def chooseFile():
global frame, dataPath
global systemPanel, chartPanel
global isTemporal
fc = JFileChooser(dataPath)
retVal = fc.showOpenDialog(frame)
if retVal != JFileChooser.APPROVE_OPTION:
return
fname = fc.getSelectedFile().getAbsolutePath()
dataPath = os.sep.join(fname.split(os.sep)[:-1])
if isTemporal:
info(frame, "We need a file with information about the temporal point of each sample")
tfc = JFileChooser(dataPath)
tRetVal = tfc.showOpenDialog(frame)
if retVal != JFileChooser.APPROVE_OPTION:
return
tname = tfc.getSelectedFile().getAbsolutePath()
systemPanel.enableChartFun = False
chartPanel.resetData()
loadGenePop(fname)
if isTemporal:
if not loadTemporal(tname):
return
updateAll()
enablePanel(empiricalPanel)
def loadTemporal(fname):
global tempSamples, popNames
f = open(fname)
l = f.readline()
i = 0
tempSamples = []
while l != '':
if i > len(popNames):
break
try:
tempSamples.append(int(l.rstrip()))
except:
error(frame, "Temporal file syntax error, please check")
return False
i += 1
l = f.readline()
f.close()
if i != len(popNames):
error(
frame,
"Number of temporal samples (%d) is less than the number of time points specified (%d)"
% (i, len(popNames)))
return False
else:
info(frame, "Temporal points set at: %s" % str(tempSamples))
return True
def actionPerformed(self, event):
global frame, chartPanel
global popNames, rec2, remLoci, remPops # , rec
global isDominant
option = event.getActionCommand()
# print option
if option == 'Open':
chooseFile()
elif option == 'LoadPop':
loadPopNames()
elif option == 'EditPop':
editPopNames()
elif option == 'SavePop':
savePopNames()
elif option == 'Example':
useExampleData()
elif option == 'Citation':
displayCitation()
elif option == 'ChooseLoci':
selLoci = rec2.loci_list[:]
for locus in remLoci:
selLoci.remove(locus)
rd = RestrictionDialog(frame, 'Choose loci', selLoci, remLoci,
updateLoci)
rd.show()
elif option == 'ChoosePops':
selPops = popNames[:]
for pop in remPops:
selPops.remove(pop)
rd = RestrictionDialog(frame, 'Choose Populations', selPops,
remPops, updatePops)
rd.show()
elif option == 'RunFDist':
runFDist()
elif option == 'CancelFDist':
cancelFDist()
elif option == 'Run5000':
runFDist(True)
elif option == 'CheckLoci':
checkLoci()
elif option == 'ConfGrp':
configChart()
elif option == 'Help':
if isDominant:
info(frame,
'For help please visit http://popgen.eu/soft/mcheza')
else:
info(frame,
'For help please visit http://popgen.eu/soft/lositan')
elif option == 'SavePNG':
chartPanel.save(frame, 'PNG')
elif option == 'SaveSVG':
chartPanel.save(frame, 'SVG')
elif option == 'SavePDF':
chartPanel.save(frame, 'PDF')
elif option == 'Exit':
sys.exit(-1)
def actionPerformed(self, event):
global frame, chartPanel
global popNames, rec2, remLoci, remPops #, rec
global isDominant
option = event.getActionCommand()
#print option
if option == 'Open':
chooseFile()
elif option == 'LoadPop':
loadPopNames()
elif option == 'EditPop':
editPopNames()
elif option == 'SavePop':
savePopNames()
elif option == 'Example':
useExampleData()
elif option == 'Citation':
displayCitation()
elif option == 'ChooseLoci':
selLoci = rec2.loci_list[:]
for locus in remLoci:
selLoci.remove(locus)
rd = RestrictionDialog(frame, 'Choose loci',
selLoci, remLoci, updateLoci)
rd.show()
elif option == 'ChoosePops':
selPops = popNames[:]
for pop in remPops:
selPops.remove(pop)
rd = RestrictionDialog(frame, 'Choose Populations',
selPops, remPops, updatePops)
rd.show()
elif option == 'RunFDist':
runFDist()
elif option == 'CancelFDist':
cancelFDist()
elif option == 'Run5000':
runFDist(True)
elif option == 'CheckLoci':
checkLoci()
elif option == 'ConfGrp':
configChart()
elif option == 'Help':
if isDominant:
info(frame, 'For help please visit http://popgen.eu/soft/mcheza')
else:
info(frame, 'For help please visit http://popgen.eu/soft/lositan')
elif option == 'SavePNG':
chartPanel.save(frame, 'PNG')
elif option == 'SaveSVG':
chartPanel.save(frame, 'SVG')
elif option == 'SavePDF':
chartPanel.save(frame, 'PDF')
elif option == 'Exit':
sys.exit(-1)
def loadTemporal(fname):
global tempSamples, popNames
f = open(fname)
l = f.readline()
i = 0
tempSamples = []
while l<>'':
if i>len(popNames):
break
tempSamples.append(int(l.rstrip()))
i += 1
l = f.readline()
f.close()
if i!=len(popNames):
error(frame, "Number of temporal samples is less than the number of time points specified")
else:
info(frame, "Temporal points set at: %s" % str(tempSamples))
def displayCitation():
if isTemporal:
info(frame, """If you use LosiTemp please cite:
...
""")
elif isDominant:
info(
frame, """If you use Mcheza please cite:
Antao T, Beaumont MA (2011)
Mcheza: A workbench to detect selection using dominant markers
Bioinformatics doi: 10.1093/bioinformatics/btr253
""")
else:
info(
frame, """If you use LOSITAN please cite both:
Beaumont MA, Nichols RA (1996)
Evaluating loci for use in the genetic analysis of population structure
Proceedings of the Royal Society of London B 263: 1619-1626
AND
LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method
Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira, Gordon Luikart
BMC Bioinformatics 2008, 9:323
""")
def loadTemporal(fname):
global tempSamples, popNames
f = open(fname)
l = f.readline()
i = 0
tempSamples = []
while l != '':
if i > len(popNames):
break
try:
tempSamples.append(int(l.rstrip()))
except:
error(frame, "Temporal file syntax error, please check")
return False
i += 1
l = f.readline()
f.close()
if i != len(popNames):
error(frame, "Number of temporal samples (%d) is less than the number of time points specified (%d)" % (i, len(popNames)))
return False
else:
info(frame, "Temporal points set at: %s" % str(tempSamples))
return True
def displayCitation():
if isTemporal:
info(frame, """If you use LosiTemp please cite:
...
""")
elif isDominant:
info(frame, """If you use Mcheza please cite:
Antao T, Beaumont MA (2011)
Mcheza: A workbench to detect selection using dominant markers
Bioinformatics doi: 10.1093/bioinformatics/btr253
""")
else:
info(frame, """If you use LOSITAN please cite both:
Beaumont MA, Nichols RA (1996)
Evaluating loci for use in the genetic analysis of population structure
Proceedings of the Royal Society of London B 263: 1619-1626
AND
LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method
Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira, Gordon Luikart
BMC Bioinformatics 2008, 9:323
""")
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 endRunDatacal(after):
global fdc, selRec2, sampSize, locusFst, lpath
global empiricalPanel, isDominant, systemPanel
global tempSamples, isTemporal
#createInfile(convert_genepop_to_fdist(selRec2))
createInfile(convert_genepop_to_fdist(selRec2, update_load_status))
if isDominant:
crit = empiricalPanel.getCrit()
beta = empiricalPanel.getBeta()
fst, sampSize, loci, pops, F, obs = fdc.run_datacal(
data_dir = lpath, version = 2,
crit_freq=crit, p=0.5, beta=beta)
elif isTemporal:
dc = Datacal()
dc.compute(lpath + os.sep + "infile", lpath + os.sep + "data_fst_outfile")
sampSize = dc.getSampleSize()
dc.computeNe(tempSamples[-1] - tempSamples[0])
ne = dc.getNe()
else:
fst, sampSize = fdc.run_datacal(data_dir = lpath)
print(fst, sampSize)
if not isTemporal:
if fst < 0.0:
systemPanel.force.setEnabled(False)
systemPanel.force.setSelected(False)
else:
systemPanel.force.setEnabled(True)
f = open(lpath + os.sep + 'data_fst_outfile')
locusFst = []
l = f.readline()
myPos = 0
while l != '':
if isDominant:
lhe, lfst, lheold, llocus = l.rstrip().split(' ')
while int(llocus)>myPos:
locusFst.append(None)
myPos += 1
myPos += 1
else:
lhe, lfst = l.rstrip().split(' ')
if lhe == "-nan":
lhe = "nan"
if lhe == "-nan":
lhe = "nan"
if lfst == "-nan":
lfst = "nan"
try:
if float(lfst) < -10.0:
lfst = "nan"
except ValueError:
lfst = 'nan'
try:
if float(lhe) < -10.0:
lhe = "nan"
except ValueError:
lhe = 'nan'
locusFst.append((float(lhe), float(lfst)))
l = f.readline()
while len(locusFst) < len(selRec2.loci_list):
locusFst.append(None)
f.close()
if sampSize > 50:
sampSize = 50
if isTemporal:
empiricalPanel.setNe(ne)
else:
empiricalPanel.setFst(fst)
empiricalPanel.setSampleSize(sampSize)
if isTemporal:
info (frame, "Dataset Ne: %d" % int(ne))
else:
info (frame, "Dataset Fst: %f" % fst)
after()
loadPanel.dispose()