[GUSDEV] questions on GUS::Supported::Plugin::InsertSequenceFeatures

[Jian Lu <jl...@vb...>]

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