old_contents: """
  this is the stuff specific to the plant studies that are loaded. It can include comments and all that. The studytreelist will be read from the load_synth_extract file. Other variables in the conf could be overridden here. 
  """
  
  from wopr_conf import *
  
  #from plants import studytreelist as plantslist
  #from goo import studytreelist as goolist
  from metazoa import studytreelist as metalist
  #from mammals import studytreelist as mammalslist
  #from birds import studytreelist as birdslist
  #from tetrapoda import studytreelist as tetrapodalist
  #from fungi import studytreelist as fungilist
  
  
  studytreelist = []
  #studytreelist.extend(plantslist)
  #studytreelist.extend(goolist)
  studytreelist.extend(metalist)
  #studytreelist.extend(mammalslist)
  #studytreelist.extend(birdslist)
  #studytreelist.extend(tetrapodalist)
  #studytreelist.extend(fungilist)
  
  import load_synth_extract
  
  # 805080 = life; 691846 = Metazoa; 81461 = Aves; 244265 = Mammalia; 229562 = Tetrapoda
  #synthottolid="805080"
  #extractottolid="691846"
  
  synthottolid = "691846"
  #extractottolid = "691846"
  
  print "loading synthottolid:",synthottolid
  print "loading studytreelist:",studytreelist
  
  # analysis name
  aname="Metazoa_test_2.3_mapcompat"
  # location of synth database
  dsynth=bdir+aname+".db"
  # location of synth treefile
  treefn=bdir+aname+"-synth.tre"
  
  #load_synth_extract.run(dott,dload,studyloc,studytreelist,javapre,treemloc,generallogfileloc,dsynth,synthottolid,treefn,extractottolid)
  load_synth_extract.run(dott,dload,studyloc,studytreelist,javapre,treemloc,generallogfileloc,dsynth,synthottolid,treefn)
  
  
new_contents: """
  this is the stuff specific to the plant studies that are loaded. It can include comments and all that. The studytreelist will be read from the load_synth_extract file. Other variables in the conf could be overridden here. 
  """
  
  from wopr_conf import *
  
  #from plants import studytreelist as plantslist
  #from goo import studytreelist as goolist
  from metazoa import studytreelist as metalist
  #from mammals import studytreelist as mammalslist
  #from birds import studytreelist as birdslist
  #from tetrapoda import studytreelist as tetrapodalist
  #from fungi import studytreelist as fungilist
  
  
  studytreelist = []
  #studytreelist.extend(plantslist)
  #studytreelist.extend(goolist)
  studytreelist.extend(metalist)
  #studytreelist.extend(mammalslist)
  #studytreelist.extend(birdslist)
  #studytreelist.extend(tetrapodalist)
  #studytreelist.extend(fungilist)
  
  import load_synth_extract
  
  # 805080 = life; 691846 = Metazoa; 81461 = Aves; 244265 = Mammalia; 229562 = Tetrapoda
  #synthottolid="805080"
  #extractottolid="691846"
  
  synthottolid = "691846"
  #extractottolid = "691846"
  
  studytreelistTF = [True] * len(studytreelist)
  
  print "loading synthottolid:",synthottolid
  print "loading studytreelist:",studytreelist
  
  # analysis name
  aname="Metazoa_test_2.3_mapcompat"
  # location of synth database
  dsynth=bdir+aname+".db"
  # location of synth treefile
  treefn=bdir+aname+"-synth.tre"
  
  #load_synth_extract.run(dott,dload,studyloc,studytreelist,javapre,treemloc,generallogfileloc,dsynth,synthottolid,treefn,extractottolid)
  load_synth_extract.run(dott,dload,studyloc,studytreelist,javapre,treemloc,generallogfileloc,dsynth,synthottolid,treefn,studytreelistTF)
  
  
subject: fix to args