<opt
  name="dmelr430"
  relid="430"
  date="20060217"
>
  <!-- see site_defaults for more included configs -->
  <include>site_defaults</include>
  
  <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="relnotes.txt"><![CDATA[

   * rename this database id to something more usable:
    "FlyBase Annotation IDs":CG2671-PD,  e.g. to FBannot: or FBAnID:CG...

   * mito chromosome: (rename to standard name: Mt) mapchr_pattern
   feature_id |           name            |        uniquename         | dbxref_id |    type    | seqlen | type_id | organism_id | is_analysis
   10711770 | dmel_mitochondrion_genome | dmel_mitochondrion_genome |    671272 | chromosome |  19517 |     204 |           1 | f

    * drop these old release chrs:
    (X..2R)_r3	chromosome_arm 
    2Rnew_11460001	chromosome_arm 

  ]]></doc>

  <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>

    ${rel} adds 
  * dpse genes - synteny info  
  * dmel_mitochondrion_genome chromosome: renamed to standard Mt

  ]]></doc>

  <include>fbreleases</include>

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

  <!-- 
    rename_child_type affects whether non-coding genes are 
    segregated at gene level or at (pseudo)rna/transcript level.
    Esp. affects which fasta files get the nc type sequence : gene, pseudogene, ncRNA
  -->
  <rename_child_type>nonesuchfeature</rename_child_type> <!-- old: pseudogene|\w+RNA -->

  <!-- "MT", "Mt", and "mt" are all used: Mt perhaps more, mt in flybase gene names -->
  <mapchr_pattern name="1mtchr" from="\w+_mitochondrion_genome" to="mt"/>
  <mapchr_pattern name="3old"   from="\w+_r3" to=""/> <!-- drop these; old chrs release 3 -->
  <mapchr_pattern name="2new"   from="2Rnew_11460001" to=""/> <!-- drop these; old chrs release 3 -->
  <mapchr_pattern name="null"   from="" to=""/>

  <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"
    >
    <target>chromosomes</target>
    <target>features</target>
    <target>analysis</target>
    <target>ests</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>
