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Re: [GUSDEV] questions on GUS::Supported::Plugin::InsertSequenceFeatures
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From: Steve F. <sfi...@pc...> - 2005-09-22 22:02:02
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Jian- great... can you send snippets of your input file that show examples of the data that is not being handled? thanks, steve Jian Lu wrote: > I have successfully run InsertSequenceFeatures for Genbank file. > > However, I have a few questions: > 1) how does this plugin deal with sequence GI number? It seems it > didn't load GI number to SECONDARY_IDENTIFIER on > DoTS.ExternalNASequence. For example, for AE011191, GI:20520280 is > missed. > 2) how does this plugin deal with locus_tag? It doesn't load locus_tag > to SOURCE_ID on all NA feature tables such as DoTS.Transcript. > 3) how does this plugin deal with sequence topology? > > > > ga GUS::Supported::Plugin::InsertSequenceFeatures > --mapFile=$GUS_HOME/config/genbank2gus.x > ml --seqFile=/home/data/BRC_genomes/bacillus/AE011191 > --fileFormat=genbank --extDbName=GenBank --extDbRlsVer=138 > --soCvsVersion 1.48 --seqType=DNA --commit > Maximum number of objects set to 500000 > Maximum number of objects set to 500000 > Thu Sep 22 15:10:54 2005 ARGS algoinvo 1 > Thu Sep 22 15:10:54 2005 ARGS comment > Thu Sep 22 15:10:54 2005 ARGS commit 1 > Thu Sep 22 15:10:54 2005 ARGS debug 0 > Thu Sep 22 15:10:54 2005 ARGS defaultOrganism > Thu Sep 22 15:10:54 2005 ARGS description > Thu Sep 22 15:10:54 2005 ARGS downloadURL > Thu Sep 22 15:10:54 2005 ARGS extDbName GenBank > Thu Sep 22 15:10:54 2005 ARGS extDbRlsDate > Thu Sep 22 15:10:54 2005 ARGS extDbRlsVer 138 > Thu Sep 22 15:10:54 2005 ARGS failDir > Thu Sep 22 15:10:54 2005 ARGS fileFormat genbank > Thu Sep 22 15:10:54 2005 ARGS filename > Thu Sep 22 15:10:54 2005 ARGS gff2GroupTag > GenePrediction Gene > Thu Sep 22 15:10:54 2005 ARGS gffFormat 2 > Thu Sep 22 15:10:54 2005 ARGS group > Thu Sep 22 15:10:54 2005 ARGS gusconfigfile > /home/brcgusts/GUS/gus_home/.gus.properties > Thu Sep 22 15:10:54 2005 ARGS help > Thu Sep 22 15:10:54 2005 ARGS helpHTML > Thu Sep 22 15:10:54 2005 ARGS isUpdateMode 0 > Thu Sep 22 15:10:54 2005 ARGS mapFile > /home/brcgusts/GUS/gus_home/config/genbank2gus.xml > Thu Sep 22 15:10:54 2005 ARGS naSequenceSubclass > Thu Sep 22 15:10:54 2005 ARGS project > Thu Sep 22 15:10:54 2005 ARGS projectName > Thu Sep 22 15:10:54 2005 ARGS restartPoint > Thu Sep 22 15:10:54 2005 ARGS seqFile > /home/data/BRC_genomes/bacillus/AE011191 > Thu Sep 22 15:10:54 2005 ARGS seqIdColumn source_id > Thu Sep 22 15:10:54 2005 ARGS seqSoTerm > Thu Sep 22 15:10:54 2005 ARGS seqType DNA > Thu Sep 22 15:10:54 2005 ARGS soCvsVersion 1.48 > Thu Sep 22 15:10:54 2005 ARGS sqlVerbose 0 > Thu Sep 22 15:10:54 2005 ARGS testNumber > Thu Sep 22 15:10:54 2005 ARGS user > Thu Sep 22 15:10:54 2005 ARGS verbose 0 > Thu Sep 22 15:10:54 2005 ARGS veryVerbose 0 > Thu Sep 22 15:10:54 2005 COMMIT commit on > Thu Sep 22 15:10:54 2005 ALGINVID 4362 > Thu Sep 22 15:11:09 2005 Inserted 100 feature trees > Thu Sep 22 15:11:11 2005 RESULT Processed: > /home/data/BRC_genomes/bacillus/AE011191 : genbank > Seqs Inserted: 1 > Features Inserted: 426 > Feature Trees Inserted: 114 > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv or your > very > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
