<opt
  name="tognomap"
  date="20040821"
  
  indexonly="0"
  >
 
  <title>Genome Feature merge (genomic and cytology features)</title>
  <about>
    These configs help merge two or more fff feature sets
    for use with gnomap,gbrowse(fb) and such feature file uses
    
    Add these to per-release-db configs.
    Cut from mergeflyfeats4.pl and .xml config, d.gilbert, aug04
  </about>

  <noIDmap>_fragment|_junction|_mutation|_peptide|_UTR|_variant|
    chromosome|golden_path\b|source|
    enhancer|EST|cDNA|intron|
    misc|match|motif|sim4|
    mRNA|CDS|oligo|processed|\bprotein\b|
    transcription_start_site|protein_binding_site|
    polyA_site|\binsertion_site|
    repeat|regulatory_region|repeat_region</noIDmap>
  <!-- keep:
  transposable_element_insertion_site
  drop:  insertion_site polyA_site protein_binding_site transcription_start_site
  -->
  
  <indexidtype>^(gene|pseudogene|\w+RNA)</indexidtype>
  <indexidpattern>[A-Z]{2}gn\d+</indexidpattern>
  <nameisid>BAC</nameisid>
  <idcutdb>^(FlyBase|Gadfly|GB_protein|GO):</idcutdb>
  
  <informat>fff</informat>  
  <informat>dna</informat>  

  <seqids
    path="tmp/chado-fb.ids"
    date="20040721" 
  />

  <seqfeat
    path="fff/[\w\-\_]+.fff"
    date="20040804"
    seqfeat="1"
    name="Annotation feature parts" 
    >
    <drop>chromosome_band</drop>
    <drop>remark</drop>
    <drop>source</drop>
  </seqfeat>
  
  
  <cytofeat
    path="tmp/cytomap/(cyto-features|cytofeat)-[\w\-\_]+.tsv"
    name="cyto-feature parts" 
    cytofeat="1"
    date="20040707" 
  />
  <sorsa
    path="tmp/cytomap/sorsa.txt"
    name="Table of genome:cytology mapping"
    note="replaced by cytomap-chr.tsv files"
    date="20020817" 
  />
  
  <!-- replace above w/ these forms cyto-features-2L.tsv 
    // dang; bulkfiles split_filename requires name format
    $org-$chr-$type-$release.$format now; rename cyto-features
    to that pattern. dmel-2L-cytofeat-r3.tsv
    Also change cytomap-chr to dmel-chr-cytomap-r1.tsv 
    
  -->
  <fileset
    name="cytofeat"
    path="tmp/cytomap/dmel\-[\w\-\_]+\-cytofeat.*.fff"
    oldpath="tmp/cytomap/cyto-features-[\w\-\_]+.tsv"
    title="cyto-feature parts" 
    cytofeat="1"
    date="20041021" 
  />
  <fileset
    name="cytomap"
    path="tmp/cytomap/cytomap-[\w\-\_]+.tsv"
    title="cyto-feature parts" 
    copy="1"
    date="20041021" 
  />
  

</opt>
