<opt
  name="dmelr420"
  relid="420"
  date="20051104"
>
  <!-- see site_defaults for more included configs -->
  <include>site_defaults</include>
  
<!--  949997852  4 Nov 13:40 chado_dmel_r4_2_16.gz =?  dmel_r4.2_20050909 at fb.net -->

  <title>FlyBase Chado DB r4 </title>
  <about>
   Configurations to extract feature and sequence data for
   bulk files from FlyBase chado databases, including various
   release information.
  </about>

  <doc name="Release.txt"><![CDATA[
    Genome data from FlyBase
    Species:  ${species}
    Release:  ${rel}, dated ${date} as ${relfull}

    See release notes at <a href="${release_url}">${release_url}</a>
  ]]></doc>

  <include>fbreleases</include>

  <org>dmel</org>
  <species>Drosophila_melanogaster</species>
  <golden_path>'chromosome_arm'</golden_path>
  <seq_ontology>SO</seq_ontology>
  <featureprops>'cyto_range','dicistronic','gbunit'</featureprops>
  <GFF_source>FlyBase</GFF_source>

  <est_where_clause>AND (an.program = 'sim4' AND
    an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros'))
  </est_where_clause>
  <analysis_where_clause>AND NOT (an.program = 'sim4' AND
    an.sourcename IN ('na_dbEST.same.dmel','na_dbEST.diff.dmel','na_DGC.in_process.dros'))
  </analysis_where_clause>

  <featdump
    path="tmp/featdump/\w+.tsv"
    config="chadofeatsql"
    tag="feature_sql"
    type="feature_table"
    splitname="chadofeat"
    >
    <!-- ENV values moved up -->
    <!-- note: ests target replaces analysis EST exclusion above -->
    <target>chromosomes</target>
    <target>features</target>
    <target>analysis</target>
    <target>ests</target>
    <!-- <target>matches</target> -->  
    <!-- <target>synteny</target> -->
  </featdump>

  <!-- use to add parent ids to features FBgn|FBti ; NOT these - FBan|CG|CR -->
  <idpattern>(FBgn|FBti)\d+</idpattern>
  <!-- rename intron,UTRs to Parent-mRNA-in/utr ? -->
  <gmodel_parts_rename>0</gmodel_parts_rename>

</opt>
