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From: Jian Lu <jl...@vb...> - 2005-09-22 21:47:53
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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
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