3.0 . >>>> I am getting an error at the initial stage of data load. It is >>>> looking >>>> for data in >>>> table called "Dots.GOASSOCIATIONINSTANCELOE" , because >>>> "Dots.GOASSOCIATIONINSTANCE" has >>>> foreign key relationship with the first table. >>>> I don't know how I am going to get data in the >>>> "Dots.GOASSOCIATIONINSTANCELOE" table. >>>> >>>> Can some one help me? >>>> >>>> Thanks >>>> Sanjeev >>>> >>>> >>>> ------------------------------------------------------- >>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>> September 19-22, 2005 * San Francisco, CA * Development >>>> Lifecycle Practices >>>> Agile & Plan-Driven Development * Managing Projects & Teams * >>>> Testing & QA >>>> Security * Process Improvement & Measurement * http:// >>>> www.sqe.com/bsce5sf >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>> >>> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * >> Testing & QA >> Security * Process Improvement & Measurement * http://www.sqe.com/ >> bsce5sf >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Mark H. <mh...@ug...> - 2005-09-08 13:56:16
|
Thanks for the info, and for your wiki posting on the subject ( http://www.gusdb.org/wiki/index.php/GusSchemaGoOntologies ). While we are on the subject... I want to store the 'with/from' annotation file field for some of our annotations. Digging around in the Bioperl2Gus module (thanks to the authors who included nice documentation in the comments) it looks such links are made via GOAssociationInstance-> Evidence-> ExternalDatabaseEntry. Is that (still) the Right Way for GUS3.5? -Mark Mark Heiges C210 Life Sciences Building Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 TEL: (706) 542-1447 FAX: (706) 542-3582 On Sep 8, 2005, at 8:10 AM, Jonathan Schug wrote: > Sanjeev: > > The table dots.GoAssociationInstanceLoe is a 'controlled' vocabulary > of that indicate the different lines of evidence one might use when > assigning a GO term to an entity. We developed it because we load GO > term associations from multiple sources. For example, the PlasmoDB > project got GO annotations from the sequencing centers and we also > made our own GO function term predictions. The link in > dots.GoAssociationInstance to this table allows us to distinguish the > two. > > I would use GUS::Common::Plugin::UpdateGusFromXML to load > dots.GoAssociationInstanceLoe. Here's an example of the XML you might > use as input to that plugin: > > <DoTS.GOAssociationInstanceLOE> > <name>Human Annotators</name> > <description>Members of a team of experts look at the gene name and > think up a GO term.</description> > </DoTS.GOAssociationInstanceLOE> > > <DoTS.GOAssociationInstanceLOE> > <name>Automatic Annotation</name> > <description>A very smart programs looks at the DNA sequence and > thinks up a GO term.</description> > </DoTS.GOAssociationInstanceLOE> > > This bit of XML defines two source of annotation; you can define more > by running the plugin again or by putting more in the file. Note that > dots.GoAssociationInstance also has an external_database_release_id > column which can pin-point the source of the data very precisely. The > goal of dots.GoAssociationInstanceLoe is a broad classification of > sources. Remember there is also the evidence code which also > indicates how the association was formed. If you don't think you'll > care about categorizing sources in this way, just enter a single 'some > method' in dots.GoAssociationInstanceLoe and use that for all > association sources. > > Hope that helped. > > Jonathan > > Jonathan Schug, Ph.D. > > Center for Bioinformatics > Computational Biology and Informatics Lab > University of Pennsylvania > > js...@pc... > (215) 573-3113 voice > (215) 573-3111 fax > > 1413 Blockley Hall, Philadelphia, PA 19014-6021 > > > > On Sep 7, 2005, at 10:51 PM, Chris Stoeckert wrote: > >> Hi Sanjeev, >> These tables were created for our GO prediction pipeline (see >> http://www.cbil.upenn.edu/GO/). You might want to check if this is >> really appropriate to what you want to do. >> The person responsible for this (Dave Barkan) has left the group. >> Jonathan, Debbie any insights to provide? >> Thanks, >> Chris >> >> On Sep 6, 2005, at 10:22 AM, Kumar, Sanjeev (Contr) wrote: >> >> >>> Hi, >>> I am trying to load GOAssociation data by usingga >>> GUS::GOPredict::Plugin::LoadGoAssoc >>> plug in in GUS3.0 . >>> I am getting an error at the initial stage of data load. It is >>> looking >>> for data in >>> table called "Dots.GOASSOCIATIONINSTANCELOE" , because >>> "Dots.GOASSOCIATIONINSTANCE" has >>> foreign key relationship with the first table. >>> I don't know how I am going to get data in the >>> "Dots.GOASSOCIATIONINSTANCELOE" table. >>> >>> Can some one help me? >>> >>> Thanks >>> Sanjeev >>> >>> >>> ------------------------------------------------------- >>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>> Practices >>> Agile & Plan-Driven Development * Managing Projects & Teams * >>> Testing & QA >>> Security * Process Improvement & Measurement * >>> http://www.sqe.com/bsce5sf >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing > & QA > Security * Process Improvement & Measurement * > http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Jonathan S. <js...@pc...> - 2005-09-08 12:10:58
|
Sanjeev: The table dots.GoAssociationInstanceLoe is a 'controlled' vocabulary of that indicate the different lines of evidence one might use when assigning a GO term to an entity. We developed it because we load GO term associations from multiple sources. For example, the PlasmoDB project got GO annotations from the sequencing centers and we also made our own GO function term predictions. The link in dots.GoAssociationInstance to this table allows us to distinguish the two. I would use GUS::Common::Plugin::UpdateGusFromXML to load dots.GoAssociationInstanceLoe. Here's an example of the XML you might use as input to that plugin: <DoTS.GOAssociationInstanceLOE> <name>Human Annotators</name> <description>Members of a team of experts look at the gene name and think up a GO term.</description> </DoTS.GOAssociationInstanceLOE> <DoTS.GOAssociationInstanceLOE> <name>Automatic Annotation</name> <description>A very smart programs looks at the DNA sequence and thinks up a GO term.</description> </DoTS.GOAssociationInstanceLOE> This bit of XML defines two source of annotation; you can define more by running the plugin again or by putting more in the file. Note that dots.GoAssociationInstance also has an external_database_release_id column which can pin-point the source of the data very precisely. The goal of dots.GoAssociationInstanceLoe is a broad classification of sources. Remember there is also the evidence code which also indicates how the association was formed. If you don't think you'll care about categorizing sources in this way, just enter a single 'some method' in dots.GoAssociationInstanceLoe and use that for all association sources. Hope that helped. Jonathan Jonathan Schug, Ph.D. Center for Bioinformatics Computational Biology and Informatics Lab University of Pennsylvania js...@pc... (215) 573-3113 voice (215) 573-3111 fax 1413 Blockley Hall, Philadelphia, PA 19014-6021 On Sep 7, 2005, at 10:51 PM, Chris Stoeckert wrote: > Hi Sanjeev, > These tables were created for our GO prediction pipeline (see > http://www.cbil.upenn.edu/GO/). You might want to check if this is > really appropriate to what you want to do. > The person responsible for this (Dave Barkan) has left the group. > Jonathan, Debbie any insights to provide? > Thanks, > Chris > > On Sep 6, 2005, at 10:22 AM, Kumar, Sanjeev (Contr) wrote: > > >> Hi, >> I am trying to load GOAssociation data by usingga >> GUS::GOPredict::Plugin::LoadGoAssoc >> plug in in GUS3.0 . >> I am getting an error at the initial stage of data load. It is >> looking >> for data in >> table called "Dots.GOASSOCIATIONINSTANCELOE" , because >> "Dots.GOASSOCIATIONINSTANCE" has >> foreign key relationship with the first table. >> I don't know how I am going to get data in the >> "Dots.GOASSOCIATIONINSTANCELOE" table. >> >> Can some one help me? >> >> Thanks >> Sanjeev >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * >> Testing & QA >> Security * Process Improvement & Measurement * http://www.sqe.com/ >> bsce5sf >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > |
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From: Chris S. <sto...@pc...> - 2005-09-08 02:51:31
|
Hi Sanjeev, These tables were created for our GO prediction pipeline (see http:// www.cbil.upenn.edu/GO/). You might want to check if this is really appropriate to what you want to do. The person responsible for this (Dave Barkan) has left the group. Jonathan, Debbie any insights to provide? Thanks, Chris On Sep 6, 2005, at 10:22 AM, Kumar, Sanjeev (Contr) wrote: > Hi, > I am trying to load GOAssociation data by usingga > GUS::GOPredict::Plugin::LoadGoAssoc > plug in in GUS3.0 . > I am getting an error at the initial stage of data load. It is > looking > for data in > table called "Dots.GOASSOCIATIONINSTANCELOE" , because > "Dots.GOASSOCIATIONINSTANCE" has > foreign key relationship with the first table. > I don't know how I am going to get data in the > "Dots.GOASSOCIATIONINSTANCELOE" table. > > Can some one help me? > > Thanks > Sanjeev > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * > Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/ > bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Kumar, S. \(Contr\) <San...@ng...> - 2005-09-06 14:23:35
|
Hi, I am trying to load GOAssociation data by usingga GUS::GOPredict::Plugin::LoadGoAssoc=20 plug in in GUS3.0 . I am getting an error at the initial stage of data load. It is looking for data in=20 table called "Dots.GOASSOCIATIONINSTANCELOE" , because "Dots.GOASSOCIATIONINSTANCE" has=20 foreign key relationship with the first table. I don't know how I am going to get data in the "Dots.GOASSOCIATIONINSTANCELOE" table. Can some one help me?=20 Thanks Sanjeev |
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From: Steve F. <sfi...@pc...> - 2005-09-05 15:35:34
|
Tony- see below - steve Tony Zhang wrote: > Hi Chris, > > Thanks for your reply. > > InsertSequenceFeatures.pm is helpful.I have more questions about this. > 1. Does InsertSequenceFeatures have the same (or more) functionality > as GBParser? Should we use InsertSequenceFeatures (supported) instead > of GBParser(community)? The functionality that GBParser supports that ISF does not support is updates. ISF is an Insert plugin, it only inserts rows, it never updates rows. GBParser can update a sequence or its features if you have new versions of them. but... we are no longer supporting GBParser (that is why it is Community). also, the current release of ISF does not yet support restart. it will very soon, hopefully next week. it will do so by providing an --undo option that will back out the previous run that failed so you can rerun it cleanly, after you have corrected whatever the problem was. > 2. To use InsertSequenceFeature, should we define "mapFile" (XML) > ourselves and pass it to InsertSequenceFeature as an argument? you can either use the provided map file or define one yourselves. but, only define one if you know that the provided one does not meet your needs > 3. Seems that there are many ways to use GUS to deal with the > relationship of "DNA->gene->CDS->AASEQUNCE". The documentation of > InsertSequenceFeatures.pm seems not very straightforward to me. Could > you or other GUS people give me a suggested method? For example, I > have an example genbank file below. ISF uses the bioperl feature parser. it includes an "unflattener" that analyzes feature locations of genes, rna, cds, etc and constructs gene feature trees of them (ie, gene models). ISF preserves those relationships in gus. AASequences are stored using the following relationship, specified by a "special case" called 'aaseq' (see the mapping file). the special cases are hard coded in the plugin, so, to understand them, read the code: Translation->TranslatedAAFeature->TranslatedAASequence with respect to the documentation, i have improved the notes provided with the plugin. here it is, what else would you like to see? ----------------snip----------------------------- The bioperl parser includes an "unflattener" that analyzes feature locations of genes, rna, cds, etc and constructs gene feature trees of them (ie, gene models). (See the bioperl API documentation for Bio::SeqFeature::Tools::Unflattener.) The plugin preserves these relationships (using the feature's parent_id to capture the tree). The mapping XML file includes five "special cases." These are cases in which some of the qualifiers are stored in tables other than the feature table. The five special cases are: 'dbxref', 'product', 'note', 'gene', and 'aaseq'. The special cases are hard-coded in the pluglin. To understand how the special cases each work, see the plugin code. ----------------------------------------------------- > > LOCUS NC_006932 2124241 bp DNA circular BCT > 08-APR-2005 > DEFINITION Brucella abortus biovar 1 str. 9-941 chromosome I, complete > sequence. > ACCESSION NC_006932 > VERSION NC_006932.1 GI:62288991 > KEYWORDS . > SOURCE Brucella abortus biovar 1 str. 9-941 > ORGANISM Brucella abortus biovar 1 str. 9-941 > <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=262698> > Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; > Brucellaceae; Brucella. > REFERENCE 1 (bases 1 to 2124241) > AUTHORS Halling,S.M., Peterson-Burch,B.D., Bricker,B.J., Zuerner,R.L., > Qing,Z., Li,L.L., Kapur,V., Alt,D.P. and Olsen,S.C. > TITLE Completion of the genome sequence of Brucella abortus and > comparison to the highly similar genomes of Brucella > melitensis and > Brucella suis > JOURNAL J. Bacteriol. 187 (8), 2715-2726 (2005) > PUBMED 15805518 > <http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi?uid=15805518&form=6&db=m&Dopt=r> > > REFERENCE 2 (bases 1 to 2124241) > AUTHORS . > CONSRTM NCBI Genome Project > TITLE Direct Submission > JOURNAL Submitted (06-APR-2005) National Center for Biotechnology > Information, NIH, Bethesda, MD 20894, USA > REFERENCE 3 (bases 1 to 2124241) > AUTHORS Halling,S.M., Bricker,B.J., Alt,D.P., Peterson-Burch,B.D., > Zuerner,R.L., Olsen,S.C., Whipple,D.L., Zhang,Q., Li,L.-L. and > Kapur,V. > TITLE Direct Submission > JOURNAL Submitted (03-FEB-2004) ARS, USDA, National Animal Disease > Center, > 2300 N. Dayton, P.O. Box 70, Ames, IA 50010, USA > COMMENT PROVISIONAL REFSEQ <http://www.ncbi.nlm.nih.gov/RefSeq/>: > This record has not yet been subject to final > NCBI review. The reference sequence was derived from > AE017223 <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=AE017223>. > COMPLETENESS: full length. > FEATURES Location/Qualifiers > source 1..2124241 > /organism="Brucella abortus biovar 1 str. 9-941" > /mol_type="genomic DNA" > /strain="9-941" > /db_xref="taxon:262698 > <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=262698>" > /chromosome="I" > /biovar="1" > gene > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=62288991&itemID=2031&view=gbwithparts> > 784..2274 > /gene="dnaA" > /locus_tag="BruAb1_0001" > /db_xref="GeneID:3339217 > <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids=3339217>" > > CDS > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=62288991&itemID=1&view=gbwithparts> > 784..2274 > /gene="dnaA" > /locus_tag="BruAb1_0001" > /note="similar to BR0001, chromosomal replication > initiator protein DnaA" > /codon_start=1 > /transl_table=11 > <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG11> > /product="DnaA, chromosomal replication initiator > protein" > /protein_id="YP_220785.1 > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=YP_220785.1>" > /db_xref="GI:62288992" > /db_xref="GeneID:3339217 > <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids=3339217>" > > > /translation="MKMDSAVSEEAFERLTAKLKARVGGEIYSSWFGRLKLDDISKSI > > VRLSVPTAFLRSWINNHYSELLTELWQEENPQILKVEVVVRGVSRVVRSAAPAETCDN > > AEAKPAVTPREKMVFPVGQSFGGQSLGEKRGSAVVAESAAATGAVLGSPLDPRYTFDT > > FVDGASNRVALAAARTIAEAGSSAVRFNPLFIHASVGLGKTHLLQAIAAAALQRQEKA > > RVVYLTAEYFMWRFATAIRDNNALSFKEQLRDIDLLVIDDMQFLQGKSIQHEFCHLLN > > TLLDSAKQVVVAADRAPSELESLDVRVRSRLQGGVALEVAAPDYEMRLEMLRRRLASA > > QCEDASLDIGEEILAHVARTVTGSGRELEGAFNQLLFRQSFEPNISIDRVDELLGHLT > > RAGEPKRIRIEEIQRIVARHYNVSKQDLLSNRRTRTIVKPRQVAMYLAKMMTPRSLPE > IGRRFGGRDHTTVLHAVRKIEDLVGADTKLAQELELLKRLINDQAA" > ... > > ORIGIN 1 ttttccacac ttatccacag ggcgcgggcg ggactcggtt > gcccctctga gtcaagcata > ... > > > I consider myself a newbie to GUS and the above questions may be naive > to many of you. However, your help is highly appreciated. > > Thanks again. > > - Tony > > > > > > Chris Stoeckert wrote: > >> Hi Tony, >> A beta release of the plugin InsertSequenceFeatures.pm is now >> available for loading GenBank records (as well as other formats). The >> semantics of how to use the GUS tables for this purpose are encoded >> in that plugin. Is that what you were asking? >> Chris >> >> On Sep 2, 2005, at 10:31 AM, Tony Zhang wrote: >> >>> This is old topic and it may have been discussed many times. Still, >>> I would like to get suggestion again about how to use GUS to store >>> DNA, CDS, and corresponding protein sequence. Suppose I have one >>> original record in Genkbank format. Thanks. >>> >>> - Tony >>> >>> >>> >>> ------------------------------------------------------- >>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>> Practices >>> Agile & Plan-Driven Development * Managing Projects & Teams * >>> Testing & QA >>> Security * Process Improvement & Measurement * >>> http://www.sqe.com/bsce5sf >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> <mailto:Gus...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> >> >> >> Chris Stoeckert, Ph.D. >> >> Research Associate Professor, Dept. of Genetics >> >> 1415 Blockley Hall, Center for Bioinformatics >> >> 423 Guardian Dr., University of Pennsylvania >> >> Philadelphia, PA 19104 >> >> Ph: 215-573-4409 FAX: 215-573-3111 >> >> > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing > & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Tony Z. <fz...@vb...> - 2005-09-05 13:49:02
|
Hi Chris,
Thanks for your reply.
InsertSequenceFeatures.pm is helpful.I have more questions about this.
1. Does InsertSequenceFeatures have the same (or more) functionality as
GBParser? Should we use InsertSequenceFeatures (supported) instead of
GBParser(community)?
2. To use InsertSequenceFeature, should we define "mapFile" (XML)
ourselves and pass it to InsertSequenceFeature as an argument?
3. Seems that there are many ways to use GUS to deal with the
relationship of "DNA->gene->CDS->AASEQUNCE". The documentation of
InsertSequenceFeatures.pm seems not very straightforward to me. Could
you or other GUS people give me a suggested method? For example, I have
an example genbank file below.
LOCUS NC_006932 2124241 bp DNA circular BCT 08-APR-2005
DEFINITION Brucella abortus biovar 1 str. 9-941 chromosome I, complete
sequence.
ACCESSION NC_006932
VERSION NC_006932.1 GI:62288991
KEYWORDS .
SOURCE Brucella abortus biovar 1 str. 9-941
ORGANISM Brucella abortus biovar 1 str. 9-941 <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=262698>
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
Brucellaceae; Brucella.
REFERENCE 1 (bases 1 to 2124241)
AUTHORS Halling,S.M., Peterson-Burch,B.D., Bricker,B.J., Zuerner,R.L.,
Qing,Z., Li,L.L., Kapur,V., Alt,D.P. and Olsen,S.C.
TITLE Completion of the genome sequence of Brucella abortus and
comparison to the highly similar genomes of Brucella melitensis and
Brucella suis
JOURNAL J. Bacteriol. 187 (8), 2715-2726 (2005)
PUBMED 15805518 <http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi?uid=15805518&form=6&db=m&Dopt=r>
REFERENCE 2 (bases 1 to 2124241)
AUTHORS .
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (06-APR-2005) National Center for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
REFERENCE 3 (bases 1 to 2124241)
AUTHORS Halling,S.M., Bricker,B.J., Alt,D.P., Peterson-Burch,B.D.,
Zuerner,R.L., Olsen,S.C., Whipple,D.L., Zhang,Q., Li,L.-L. and
Kapur,V.
TITLE Direct Submission
JOURNAL Submitted (03-FEB-2004) ARS, USDA, National Animal Disease Center,
2300 N. Dayton, P.O. Box 70, Ames, IA 50010, USA
COMMENT PROVISIONAL REFSEQ <http://www.ncbi.nlm.nih.gov/RefSeq/>: This record has not yet been subject to final
NCBI review. The reference sequence was derived from AE017223 <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=AE017223>.
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..2124241
/organism="Brucella abortus biovar 1 str. 9-941"
/mol_type="genomic DNA"
/strain="9-941"
/db_xref="taxon:262698 <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=262698>"
/chromosome="I"
/biovar="1"
gene <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=62288991&itemID=2031&view=gbwithparts> 784..2274
/gene="dnaA"
/locus_tag="BruAb1_0001"
/db_xref="GeneID:3339217 <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids=3339217>"
CDS <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=62288991&itemID=1&view=gbwithparts> 784..2274
/gene="dnaA"
/locus_tag="BruAb1_0001"
/note="similar to BR0001, chromosomal replication
initiator protein DnaA"
/codon_start=1
/transl_table=11 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG11>
/product="DnaA, chromosomal replication initiator protein"
/protein_id="YP_220785.1 <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=YP_220785.1>"
/db_xref="GI:62288992"
/db_xref="GeneID:3339217 <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids=3339217>"
/translation="MKMDSAVSEEAFERLTAKLKARVGGEIYSSWFGRLKLDDISKSI
VRLSVPTAFLRSWINNHYSELLTELWQEENPQILKVEVVVRGVSRVVRSAAPAETCDN
AEAKPAVTPREKMVFPVGQSFGGQSLGEKRGSAVVAESAAATGAVLGSPLDPRYTFDT
FVDGASNRVALAAARTIAEAGSSAVRFNPLFIHASVGLGKTHLLQAIAAAALQRQEKA
RVVYLTAEYFMWRFATAIRDNNALSFKEQLRDIDLLVIDDMQFLQGKSIQHEFCHLLN
TLLDSAKQVVVAADRAPSELESLDVRVRSRLQGGVALEVAAPDYEMRLEMLRRRLASA
QCEDASLDIGEEILAHVARTVTGSGRELEGAFNQLLFRQSFEPNISIDRVDELLGHLT
RAGEPKRIRIEEIQRIVARHYNVSKQDLLSNRRTRTIVKPRQVAMYLAKMMTPRSLPE
IGRRFGGRDHTTVLHAVRKIEDLVGADTKLAQELELLKRLINDQAA"
...
ORIGIN
1 ttttccacac ttatccacag ggcgcgggcg ggactcggtt gcccctctga gtcaagcata
...
I consider myself a newbie to GUS and the above questions may be naive to many of you. However, your help is highly appreciated.
Thanks again.
- Tony
Chris Stoeckert wrote:
> Hi Tony,
> A beta release of the plugin InsertSequenceFeatures.pm is now
> available for loading GenBank records (as well as other formats). The
> semantics of how to use the GUS tables for this purpose are encoded in
> that plugin. Is that what you were asking?
> Chris
>
> On Sep 2, 2005, at 10:31 AM, Tony Zhang wrote:
>
>> This is old topic and it may have been discussed many times. Still, I
>> would like to get suggestion again about how to use GUS to store DNA,
>> CDS, and corresponding protein sequence. Suppose I have one original
>> record in Genkbank format. Thanks.
>>
>> - Tony
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing
>> & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> <mailto:Gus...@li...>
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
> Chris Stoeckert, Ph.D.
>
> Research Associate Professor, Dept. of Genetics
>
> 1415 Blockley Hall, Center for Bioinformatics
>
> 423 Guardian Dr., University of Pennsylvania
>
> Philadelphia, PA 19104
>
> Ph: 215-573-4409 FAX: 215-573-3111
>
>
|
|
From: Steve F. <sfi...@pc...> - 2005-09-04 16:39:39
|
folks- The NASequence table has two columns dealing with the type of the sequence, one a link to Dots.SequenceType, the other a link to SRes.SequenceOntology. The new InsertSequenceFeatures plugin allows you so specify either or both of these. The plugin requires you to have already loaded the SO, even if you don't use it for the sequence type, because it is needed for the features. however, if you want to use SequenceType, you will have needed to populate the SequenceType table. There is no standard or agreed upon vocabulary to use. Nor is there a plugin to load this CV. I am wondering: why do we need SequenceType when we now have the SO? Perhaps it is time to abandon SequenceType. steve |
|
From: Steve F. <sfi...@pc...> - 2005-09-04 16:28:49
|
folks- when we load feature data, especially from genbank, it is possible that almost any feature might be associated with a gene name. note, this is different than the feature being in a feature tree rooted at a gene feature. fewer features are in those. as it stands now, gus has two ways of dealing with this: 1. some features have a view-column for name called 'gene' 2. there is also the NAGene table (which should be renamed GeneName, because 'name' is its only attribute) and features can be linked to it via NAFeatureNAGene. I propose that in 3.5 we: 1. ignore the 'gene' attribute 2. instead, only use the NAGene table to store gene names In 3.6 I propose that we: 1. lose the 'gene' attribute in all feature subclasses 2. rename NAGene to GeneName and NAFeatureNAGene to NAFeatureGeneName objections, encouragements? steve |
|
From: Chris S. <sto...@pc...> - 2005-09-02 20:32:51
|
Hi Tony, A beta release of the plugin InsertSequenceFeatures.pm is now available for loading GenBank records (as well as other formats). The semantics of how to use the GUS tables for this purpose are encoded in that plugin. Is that what you were asking? Chris On Sep 2, 2005, at 10:31 AM, Tony Zhang wrote: > This is old topic and it may have been discussed many times. Still, > I would like to get suggestion again about how to use GUS to store > DNA, CDS, and corresponding protein sequence. Suppose I have one > original record in Genkbank format. Thanks. > > - Tony > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * > Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/ > bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 |
|
From: Tony Z. <fz...@vb...> - 2005-09-02 14:31:25
|
This is old topic and it may have been discussed many times. Still, I would like to get suggestion again about how to use GUS to store DNA, CDS, and corresponding protein sequence. Suppose I have one original record in Genkbank format. Thanks. - Tony |
|
From: Deborah P. <pi...@pc...> - 2005-08-31 17:43:44
|
Wouldn't it be better to avoid using dots.SequenceType, a table for
which there is no controlled vocabulary, and instead use the
sres.sequenceontology.term_name to get a
sequenceontology.sequence_ontology_id? Especially since the SO file will
have been loaded. It seems as if that would be a minor change to the plugin.
Debbie
Steve Fischer wrote:
> for those of you who are using the beta version of the ISF plugin:
> 1. i will improve its documentation to indicate what it expects to
> already be in the database:
> - SequenceOntology (InsertSequenceOntology plugin)
> - NCBI Taxon (LoadTaxon plugin)
> - External database and release (InsertExternalDatabase and
> InsertExternalDatabaseRls plugins)
> - at least one row in SequenceType so you can say what type of
> sequence you are loading (you can use LoadRow plugin for this)
>
> 2. i will improve the error messages so that it better detects the
> absence of these, and makes it more clear what to do.
>
> About loading SO:
> 1. can you send the SO term with definition that is too big?
>
> 2. i understand about the rollback. we have been discussing how to
> undo a plugin. for now, you need to do it with sql.
>
> Thanks for helping us make this plugin better.
>
> steve
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing
> & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
|
|
From: Steve F. <sfi...@pc...> - 2005-08-31 17:32:55
|
for those of you who are using the beta version of the ISF plugin:
1. i will improve its documentation to indicate what it expects to
already be in the database:
- SequenceOntology (InsertSequenceOntology plugin)
- NCBI Taxon (LoadTaxon plugin)
- External database and release (InsertExternalDatabase and
InsertExternalDatabaseRls plugins)
- at least one row in SequenceType so you can say what type of
sequence you are loading (you can use LoadRow plugin for this)
2. i will improve the error messages so that it better detects the
absence of these, and makes it more clear what to do.
About loading SO:
1. can you send the SO term with definition that is too big?
2. i understand about the rollback. we have been discussing how to
undo a plugin. for now, you need to do it with sql.
Thanks for helping us make this plugin better.
steve
|
|
From: <fab...@de...> - 2005-08-31 16:15:18
|
Hello, We're now trying to use the new plugin InsertSequenceFeatures. We were tr= ying to load c.hom.gb with it, but an error ocurred. The command: ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile /usr/local/GUS/gus_home/config/genbank2gus.xml --seqFile c.hom.gb --fileF= ormat 'genbank' --extDbName 'genbank' --extDbRlsVer 'unknown' --soCvsVersion '1= .42' And error: ERROR: null value in column "aa_sequence_id" violates not-null constrain= t DBD::Pg::st execute failed: ERROR: null value in column "aa_sequence_id" violates not-null constraint at /usr/local/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147, <GE= N12> line 2179. So, we tryed to load a nucleotide genbank and the error changes: ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile /usr/local/GUS/gus_home/config/genbank2gus.xml --seqFile c.hom.gb --fileF= ormat 'genbank' --extDbName 'genbank' --extDbRlsVer 'unknown' --soCvsVersion '1= .42' And the error was: ERROR: Can't locate object method "geneNameIds" via package "GUS::Supported::Plugin::InsertSequenceFeatures" at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatu= res.pm line 886, <GEN12> line 58. I saw in the InsertSequenceFeatures.pm that the function "geneNameIds" is= n't defined. It's been used but the function doesn't exist. Is it ok? Thanks a lot, Fabricio. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
|
From: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-31 15:04:10
|
Hi Steve,
Thanks for your reply.Even after using new genbank2gus.xml file it
requires SO=20
definition data in the SRES.SequenceOntology table.
Any way, I downloaded the SO definition data and loaded in the system
using
InsertSequenceOntology.pm.
Problem noticed in tn loading SO data :
1. Field size in SRES.sequenceOntology table for "definition" column
is 255, which is=20
insufficient to hold some of definition whose size is about 1004.=20
So, pl. take appropriate action to increase the field size for
future GUS releases.
2. Even after the plugin was failing, it loaded data partially in the
table.
(I think it should rollback entirely)
Again back to InsertSequenceFeatures plugin, it is failing even after
loading the
sequence ontology data. This time it is throwing error message
mentioned below.
It looks to me that this pluin requires some master data in the
system prior to run,
Do we have any kind of writeup about the prerequisite data.
[oragus35@rdevse02 oragus35]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --seqFile
/u02/Downloads/data/Fra6570.genbank --mapFile
/home/oragus35/genbank2gus.xml --fileFormat 'genbank' --extDbName
'genBank' --extDbRlsVer 147 --soCvsVersion 3354
Wed Aug 31 10:58:36 2005 ARGS algoinvo 1
Wed Aug 31 10:58:36 2005 ARGS comment
Wed Aug 31 10:58:36 2005 ARGS commit 0
Wed Aug 31 10:58:36 2005 ARGS debug 0
Wed Aug 31 10:58:36 2005 ARGS description
Wed Aug 31 10:58:36 2005 ARGS downloadURL
Wed Aug 31 10:58:36 2005 ARGS extDbName genBank
Wed Aug 31 10:58:36 2005 ARGS extDbRlsDate
Wed Aug 31 10:58:36 2005 ARGS extDbRlsVer 147
Wed Aug 31 10:58:36 2005 ARGS failDir
Wed Aug 31 10:58:36 2005 ARGS fileFormat genbank
Wed Aug 31 10:58:36 2005 ARGS filename
Wed Aug 31 10:58:36 2005 ARGS gff2GroupTag GenePrediction
Gene
Wed Aug 31 10:58:36 2005 ARGS gffFormat 2
Wed Aug 31 10:58:36 2005 ARGS group
Wed Aug 31 10:58:36 2005 ARGS gusconfigfile =20
/home/oragus35/GUS/gus.properties
Wed Aug 31 10:58:36 2005 ARGS help
Wed Aug 31 10:58:36 2005 ARGS helpHTML
Wed Aug 31 10:58:36 2005 ARGS isUpdateMode 0
Wed Aug 31 10:58:36 2005 ARGS mapFile=20
/home/oragus35/genbank2gus.xml
Wed Aug 31 10:58:36 2005 ARGS naSequenceSubclass
Wed Aug 31 10:58:36 2005 ARGS project
Wed Aug 31 10:58:36 2005 ARGS projectName
Wed Aug 31 10:58:36 2005 ARGS restartPoint
Wed Aug 31 10:58:36 2005 ARGS seqFile=20
/u02/Downloads/data/Fra6570.genbank
Wed Aug 31 10:58:36 2005 ARGS seqIdColumn source_id
Wed Aug 31 10:58:36 2005 ARGS seqSoTerm
Wed Aug 31 10:58:36 2005 ARGS seqType DNA
Wed Aug 31 10:58:36 2005 ARGS soCvsVersion 3354
Wed Aug 31 10:58:36 2005 ARGS sqlVerbose 0
Wed Aug 31 10:58:36 2005 ARGS testNumber
Wed Aug 31 10:58:36 2005 ARGS user
Wed Aug 31 10:58:36 2005 ARGS verbose 0
Wed Aug 31 10:58:36 2005 ARGS veryVerbose 0
Wed Aug 31 10:58:36 2005 COMMIT commit off
Wed Aug 31 10:58:36 2005 ALGINVID 427
ERROR:
Failed to retrieve GUS::Model::DoTS::SequenceType id for name =3D 'DNA' =
at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 1063, <GEN0> line 73767.
STACK TRACE:
at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 1063
=20
GUS::Supported::Plugin::InsertSequenceFeatures::getIdFromCache('GUS::Sup
ported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'seqTypeCache', 'DNA', 'GUS::Model::DoTS::SequenceType', 'name') called
at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 800
=20
GUS::Supported::Plugin::InsertSequenceFeatures::getSeqTypeId('GUS::Suppo
rted::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'DNA') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 580
=20
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS
::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'Bio::Seq::RichSeq=3DHASH(0xa064044)', 42) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 547
=20
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS:
:Supported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'Bio::Seq::RichSeq=3DHASH(0xa064044)') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 348
=20
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
gin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'HASH(0x90288dc)') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 469
eval {...} called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 461
=20
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
:GusApplication=3DHASH(0x811e180)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
=20
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
ication=3DHASH(0x811e180)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
=20
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x811e180)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
=20
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x811e180)',
'ARRAY(0x811e918)') called at /home/oragus35/GUS/gus_home/bin/ga line 11
Thanks
Sanjeev=20
-----Original Message-----
From: Steve Fischer [mailto:sfi...@pc...]=20
Sent: Tuesday, August 30, 2005 6:21 PM
To: Kumar, Sanjeev (Contr)
Cc: gus...@li...
Subject: Re: [GUSDEV] Problem in running "InsertSequenceFeatures.pm'
sanjeev-
use this mapping file:
$GUS_HOME/config/genbank2gus.xml
the one you are using is old and is using SO ids instead of SO terms,
which are what is needed.
steve
Kumar, Sanjeev (Contr) wrote:
> Hi,
> Can anyone help me in uns=3Dderstanding and resolving the problem.
> I am getting this problem when I am trying to run and load genbank=20
>sequence file.
>
>Thanks
>Sanjeev
>
>-----Original Message-----
>From: Sanjeev Kumar [mailto:sk...@bi...]
>Sent: Tuesday, August 30, 2005 5:51 PM
>To: Kumar, Sanjeev (Contr)
>Subject: (no subject)
>
>[oragus35@rdevse02 oragus35]$ ga
>GUS::Supported::Plugin::InsertSequenceFeatures --seqFile=20
>/u02/Downloads/data/Fra6570.genbank --mapFile=20
>/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
>--fileFormat 'genbank' --extDbName 'genBank' --extDbRlsVer 147=20
>--soCvsVersion 3354
>Tue Aug 30 18:10:56 2005 ARGS algoinvo 1
>Tue Aug 30 18:10:56 2005 ARGS comment
>Tue Aug 30 18:10:56 2005 ARGS commit 0
>Tue Aug 30 18:10:56 2005 ARGS debug 0
>Tue Aug 30 18:10:56 2005 ARGS description
>Tue Aug 30 18:10:56 2005 ARGS downloadURL
>Tue Aug 30 18:10:56 2005 ARGS extDbName genBank
>Tue Aug 30 18:10:56 2005 ARGS extDbRlsDate
>Tue Aug 30 18:10:56 2005 ARGS extDbRlsVer 147
>Tue Aug 30 18:10:56 2005 ARGS failDir
>Tue Aug 30 18:10:56 2005 ARGS fileFormat genbank
>Tue Aug 30 18:10:56 2005 ARGS filename
>Tue Aug 30 18:10:56 2005 ARGS gff2GroupTag GenePrediction
>Gene
>Tue Aug 30 18:10:56 2005 ARGS gffFormat 2
>Tue Aug 30 18:10:56 2005 ARGS group
>Tue Aug 30 18:10:56 2005 ARGS gusconfigfile =20
>/home/oragus35/GUS/gus.properties
>Tue Aug 30 18:10:56 2005 ARGS help
>Tue Aug 30 18:10:56 2005 ARGS helpHTML
>Tue Aug 30 18:10:56 2005 ARGS isUpdateMode 0
>Tue Aug 30 18:10:56 2005 ARGS mapFile=20
>/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
>Tue Aug 30 18:10:56 2005 ARGS naSequenceSubclass
>Tue Aug 30 18:10:56 2005 ARGS project
>Tue Aug 30 18:10:56 2005 ARGS projectName
>Tue Aug 30 18:10:56 2005 ARGS restartPoint
>Tue Aug 30 18:10:56 2005 ARGS seqFile=20
>/u02/Downloads/data/Fra6570.genbank
>Tue Aug 30 18:10:56 2005 ARGS seqIdColumn source_id
>Tue Aug 30 18:10:56 2005 ARGS seqSoTerm
>Tue Aug 30 18:10:56 2005 ARGS seqType DNA
>Tue Aug 30 18:10:56 2005 ARGS soCvsVersion 3354
>Tue Aug 30 18:10:56 2005 ARGS sqlVerbose 0
>Tue Aug 30 18:10:56 2005 ARGS testNumber
>Tue Aug 30 18:10:56 2005 ARGS user
>Tue Aug 30 18:10:56 2005 ARGS verbose 0
>Tue Aug 30 18:10:56 2005 ARGS veryVerbose 0
>Tue Aug 30 18:10:56 2005 COMMIT commit off
>Tue Aug 30 18:10:56 2005 ALGINVID 406
>
>ERROR:
>
>USER ERROR: Mapping file
>'/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml' or cmd
>line args are using the following SO terms that are not found in the=20
>database for SO CVS version '3354': SO:0000297, SO:0000234, SO:0000725,
>SO:0000110, SO:0000704, SO:0000172, SO:0000418, SO:0000204, SO:0000557,
>SO:0000313, SO:0000141, SO:0000298, SO:0000657, SO:0000176, SO:0000185,
>SO:0000013, SO:0005836, SO:0000413, SO:0000173, SO:0000275, SO:0000140,
>SO:0000331, SO:0000274, SO:0000555, SO:0000188, SO:0000252, SO:0000167,
>SO:0000005, SO:0000410, SO:0000109, SO:0000492, SO:0000139, SO:0000174,
>SO:0000286, SO:0000673, SO:0000724, SO:0000178, SO:0000553, SO:0000563,
>SO:0000305, SO:0000147, SO:0000253, SO:0000478, SO:0000205, SO:0000723,
>SO:0000316, SO:0000302, SO:0000413, SO:0005850, SO:0000296, SO:0000185,
>SO:0000551, SO:0000175, SO:0000409, SO:0000419, SO:0000002
>
>STACK TRACE:
> at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line
>1189
> =20
>GUS::PluginMgr::Plugin::userError('GUS::Supported::Plugin::InsertSequen
>c
>eFeatures=3DHASH(0x85bea48)',
>'Mapping file \'/home/oragus35/ApiComplexa/DataLoad/doc/config...')
>called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc
>e
>Features.pm
>line 1108
> =20
>GUS::Supported::Plugin::InsertSequenceFeatures::getSoPrimaryKeys('GUS::
>S
>upported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)')
>called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenc
>e
>Features.pm
>line 335
> =20
>GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Pl
>u gin::InsertSequenceFeatures=3DHASH(0x85bea48)',
>'HASH(0x902894c)') called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 469
> eval {...} called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 461
> =20
>GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr
:
>:GusApplication=3DHASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 380
> =20
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApp
>l
>ication=3DHASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 288
> =20
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplica
>t
>ion=3DHASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 197
> =20
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplica
>t
>ion=3DHASH(0x811e180)',
>'ARRAY(0x811e918)') called at /home/oragus35/GUS/gus_home/bin/ga line=20
>11
>
>
>
>
>-------------------------------------------------------
>SF.Net email is Sponsored by the Better Software Conference & EXPO=20
>September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20
>Practices Agile & Plan-Driven Development * Managing Projects & Teams *
>Testing & QA Security * Process Improvement & Measurement *=20
>http://www.sqe.com/bsce5sf=20
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>
|
|
From: <hen...@gm...> - 2005-08-31 14:00:44
|
Hi Steve,
I tried uploading the file you provided in your email (at least part of it)=
,=20
and I got the following error:
(this WARNING repeats several times)
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for Skipping feature, attempting to=
=20
recover
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for Skipping feature, attempting to=
=20
recover
---------------------------------------------------
ERROR:
Can't call method "genus" on an undefined value at=20
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeature=
s.pm=20
line 812, <GEN29> line 1473.
STACK TRACE:
at=20
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeature=
s.pm=20
line 812
GUS::Supported::Plugin::InsertSequenceFeatures::getTaxonId('GUS::Supported:=
:Plugin::InsertSequenceFeatures=3DHASH(0x87071b0)',
'Bio::Seq::RichSeq=3DHASH(0x9414818)') called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeature=
s.pm=20
line 587
GUS::Supported::Plugin::InsertSequenceFeatures::constructNASequence('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x87071b0)',
'Bio::Seq::RichSeq=3DHASH(0x9414818)', 3734) called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeature=
s.pm=20
line 547
GUS::Supported::Plugin::InsertSequenceFeatures::bioperl2NASequence('GUS::Su=
pported::Plugin::InsertSequenceFeatures=3DHASH(0x87071b0)',
'Bio::Seq::RichSeq=3DHASH(0x9414818)') called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeature=
s.pm=20
line 348
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x87071b0)',
'HASH(0x91cf374)') called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 469
eval {...} called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x81bac20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 380
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x81bac20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 288
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x81bac20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at=20
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 197
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x81bac20)',
'ARRAY(0x81ce520)') called at /usr/local/GUS/gus_home/bin/ga line 1
When I did the build, as you instructed, I did not recreate the schema.=20
Should I do that?
Thanks,
Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
"As soon as you concern yourself with the "good" and "bad" of your fellows,=
=20
you create an opening in your heart for maliciousness to enter. Testing,=20
competing with, and criticizing others weaken and defeat you."
Morihei Ueshiba, O-Sensei (1883-1969)
|
|
From: Steve F. <sfi...@pc...> - 2005-08-30 22:21:26
|
sanjeev-
use this mapping file:
$GUS_HOME/config/genbank2gus.xml
the one you are using is old and is using SO ids instead of SO terms,
which are what is needed.
steve
Kumar, Sanjeev (Contr) wrote:
> Hi,
> Can anyone help me in uns=derstanding and resolving the problem.
> I am getting this problem when I am trying to run and load genbank
>sequence file.
>
>Thanks
>Sanjeev
>
>-----Original Message-----
>From: Sanjeev Kumar [mailto:sk...@bi...]
>Sent: Tuesday, August 30, 2005 5:51 PM
>To: Kumar, Sanjeev (Contr)
>Subject: (no subject)
>
>[oragus35@rdevse02 oragus35]$ ga
>GUS::Supported::Plugin::InsertSequenceFeatures --seqFile
>/u02/Downloads/data/Fra6570.genbank --mapFile
>/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
>--fileFormat 'genbank' --extDbName 'genBank' --extDbRlsVer 147
>--soCvsVersion 3354
>Tue Aug 30 18:10:56 2005 ARGS algoinvo 1
>Tue Aug 30 18:10:56 2005 ARGS comment
>Tue Aug 30 18:10:56 2005 ARGS commit 0
>Tue Aug 30 18:10:56 2005 ARGS debug 0
>Tue Aug 30 18:10:56 2005 ARGS description
>Tue Aug 30 18:10:56 2005 ARGS downloadURL
>Tue Aug 30 18:10:56 2005 ARGS extDbName genBank
>Tue Aug 30 18:10:56 2005 ARGS extDbRlsDate
>Tue Aug 30 18:10:56 2005 ARGS extDbRlsVer 147
>Tue Aug 30 18:10:56 2005 ARGS failDir
>Tue Aug 30 18:10:56 2005 ARGS fileFormat genbank
>Tue Aug 30 18:10:56 2005 ARGS filename
>Tue Aug 30 18:10:56 2005 ARGS gff2GroupTag GenePrediction
>Gene
>Tue Aug 30 18:10:56 2005 ARGS gffFormat 2
>Tue Aug 30 18:10:56 2005 ARGS group
>Tue Aug 30 18:10:56 2005 ARGS gusconfigfile
>/home/oragus35/GUS/gus.properties
>Tue Aug 30 18:10:56 2005 ARGS help
>Tue Aug 30 18:10:56 2005 ARGS helpHTML
>Tue Aug 30 18:10:56 2005 ARGS isUpdateMode 0
>Tue Aug 30 18:10:56 2005 ARGS mapFile
>/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
>Tue Aug 30 18:10:56 2005 ARGS naSequenceSubclass
>Tue Aug 30 18:10:56 2005 ARGS project
>Tue Aug 30 18:10:56 2005 ARGS projectName
>Tue Aug 30 18:10:56 2005 ARGS restartPoint
>Tue Aug 30 18:10:56 2005 ARGS seqFile
>/u02/Downloads/data/Fra6570.genbank
>Tue Aug 30 18:10:56 2005 ARGS seqIdColumn source_id
>Tue Aug 30 18:10:56 2005 ARGS seqSoTerm
>Tue Aug 30 18:10:56 2005 ARGS seqType DNA
>Tue Aug 30 18:10:56 2005 ARGS soCvsVersion 3354
>Tue Aug 30 18:10:56 2005 ARGS sqlVerbose 0
>Tue Aug 30 18:10:56 2005 ARGS testNumber
>Tue Aug 30 18:10:56 2005 ARGS user
>Tue Aug 30 18:10:56 2005 ARGS verbose 0
>Tue Aug 30 18:10:56 2005 ARGS veryVerbose 0
>Tue Aug 30 18:10:56 2005 COMMIT commit off
>Tue Aug 30 18:10:56 2005 ALGINVID 406
>
>ERROR:
>
>USER ERROR: Mapping file
>'/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml' or cmd
>line args are using the following SO terms that are not found in the
>database for SO CVS version '3354': SO:0000297, SO:0000234, SO:0000725,
>SO:0000110, SO:0000704, SO:0000172, SO:0000418, SO:0000204, SO:0000557,
>SO:0000313, SO:0000141, SO:0000298, SO:0000657, SO:0000176, SO:0000185,
>SO:0000013, SO:0005836, SO:0000413, SO:0000173, SO:0000275, SO:0000140,
>SO:0000331, SO:0000274, SO:0000555, SO:0000188, SO:0000252, SO:0000167,
>SO:0000005, SO:0000410, SO:0000109, SO:0000492, SO:0000139, SO:0000174,
>SO:0000286, SO:0000673, SO:0000724, SO:0000178, SO:0000553, SO:0000563,
>SO:0000305, SO:0000147, SO:0000253, SO:0000478, SO:0000205, SO:0000723,
>SO:0000316, SO:0000302, SO:0000413, SO:0005850, SO:0000296, SO:0000185,
>SO:0000551, SO:0000175, SO:0000409, SO:0000419, SO:0000002
>
>STACK TRACE:
> at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line
>1189
>
>GUS::PluginMgr::Plugin::userError('GUS::Supported::Plugin::InsertSequenc
>eFeatures=HASH(0x85bea48)',
>'Mapping file \'/home/oragus35/ApiComplexa/DataLoad/doc/config...')
>called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
>Features.pm
>line 1108
>
>GUS::Supported::Plugin::InsertSequenceFeatures::getSoPrimaryKeys('GUS::S
>upported::Plugin::InsertSequenceFeatures=HASH(0x85bea48)')
>called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
>Features.pm
>line 335
>
>GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
>gin::InsertSequenceFeatures=HASH(0x85bea48)',
>'HASH(0x902894c)') called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 469
> eval {...} called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 461
>
>GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
>:GusApplication=HASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 380
>
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
>ication=HASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 288
>
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
>ion=HASH(0x811e180)',
>'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 197
>
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
>ion=HASH(0x811e180)',
>'ARRAY(0x811e918)') called at /home/oragus35/GUS/gus_home/bin/ga line 11
>
>
>
>
>-------------------------------------------------------
>SF.Net email is Sponsored by the Better Software Conference & EXPO
>September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
>Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
>Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
|
|
From: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-30 21:57:19
|
Hi,
Can anyone help me in uns=3Dderstanding and resolving the problem.
I am getting this problem when I am trying to run and load genbank
sequence file.
Thanks
Sanjeev
-----Original Message-----
From: Sanjeev Kumar [mailto:sk...@bi...]=20
Sent: Tuesday, August 30, 2005 5:51 PM
To: Kumar, Sanjeev (Contr)
Subject: (no subject)
[oragus35@rdevse02 oragus35]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --seqFile
/u02/Downloads/data/Fra6570.genbank --mapFile
/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
--fileFormat 'genbank' --extDbName 'genBank' --extDbRlsVer 147
--soCvsVersion 3354
Tue Aug 30 18:10:56 2005 ARGS algoinvo 1
Tue Aug 30 18:10:56 2005 ARGS comment
Tue Aug 30 18:10:56 2005 ARGS commit 0
Tue Aug 30 18:10:56 2005 ARGS debug 0
Tue Aug 30 18:10:56 2005 ARGS description
Tue Aug 30 18:10:56 2005 ARGS downloadURL
Tue Aug 30 18:10:56 2005 ARGS extDbName genBank
Tue Aug 30 18:10:56 2005 ARGS extDbRlsDate
Tue Aug 30 18:10:56 2005 ARGS extDbRlsVer 147
Tue Aug 30 18:10:56 2005 ARGS failDir
Tue Aug 30 18:10:56 2005 ARGS fileFormat genbank
Tue Aug 30 18:10:56 2005 ARGS filename
Tue Aug 30 18:10:56 2005 ARGS gff2GroupTag GenePrediction
Gene
Tue Aug 30 18:10:56 2005 ARGS gffFormat 2
Tue Aug 30 18:10:56 2005 ARGS group
Tue Aug 30 18:10:56 2005 ARGS gusconfigfile =20
/home/oragus35/GUS/gus.properties
Tue Aug 30 18:10:56 2005 ARGS help
Tue Aug 30 18:10:56 2005 ARGS helpHTML
Tue Aug 30 18:10:56 2005 ARGS isUpdateMode 0
Tue Aug 30 18:10:56 2005 ARGS mapFile=20
/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml
Tue Aug 30 18:10:56 2005 ARGS naSequenceSubclass
Tue Aug 30 18:10:56 2005 ARGS project
Tue Aug 30 18:10:56 2005 ARGS projectName
Tue Aug 30 18:10:56 2005 ARGS restartPoint
Tue Aug 30 18:10:56 2005 ARGS seqFile=20
/u02/Downloads/data/Fra6570.genbank
Tue Aug 30 18:10:56 2005 ARGS seqIdColumn source_id
Tue Aug 30 18:10:56 2005 ARGS seqSoTerm
Tue Aug 30 18:10:56 2005 ARGS seqType DNA
Tue Aug 30 18:10:56 2005 ARGS soCvsVersion 3354
Tue Aug 30 18:10:56 2005 ARGS sqlVerbose 0
Tue Aug 30 18:10:56 2005 ARGS testNumber
Tue Aug 30 18:10:56 2005 ARGS user
Tue Aug 30 18:10:56 2005 ARGS verbose 0
Tue Aug 30 18:10:56 2005 ARGS veryVerbose 0
Tue Aug 30 18:10:56 2005 COMMIT commit off
Tue Aug 30 18:10:56 2005 ALGINVID 406
ERROR:
USER ERROR: Mapping file
'/home/oragus35/ApiComplexa/DataLoad/doc/config/genbank2gus.xml' or cmd
line args are using the following SO terms that are not found in the
database for SO CVS version '3354': SO:0000297, SO:0000234, SO:0000725,
SO:0000110, SO:0000704, SO:0000172, SO:0000418, SO:0000204, SO:0000557,
SO:0000313, SO:0000141, SO:0000298, SO:0000657, SO:0000176, SO:0000185,
SO:0000013, SO:0005836, SO:0000413, SO:0000173, SO:0000275, SO:0000140,
SO:0000331, SO:0000274, SO:0000555, SO:0000188, SO:0000252, SO:0000167,
SO:0000005, SO:0000410, SO:0000109, SO:0000492, SO:0000139, SO:0000174,
SO:0000286, SO:0000673, SO:0000724, SO:0000178, SO:0000553, SO:0000563,
SO:0000305, SO:0000147, SO:0000253, SO:0000478, SO:0000205, SO:0000723,
SO:0000316, SO:0000302, SO:0000413, SO:0005850, SO:0000296, SO:0000185,
SO:0000551, SO:0000175, SO:0000409, SO:0000419, SO:0000002
STACK TRACE:
at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line
1189
=20
GUS::PluginMgr::Plugin::userError('GUS::Supported::Plugin::InsertSequenc
eFeatures=3DHASH(0x85bea48)',
'Mapping file \'/home/oragus35/ApiComplexa/DataLoad/doc/config...')
called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 1108
=20
GUS::Supported::Plugin::InsertSequenceFeatures::getSoPrimaryKeys('GUS::S
upported::Plugin::InsertSequenceFeatures=3DHASH(0x85bea48)')
called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
Features.pm
line 335
=20
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
gin::InsertSequenceFeatures=3DHASH(0x85bea48)',
'HASH(0x902894c)') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 469
eval {...} called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 461
=20
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
:GusApplication=3DHASH(0x811e180)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
=20
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
ication=3DHASH(0x811e180)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
=20
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x811e180)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
=20
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x811e180)',
'ARRAY(0x811e918)') called at /home/oragus35/GUS/gus_home/bin/ga line 11
|
|
From: Steve F. <sfi...@pc...> - 2005-08-30 18:54:31
|
it is now available for beta use in the svn repository. we will begin
our final testing of it this week.
you need these files:
$PROJECT_HOME/Gus/Supported/
config/genbank2gus.xml
lib/perl/BioFeatMapper.pm
lib/perl/BioFeatMapperSet.pm
lib/perl/SequenceIterator.pm
plugin/perl/InsertSequenceFeatures.pm
steve
Kumar, Sanjeev (Contr) wrote:
>Hi Steve,
> What is the status of the below mention Plugin?
> Can we have some kind of release time line for the same?
> I am not able to utilize the GUS3.5 because we don't have any kind of
>parser to parser
> GenBank genome sequence file.
>
>
>Thanks
>Sanjeev
>
>-----Original Message-----
>From: Steve Fischer [mailto:sfi...@pc...]
>Sent: Friday, August 12, 2005 12:08 PM
>To: Kumar, Sanjeev (Contr)
>Cc: Chris Stoeckert; Michael Saffitz
>Subject: Re: [GUSDEV] Issue in running new Plugin
>
>sanjeev-
>
>you'll have to work with ed on that. he has given you a pre-release
>version. i am working (starting today) to complete the testing of the
>supported plugin, which is
>GUS::Supported::Plugin::InsertSequenceFeatures.
>
>i hope to have it done in a couple of days.
>
>steve
>
>Kumar, Sanjeev (Contr) wrote:
>
>
>
>>Hi Chris,
>> Thanks for checking.I think all issues raised by me earlier are
>>resolved. I am working
>> on writing Plugin to load Prosite data.
>> I have a question regarding the new GBParser development status.
>> Although I got this new GBParser for testing with GUS3.5 from ED
>>Robinson.
>> It is not loading any sequence data, but I see some insert sql
>>generated for CORE
>> schema tables.
>> Steve, can you help me in this.
>>
>>Thanks
>>Sanjeev
>>
>>-----Original Message-----
>>From: Chris Stoeckert [mailto:sto...@pc...]
>>Sent: Wednesday, August 10, 2005 4:57 PM
>>To: Kumar, Sanjeev (Contr)
>>Cc: Steve Fischer; Michael Saffitz
>>Subject: Re: [GUSDEV] Issue in running new Plugin
>>
>>Hi Sanjeev,
>>Steve thinks this was a permission problem. Mike has granted you
>>permission now with your Wiki username and password so please try
>>
>>
>again.
>
>
>>Are you Ok with the other issues you raised?
>>Cheers,
>>Chris
>>
>>On Aug 5, 2005, at 10:41 AM, Kumar, Sanjeev (Contr) wrote:
>>
>>
>>
>>
>>
>>>Hi,
>>> I am having issue in running newly registered plugin.
>>> I have one new plug in which I registered and I tested it , it ran
>>>fine.
>>> AFter that I fixed some bug and then tried to run it gave me error
>>>saying that plugin has change I need to update it. But when I am
>>>trying to update the plug in it is not letting me do so. Errors are
>>>listed below :
>>>***************************************
>>>[oragus35@rdevse02 oragus35]$ ga GUS::Supported::Plugin::LoadPrositeDB
>>>--file /home/oragus35/prosite.dat --commit
>>>
>>>USER ERROR: The md5 checksum of
>>>GUS::Supported::Plugin::LoadPrositeDB's
>>>executable file (cvs revision 2943) doesn't match the md5 checksum in
>>>the database for that plugin and revision. IE, the plugin has been
>>>changed but not commited and updated. Please:
>>> - cvs commit the plugin file
>>> - use the build system to install it
>>> - run 'ga +update
>>>GUS::Supported::Plugin::LoadPrositeDB --commit'
>>>Aborting
>>>Issuing rollback() for database handle being DESTROY'd without
>>>explicit disconnect().
>>>Issuing rollback() for database handle being DESTROY'd without
>>>explicit disconnect().
>>>[oragus35@rdevse02 oragus35]$ ga +update
>>>GUS::Supported::Plugin::LoadPrositeDB --commit;
>>>Error: GUS::Supported::Plugin::LoadPrositeDB with CVS revision
>>>2943 is
>>>already registered. You don't need to do a +update.
>>>
>>>******************************************************************
>>>Pl. suggest me what needs to be done.
>>>
>>>Thanks
>>>Sanjeev
>>>
>>>
>>>-------------------------------------------------------
>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>>>Practices Agile & Plan-Driven Development * Managing Projects & Teams
>>>* Testing & QA Security * Process Improvement & Measurement *
>>>http://www.sqe.com/ bsce5sf
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
|
|
From: Ed R. <ero...@ug...> - 2005-08-30 16:42:56
|
I would wait for Steve's version for use in 3.5. -ed ---- Original message ---- >Date: Tue, 30 Aug 2005 12:24:51 -0400 >From: "Kumar, Sanjeev (Contr)" <San...@ng...> >Subject: RE: [GUSDEV] Issue in running new Plugin >To: "Steve Fischer" <sfi...@pc...> >Cc: "Chris Stoeckert" <sto...@pc...>, "Michael Saffitz" <msa...@pc...>, <gus...@li...> > >Hi Steve, > What is the status of the below mention Plugin? > Can we have some kind of release time line for the same? > I am not able to utilize the GUS3.5 because we don't have any kind of >parser to parser > GenBank genome sequence file. > > >Thanks >Sanjeev > >-----Original Message----- >From: Steve Fischer [mailto:sfi...@pc...] >Sent: Friday, August 12, 2005 12:08 PM >To: Kumar, Sanjeev (Contr) >Cc: Chris Stoeckert; Michael Saffitz >Subject: Re: [GUSDEV] Issue in running new Plugin > >sanjeev- > >you'll have to work with ed on that. he has given you a pre-release >version. i am working (starting today) to complete the testing of the >supported plugin, which is >GUS::Supported::Plugin::InsertSequenceFeatures. > >i hope to have it done in a couple of days. > >steve > >Kumar, Sanjeev (Contr) wrote: > >>Hi Chris, >> Thanks for checking.I think all issues raised by me earlier are >>resolved. I am working >> on writing Plugin to load Prosite data. >> I have a question regarding the new GBParser development status. >> Although I got this new GBParser for testing with GUS3.5 from ED >>Robinson. >> It is not loading any sequence data, but I see some insert sql >>generated for CORE >> schema tables. >> Steve, can you help me in this. >> >>Thanks >>Sanjeev >> >>-----Original Message----- >>From: Chris Stoeckert [mailto:sto...@pc...] >>Sent: Wednesday, August 10, 2005 4:57 PM >>To: Kumar, Sanjeev (Contr) >>Cc: Steve Fischer; Michael Saffitz >>Subject: Re: [GUSDEV] Issue in running new Plugin >> >>Hi Sanjeev, >>Steve thinks this was a permission problem. Mike has granted you >>permission now with your Wiki username and password so please try >again. >>Are you Ok with the other issues you raised? >>Cheers, >>Chris >> >>On Aug 5, 2005, at 10:41 AM, Kumar, Sanjeev (Contr) wrote: >> >> >> >>>Hi, >>> I am having issue in running newly registered plugin. >>> I have one new plug in which I registered and I tested it , it ran >>>fine. >>> AFter that I fixed some bug and then tried to run it gave me error >>>saying that plugin has change I need to update it. But when I am >>>trying to update the plug in it is not letting me do so. Errors are >>>listed below : >>>*************************************** >>>[oragus35@rdevse02 oragus35]$ ga GUS::Supported::Plugin::LoadPrositeDB >>>--file /home/oragus35/prosite.dat --commit >>> >>>USER ERROR: The md5 checksum of >>>GUS::Supported::Plugin::LoadPrositeDB's >>>executable file (cvs revision 2943) doesn't match the md5 checksum in >>>the database for that plugin and revision. IE, the plugin has been >>>changed but not commited and updated. Please: >>> - cvs commit the plugin file >>> - use the build system to install it >>> - run 'ga +update >>>GUS::Supported::Plugin::LoadPrositeDB --commit' >>>Aborting >>>Issuing rollback() for database handle being DESTROY'd without >>>explicit disconnect(). >>>Issuing rollback() for database handle being DESTROY'd without >>>explicit disconnect(). >>>[oragus35@rdevse02 oragus35]$ ga +update >>>GUS::Supported::Plugin::LoadPrositeDB --commit; >>>Error: GUS::Supported::Plugin::LoadPrositeDB with CVS revision >>>2943 is >>>already registered. You don't need to do a +update. >>> >>>****************************************************************** >>>Pl. suggest me what needs to be done. >>> >>>Thanks >>>Sanjeev >>> >>> >>>------------------------------------------------------- >>>SF.Net email is Sponsored by the Better Software Conference & EXPO >>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>>Practices Agile & Plan-Driven Development * Managing Projects & Teams >>>* Testing & QA Security * Process Improvement & Measurement * >>>http://www.sqe.com/ bsce5sf >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >> >> >> > > >------------------------------------------------------- >SF.Net email is Sponsored by the Better Software Conference & EXPO >September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices >Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA >Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
|
From: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-30 16:25:44
|
Hi Steve, What is the status of the below mention Plugin? Can we have some kind of release time line for the same? I am not able to utilize the GUS3.5 because we don't have any kind of parser to parser=20 GenBank genome sequence file.=20 =20 Thanks Sanjeev =20 -----Original Message----- From: Steve Fischer [mailto:sfi...@pc...]=20 Sent: Friday, August 12, 2005 12:08 PM To: Kumar, Sanjeev (Contr) Cc: Chris Stoeckert; Michael Saffitz Subject: Re: [GUSDEV] Issue in running new Plugin sanjeev- you'll have to work with ed on that. he has given you a pre-release=20 version. i am working (starting today) to complete the testing of the=20 supported plugin, which is GUS::Supported::Plugin::InsertSequenceFeatures. i hope to have it done in a couple of days. steve Kumar, Sanjeev (Contr) wrote: >Hi Chris, > Thanks for checking.I think all issues raised by me earlier are=20 >resolved. I am working > on writing Plugin to load Prosite data. > I have a question regarding the new GBParser development status. > Although I got this new GBParser for testing with GUS3.5 from ED=20 >Robinson. > It is not loading any sequence data, but I see some insert sql=20 >generated for CORE > schema tables. > Steve, can you help me in this. > =20 >Thanks >Sanjeev > >-----Original Message----- >From: Chris Stoeckert [mailto:sto...@pc...] >Sent: Wednesday, August 10, 2005 4:57 PM >To: Kumar, Sanjeev (Contr) >Cc: Steve Fischer; Michael Saffitz >Subject: Re: [GUSDEV] Issue in running new Plugin > >Hi Sanjeev, >Steve thinks this was a permission problem. Mike has granted you=20 >permission now with your Wiki username and password so please try again. >Are you Ok with the other issues you raised? >Cheers, >Chris > >On Aug 5, 2005, at 10:41 AM, Kumar, Sanjeev (Contr) wrote: > > =20 > >>Hi, >> I am having issue in running newly registered plugin. >> I have one new plug in which I registered and I tested it , it ran=20 >>fine. >> AFter that I fixed some bug and then tried to run it gave me error=20 >>saying that plugin has change I need to update it. But when I am=20 >>trying to update the plug in it is not letting me do so. Errors are=20 >>listed below : >>*************************************** >>[oragus35@rdevse02 oragus35]$ ga GUS::Supported::Plugin::LoadPrositeDB >>--file /home/oragus35/prosite.dat --commit >> >>USER ERROR: The md5 checksum of >>GUS::Supported::Plugin::LoadPrositeDB's >>executable file (cvs revision 2943) doesn't match the md5 checksum in=20 >>the database for that plugin and revision. IE, the plugin has been=20 >>changed but not commited and updated. Please: >> - cvs commit the plugin file >> - use the build system to install it >> - run 'ga +update >>GUS::Supported::Plugin::LoadPrositeDB --commit' >>Aborting >>Issuing rollback() for database handle being DESTROY'd without=20 >>explicit disconnect(). >>Issuing rollback() for database handle being DESTROY'd without=20 >>explicit disconnect(). >>[oragus35@rdevse02 oragus35]$ ga +update=20 >>GUS::Supported::Plugin::LoadPrositeDB --commit; >>Error: GUS::Supported::Plugin::LoadPrositeDB with CVS revision =20 >>2943 is >>already registered. You don't need to do a +update. >> >>****************************************************************** >>Pl. suggest me what needs to be done. >> >>Thanks >>Sanjeev >> >> >>------------------------------------------------------- >>SF.Net email is Sponsored by the Better Software Conference & EXPO=20 >>September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 >>Practices Agile & Plan-Driven Development * Managing Projects & Teams >>* Testing & QA Security * Process Improvement & Measurement *=20 >>http://www.sqe.com/ bsce5sf=20 >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> =20 >> > > =20 > |
|
From: Steve F. <sfi...@pc...> - 2005-08-29 19:44:28
|
henrique-
can you look in the plugin code and send the new() method. here is=20
what i have in the latest from svn:
sub new {
my ($class) =3D @_;
my $self =3D {};
bless($self,$class);
=
=20
$self->initialize({requiredDbVersion =3D> 3.5,
cvsRevision =3D> '$Revision: 3057 $', # cvs fills=20
this in!
name =3D> ref($self),
argsDeclaration =3D> $argsDeclaration,
documentation =3D> $documentation
});
=20
return $self;
}
=20
Henrique Juc=E1 wrote:
>Hi everyone,
>
>
>I'm trying to use LoadNRDB (rev. 2976)from GUS::Supported::Plugins.
>Before starting to use it, I decided to update it to the current
>version (rev. 3115). But when trying to update it (w/ 'ga +update ....
>--commit'), I got the following message:
>
>"[juca@desterrensis Plugin]$ ga +update
>GUS::Supported::Plugin::LoadNRDB --commit
>
>The plugin has an illegal cvs revision: '$Revision$'. If that doesn't
>include a revision number, then the plugin has never been checked into
>CVS. Please do so to give it an intial revision at
>/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 347."
>
>I saw the the $Id:$ line from the newest revision was empty in
>comparison the older revision that I'm using (in rv. 2976 the line was
>'$Id: LoadNRDB.pm 2976 2005-06-20 19:26:19Z jldommer $'). Is the
>latest (of all GUS) revision working? And if it is, how do I "give it
>a initial revision" (if I'm the one who has to do it)?
>
>
>Thanks,
>
> =20
>
|
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