<opt
  name="featuresets"
  date="20040821"
  >
 
  <title>Chado Feature mapping info</title>
 
  <about>
    
    These are configurations for converting chado feature table dumps to
    standard feature/sequence files. Much of below specifies how to
    process different features (tied to methods in ChadoFeatDump.pm
    
    These configs are mostly data-set independent, but may
    need changing for some genome data sets.
    
    Used mostly now by Bulkfiles/FastaWriter.pm

   featmap for feature sets that need reprocessing, attributes: 
    name = feature set name
    types = feature types, space delimited (in fff/gff)
    typelabel = type to use in output header, paired with types list
    subrange = expansion/extraction range to add to feature location;
             readseq syntax not yet supported, i.e. {start,end}+/-offset)
    fromdb = extract from chado database feature.residues field
             rather than chromosome dna file,
             for curated residues - transcript, translation)
    get_id = save id, dbxref fields for add to other (genemodel) features
    add_id = add id of parent feature (genemodel)
    note: translation type=protein is coded into various seq fetch programs

  </about>

  <!-- feature sets to make fasta bulk files -->
  <featset>gene</featset>
<!--   <featset>mRNA</featset> // duplicates transcript -->
  <featset>transcript</featset>
  <featset>CDS</featset>  <!-- dna of protein coding sequence -->
  <featset>translation</featset> <!-- protein aminos -->
<!--  <featset>CDS_translation</featset> --> <!-- alternate, create protein from dna -->
<!--   <featset>tRNA</featset>  -->
<!--   <featset>miscRNA</featset> -->
  <featset>ncRNA</featset> <!-- combines tRNA, miscRNA -->
  <featset>transposon</featset>
  <featset>pseudogene</featset>
  <featset>gene_extended2000</featset>
<!--   <featset>five_prime_UTR</featset> -->
<!--   <featset>three_prime_UTR</featset> -->
<!--   <featset>intron</featset> -->
  <featset>intergenic</featset>
  <featset>syntenic_region</featset> 
<!--   <featset>scaffold</featset>  --> <!-- see below confusion -->
  <featset>chromosome</featset>  <!-- stands for all ${golden_path} -->
<!--   <featset>EST</featset> --> <!-- if wanted; reagent seqs not on chromosomes -->
  
  <featmap id="gene" get_id="1" />
  <featmap id="five_prime_UTR" add_id="gene" />
  <featmap id="three_prime_UTR" add_id="gene" />
  <featmap id="intron" add_id="gene" />
  <featmap id="mRNA" add_id="gene" />
  <featmap id="CDS" add_id="gene" />

  <featmap id="translation"
    types="CDS protein"
    ALSO_types="polypeptide"
    typelabel="protein"
    dotranslate="1"
    fromdb="1"
    />
  <featmap id="CDS_translation"
    types="CDS"
    typelabel="protein"
    dotranslate="1"
    fromdb="0"
    />
  <featmap id="gene"
    types="gene"
    />
  <!-- feb05: problems here with mRNA vs ncRNA snRNA snoRNA rRNA tRNA 
    need a 'transcript' equivalent type in input data - fff ? 
    but for gff, other public files, need to use real RNA type.
    -->
  <featmap  name="transcript"
    types="mRNA"
    typelabel="transcript"
    fromdb="1"
    />
  <featmap  name="transposon"
    types="transposable_element"
    typelabel="transposable_element"
    />
  <featmap id="miscRNA"
    types="ncRNA snRNA snoRNA rRNA miRNA" 
    />
    <!-- this variant includes all non-prot-coding rnas -->
  <featmap id="ncRNA"
    types="ncRNA snRNA snoRNA rRNA tRNA miRNA" 
    />
  <featmap id="gene_extended2000"
    types="gene"
    typelabel="gene_ex2000"
    subrange="-2000..2000"
    />
  <featmap id="intergenic"
    types="gene"
    typelabel="intergenic"
    method="between"
    />
  <featmap id="EST"
    types="EST"
    fromdb="1"
    onlydb="1"
    />

  <!-- 200710: no_csomesplit config -->
  <featmap id="chromosome"
    types="${golden_path}"
    fromdb="1"
    onlydb="1"
    />

  <!-- many names used for this: 
    golden_path_region may be alternate, or supercontig 
    // use above chromosome, type=${golden_path} variable
  -->
  <featmap id="scaffold"   
    alt_name0 = "golden_path_region" 
    alt_name1 = "golden_path_fragment" 
    alt_name2 = "databank_scaffold"
    alt_name3 = "scaffold"
    alt_name4 = "supercontig"
    types="golden_path_region scaffold"
    typelabel="scaffold"
    NOT_fromdb="1"
    />

</opt>
