<opt
  name="sgdbulk1"
  relid="1"
  >
  <!-- see site_defaults for more included configs -->
  <include>site_defaults</include>
  
  <title>SGD Lite rel 1</title>
  
  <doc name="Release.txt"><![CDATA[
  Genome file output for Chado genome databases
  Database: SGD Lite rel 1
  Software: Bio::GMOD::Bulkfiles
  
  Chado genome databases available (aug 2004) are
  ftp://flybase.net/genomes/Drosophila_melanogaster/current/pgsql/chado_r3_2_26_s.gz
  http://sgdlite.princeton.edu/download/sgdlite/2004_05_19_sgdlite.sql.gz

  QUICK TEST:
  # get soft
  cvs -d :pserver:anonymous@cvs.sourceforge.net:/cvsroot/gmod \
    co -d GMODTools schema/GMODTools 
  
  # load chado db to Postgres
  createdb sgdlite_20040519
  wget http://sgdlite.princeton.edu/download/sgdlite/2004_05_19_sgdlite.sql.gz
  (zcat *sgdlite.sql.gz | psql -d sgdlite_20040519 -f - ) >& log.load 
  
  # set root path to here and make bulkfiles
  env GMOD_ROOT=$PWD  ARGOS_ROOT=$PWD \
   perl -I./GMODTools/lib/ GMODTools/bin/bulkfiles.pl sgdbulk1
  ]]></doc>
  

  <release id="1" rel="sgdr1"  dbname="sgdlite_20040519" date="20040519"
    relfull="sgdlite_20040519"
    release_url="/annot/sgdlite-release1.html"
    />
  <release id="0" rel="sgdr1"  dbname="sgdlite_20040519" date="20040519"
    relfull="sgdlite_20040519"
    release_url="/annot/sgdlite-release1.html"
    />
  <!-- need two+ release entries for config reader .. -->


  <db
    driver="Pg"
    name="sgdlite_20040519"
    host="localhost"
    port="7302"
    user=""
    password=""
    />

  <org>scer</org>
  <species>Saccharomyces cerevisiae</species>
  

  <featdump
    path="tmp/featdump/\w+.tsv"
    config="chadofeatsql"
    tag="feature_sql"
    type="feature_table"
    splitname="chadofeat"
    >
    <target>chromosomes</target>
    <target>features</target>
<!--  //none in sgdlite1//  <target>matches</target> -->
<!--  //none in sgdlite1//  <target>analysis</target> -->
  </featdump>
  

  <fileset_override
    name="fff"
    path="fff/.+\.fff"
    title="FFF Genome features"
    config="sgdfeatconf"
    handler="FeatureWriter"
    dogzip="1"
    />
  <fileset_override name="dummy"/>
  

  <idpattern></idpattern>

  <!-- feature sets to make fasta bulk files -->
  <featset>chromosome</featset>

  <featset>gene</featset>
  <featset>CDS</featset>
<!--   <featset>translation</featset> // no translations in sgdlite db -->
  <featset>tRNA</featset>
  <featset>miscRNA</featset>
  <featset>transposon</featset>
  <featset>gene_extended2000</featset>
  <featset>intergenic</featset>


  <!-- featmap moved to common bulkfiles/chadofeatconv
    but can override here if desired to add/replace/delete -->

<!-- sgd variant for this feature -->
  <featmap
    name="transposon"
    types="transposable_element_gene"
    typelabel="transposable_element"
    />

  <doc name="Test-results.txt"><![CDATA[
  Test for GMOD::Bulkfile processor
  aug 04, d.gilbert 
  
  dghome2% ls $sgr
  /bio/biodb/flybase/data2/fban/sgdlite_20040519:
  chadofeat-summary.txt  fasta/                 gff/                   tmp/
  dna/                   fff/                   gnomap/                
  
  dghome2% du $sgr
  24052   /bio/biodb/flybase/data2/fban/sgdlite_20040519/dna
  9928    /bio/biodb/flybase/data2/fban/sgdlite_20040519/fasta
  944     /bio/biodb/flybase/data2/fban/sgdlite_20040519/fff
  924     /bio/biodb/flybase/data2/fban/sgdlite_20040519/gff
  0       /bio/biodb/flybase/data2/fban/sgdlite_20040519/gnomap
  3980    /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp/featdump
  3980    /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp
  39836   /bio/biodb/flybase/data2/fban/sgdlite_20040519

  # Summary of features for Saccharomyces cerevisiae from SGD Chado DB Lite r1  [20040519]
  # ALL chromosomes
  ARS     59     
  CDS     7050
  centromere      16
  chromosome      17
  gene    13645
  long_terminal_repeat    382
  ncRNA   14
  non_transcribed_region  3
  noncoding_exon  466
  rRNA    56
  region  78
  repeat_family   110
  retrotransposon 50
  snRNA   14
  snoRNA  135
  tRNA    347
  telomere        32
  transcribed_spacer_region       16
  transposable_element_gene       100

  == process log ==
  DBI->connect( dbi:Pg:dbname=sgdlite_20040519;host=localhost;port=7302 )
  do sql  views view
  sql dump chromosomes feature_table /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp/featdump/
  chromosomes.tsv
  sql dump chromosomes n rows=17
  sql dump features feature_table /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp/featdump/fea
  tures.tsv
  sql dump features n rows=22573
  sortNSplitByChromosome:

  dumpChromosomeBases /bio/biodb/flybase/data2/fban/sgdlite_20040519/dna/scer_chrI_dna_sgdr1.raw
  ...

  makeFiles: outformats= fff gff fasta
  openInput: type=feature/table part=0 
  openInput: name=chrI, type=feature/table, /bio/biodb/flybase/data2/fban/sgdlite_20040519/tmp/fe
  atdump/chadofeat-chrI.tsv
  # output /bio/biodb/flybase/data2/fban/sgdlite_20040519/fff/scer_chrI_sgdr1.fff (append=0)
  # output /bio/biodb/flybase/data2/fban/sgdlite_20040519/gff/scer_chrI_sgdr1.gff (append=0)
  # output /bio/biodb/flybase/data2/fban/sgdlite_20040519/fasta/scer_chrI_sgdr1.fasta (append=0)
  putFeats n=11, total=11, oid1=126750
  open dnafile /bio/biodb/flybase/data2/fban/sgdlite_20040519/dna/scer_chrI_dna_sgdr1.raw, length
  =230210
  putFeats n=17, total=25, oid1=126761

  processChadoTable ndone = 1737
  openInput: type=feature/table part=18 
  openInput: nothing matches part=18
  makeFiles: done
  ]]></doc>

</opt>
