def __init__(self, fdist_dir="", ext=None):
"""Constructor.
Parameters:
fdist_dir - Where fdist can be found, if = "", then it
should be on the path.
ext - Extension of binary names (e.g. nothing on Unix,
".exe" on Windows
"""
FDistController.__init__(self, fdist_dir, ext)
def __init__(self, fdist_dir="", ext=None):
"""Constructor.
Parameters:
fdist_dir - Where fdist can be found, if = "", then it
should be on the path.
ext - Extension of binary names (e.g. nothing on Unix,
".exe" on Windows
"""
FDistController.__init__(self, fdist_dir, ext)
def report(fst):
global numAttempts
global fda, fdc, fdRequest, runState, selRec2, splitSize
global chartPanel, simsDonePanel, systemPanel, empiricalPanel
global empiricalPanel, menuHandles, statusPanel, frame
global myFst, maxRun, minRun # This is really a private var to be reused
global isTemporal, tempSamples, fdt
if isTemporal:
fdt.acquire()
else:
fda.acquire()
if myFst < 0:
myFst = empiricalPanel.getFst()
if maxRun < 0:
maxRun = 1.0
minRun = 0.0
ext = FDistExtra.getExt()
fdc = FDistController('.', ext)
ci = systemPanel.getCI()
chartPanel.drawCI = True
confLines = changeChartCI(False)
simsDonePanel.increment(splitSize / 1000.0)
if isTemporal:
desiredNe = empiricalPanel.getNe()
else:
desiredFst = empiricalPanel.getFst()
if simsDonePanel.getRange() == simsDonePanel.getValue():
#print runState
if isTemporal:
fdt.release() # We are the last one, this is safe
else:
fda.release() # We are the last one, this is safe
if runState == 'ForceBeforeNeutral' or runState == 'Force':
os.remove(lpath + os.sep + 'out.dat') #careful, not for 5000 case
#print "max", maxRun, "min", minRun
nextFst, maxRun, minRun = approximate_fst(desiredFst, fst, myFst,
maxRun, minRun)
#print "obtained", fst, "desired", desiredFst, "next", nextFst, "max", maxRun, "min", minRun
numAttempts += 1
if nextFst == myFst or numAttempts == 20:
numSims = systemPanel.getNumSims()
if runState == 'Force':
statusPanel.setStatus('Running final simulation', Color.YELLOW)
runState = 'Final'
else:
runState = 'Neutral'
statusPanel.setStatus('Simulation pass to determine initial neutral set', Color.CYAN)
else:
statusPanel.setStatus('Forcing correct mean Fst, current error is ' +
str(round(abs(fst - desiredFst), 3)), Color.RED)
numSims = 50000
myFst = nextFst
npops = empiricalPanel.getTotalPops()
nsamples = countPops(selRec2)
numCores = systemPanel.getNumCores()
sampSize = empiricalPanel.getSampleSize()
if isDominant:
theta = empiricalPanel.getTheta()
beta = empiricalPanel.getBeta()
crit = empiricalPanel.getCrit()
mut = None
else:
theta = beta = crit = None
mutStr = empiricalPanel.mut.getSelectedItem()
mut = getMut(mutStr)
if isTemporal:
pass #XXX
else:
runFDistPart(False, selRec2, mut, numSims, npops, nsamples,
myFst, sampSize, theta, beta, crit, numCores)
elif runState == 'Neutral':
maxRun = -1
minRun = -1
myFst = -1
if isDominant:
pv = fdc.run_pv(data_dir = lpath, version=2)
else:
pv = fdc.run_pv(data_dir = lpath, version=1)
#pv = get_pv(data_dir = lpath)
selLoci = getSelLoci(pv)
if fdRequest == 'Neutral':
runState = 'Final'
numSims = systemPanel.getNumSims()
statusPanel.setStatus('Running final simulation', Color.YELLOW)
else:
runState = 'Force'
numAttempts = 0
statusPanel.setStatus('Forcing correct mean Fst for final pass', Color.RED)
numSims = 50000
neutralRec = FileParser.read(selRec2.fname)
#for locus in selLoci:
neutralRec.remove_loci_by_name(selLoci, lpath+os.sep+"nr.tmp")
shutil.copyfile(lpath + os.sep + "nr.tmp",
lpath + os.sep + "nr")
neutralRec = FileParser.read(lpath + os.sep + "nr")
createInfile(convert_genepop_to_fdist(neutralRec))
if isTemporal:
dc = Datacal()
dc.compute(lpath + os.sep + "infile", lpath + os.sep + "data_fst_outfile")
dc.computeNe(tempSamples[-1] - tempSamples[0])
myNe = dc.getNe()
elif isDominant:
crit = empiricalPanel.getCrit()
beta = empiricalPanel.getBeta()
myFst, _sampSize, _loci, _pops, _F, _obs = \
fdc.run_datacal(data_dir = lpath,
version=2, crit_freq=crit, p=0.5, beta=beta)
else:
myFst, _sampSize = fdc.run_datacal(data_dir = lpath)
#if myFst < 0.005:
# myFst = 0.005
if isTemporal:
empiricalPanel.setNe(myNe) #actually it is Ne
else:
empiricalPanel.setFst(myFst)
if not isDominant:
mutStr = empiricalPanel.mut.getSelectedItem()
mut = getMut(mutStr)
else:
mut = None
npops = empiricalPanel.getTotalPops()
nsamples = countPops(selRec2)
numCores = systemPanel.getNumCores()
sampSize = empiricalPanel.getSampleSize()
if isDominant:
theta = empiricalPanel.getTheta()
beta = empiricalPanel.getBeta()
crit = empiricalPanel.getCrit()
else:
theta = beta = crit = None
os.remove(lpath + os.sep + 'out.dat') #careful, not for 5000 case
createInfile(convert_genepop_to_fdist(selRec2))
if isTemporal:
dc = Datacal()
dc.compute(lpath + os.sep + "infile", lpath + os.sep + "data_fst_outfile")
dc.computeNe(tempSamples[-1] - tempSamples[0])
ne = dc.getNe()
elif isDominant:
_fst, _sampSize, _loci, _pops, _F, _obs = \
fdc.run_datacal(data_dir = lpath, version=2,
crit_freq = crit, p=0.5, beta=beta)
else:
_fst, _sampSize = fdc.run_datacal(data_dir = lpath)
if isTemporal:
runFtempPart(False, selRec2, numSims, npops, nsamples, ne,
sampSize, numCores)
else:
runFDistPart(False, selRec2, mut, numSims, npops, nsamples,
myFst, sampSize, theta, beta, crit, numCores)
elif runState == 'Final':
maxRun = -1
minRun = -1
myFst = -1
statusPanel.setStatus('Done (preparing selection table, please wait...)', Color.GRAY)
if isDominant:
pv = fdc.run_pv(data_dir = lpath, version=2)
else:
pv = fdc.run_pv(data_dir = lpath, version=1)
selLoci = getSelLoci(pv)
chartPanel.setSelLoci(pv, selRec2.loci_list, selLoci)
sp = SelPanel(frame, chartPanel, selRec2.loci_list, pv,
systemPanel.getCI(), confLines, locusFst, isDominant,
systemPanel.getFDR())
if isTemporal:
info(frame, "Done")
else:
info(frame, "Simulated Fst: %f" % (fst,))
statusPanel.setStatus('Done')
sp.show()
enablePanel(empiricalPanel)
enablePanel(systemPanel)
enableAllMenus(True)
systemPanel.enableChartFun = True
else:
if isTemporal:
fdt.release()
else:
fda.release()
def prepareFDist():
global fdc
#print lpath
FDistExtra.compile(lpath)
ext = FDistExtra.getExt()
fdc = FDistController('.', ext)