<opt
  name="spbase"
  relid="1"
  date="20071228"
  make_current="1"
  >

  <no_csomesplit>1</no_csomesplit>
  <valid>1</valid> <!-- set 1 to skip db checks of above variables -->
  
  <about id="spbase"><![CDATA[
   See bulkfiles_template.xml for further documentation. 
   See site_defaults for included configurations.
  ]]></about>
  
  <include>site_defaults</include>
  
  <title>SpBase</title>
  
  <doc id="Release.txt"><![CDATA[
  Bulk output for Chado genome databases
  Database: ${title} 
  Species:  ${species}
  Release:  ${rel}, dated ${date} as ${relfull}
  ]]></doc>
    
  <release id="1" rel="spbase1"  dbname="SpBase" date="20071005"
    relfull="spbase_20071005"
    release_url="/genome/spbase/spbase-release1.html"
    />
  <release id="dummy" title="placeholder for xmlsimple"/>

  <GFF_source>SpBase</GFF_source>
  <org>spur</org>
  <species>Strongylocentrotus_purpuratus</species>
  <seq_ontology>sequence</seq_ontology> 
  <!-- see chadofeatsql ENV_default -->
  <golden_path>'supercontig'</golden_path>
  <featureprops>'Note','orf_classification'</featureprops>
  
  <featdump
    path="tmp/featdump/\w+.tsv"
    config="chadofeatsql"
    tag="feature_sql"
    type="feature_table"
    splitname="chadofeat"
    >
    <target>chromosomes</target>
    <target>features</target>
    <target>matches</target> <!--  //none in sgdlite1//  -->
    <target>analysis</target> <!--  //none in sgdlite1//  -->
  </featdump>

  <fileset_override
    name="fff"
    path="fff/.+\.fff"
    input="feature_table"
    title="Genome features"
    config="spbasefeatconf"
    handler="FeatureWriter"
    dogzip="0"
    />
  <fileset_override id="dummy" title="placeholder for xmlsimple"/>


  
  <!-- feature sets to make fasta bulk files -->
  <featset>chromosome</featset>
  <featset>gene</featset>
  <!-- <featset>CDS</featset> -->
  <featset>CDS_translation</featset>
  <featset>ncRNA</featset>
  <featset>transposon</featset>
  <featset>gene_extended2000</featset>
  <featset>intergenic</featset>
<!--   <featset>translation</featset> // none in sgdlite; make from CDS ? -->

  <!-- feature sets to make blast indices -->
  <blastset>chromosome</blastset>
  <blastset>gene</blastset>
  <blastset>CDS_translation</blastset>
  <blastset>ncRNA</blastset>
  <blastset>intergenic</blastset>

<!-- 
dgg: 0712: is there bug in chr dna dump requiring organism entry in organisms.xml
when found in main conf.xml and also in chado organism table?

12      S.purpuratus    Strongylocentrotus      purpuratus      sea urchin      1525779 

log:

Automaking dna files
make chromosomes= all scaffold1 scaffold10 scaffold100 scaffold1000 scaffold10000 scaffold100000 scaffol
d100001 scaffold100002 scaffold100003 scaffold100004 scaffold100005 scaffold100006 scaffold100007 scaffo
ld100008 scaffold100009 scaffold10001 scaffold100010 scaffold100011 scaffold100012 scaffold100013 .. mor
e ..
with featfiles= spur-all-spbase1.fff
with dnafiles= 
Missing dna files; make with -dnadump

Config2: read: conf/bulkfiles/fastawriter.xml ok=1
Config: title = Fasta file writer; date = 20051217;  from conf/bulkfiles/fastawriter.xml
readConfig:pass2 for variables=species org date title datadir rel relfull relid release_url release_id r
elease_date GFF_source taxon ftp_url golden_path seq_ontology addids title addmd5sum writeemptyrecords a
ddcrc64 perchr about makeall outformats date allowanyfeat informat dropnotes dogzip name

FastaWriter::makeFiles
openInput[0]: name=spur-all-spbase1.fff, type=feature/fff, /usr/local/bio/argos/gmod/gmtmp/GMODTools/dat
a/genomes/Strongylocentrotus_purpuratus/spbase_20071005/fff/spur-all-spbase1.fff
procFasta featset=chromosome,gene,CDS_translation,ncRNA,transposon,gene_extended2000,intergenic

procFasta chromosome outh=/usr/local/bio/argos/gmod/gmtmp/GMODTools/data/genomes/Strongylocentrotus_purp
uratus/spbase_20071005/fasta/spur-all-chromosome-spbase1.fasta
     ^^ empty file
procFasta gene outh=/usr/local/bio/argos/gmod/gmtmp/GMODTools/data/genomes/Strongylocentrotus_purpuratus
/spbase_20071005/fasta/spur-all-gene-spbase1.fasta

...
fastaFromFFFloop: ft=gene,CDS_translation,ncRNA,transposon,gene_extended2000,intergenic
fastaFromDb featn=chromosome ?
fastaFromDb sql= 
select f.feature_id, t.name as type, f.residues, f.md5checksum, f.seqlen, f.name, f.uniquename
from feature f, organism o, cvterm t
where t.name in ('supercontig') and t.cvterm_id = f.type_id
and o.genus = '' and o.species = '' and o.organism_id = f.organism_id
            ^^^^^              ^^^^^^   
in FastaWriter:fastaFromDb:
  my $org= $self->{org};  
  my $rel= $self->{rel};  
  my($species,$genus) = ($self->handler->speciesFull($org),'');
  ($genus,$species)= split(/[_ ]/,$species,2);  


-->


</opt>
