class GenericTable(QtCore.QAbstractTableModel):
def __init__(self, data, headers, parent=None, *args):
QtCore.QAbstractTableModel.__init__(self, parent, *args)
self.arraydata = data
self.headerdata = headers
def rowCount(self, parent):
return len(self.arraydata)
def columnCount(self, parent):
if len(self.arraydata) > 0:
return len(self.arraydata[0])
else:
return -1
def data(self, index, role):
if index.isValid() and role == QtCore.Qt.DisplayRole:
return QtCore.QVariant(self.arraydata[index.row()][index.column()])
return QtCore.QVariant()
def headerData(self, col, orientation, role):
if orientation == QtCore.Qt.Horizontal and role == QtCore.Qt.DisplayRole:
return QtCore.QVariant(self.headerdata[col])
return QtCore.QVariant()
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = SortTableNumericStrCol(self.arraydata, Ncol)
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
def save(self, filename):
fout = open(filename, 'w')
for header in self.headerdata:
fout.write(str(header) + '\t')
fout.write('\n')
for row in self.arraydata:
for item in row:
fout.write(str(item) + '\t')
fout.write('\n')
fout.close()
class GenericTable(QtCore.QAbstractTableModel):
def __init__(self, data, headers, parent=None, *args):
QtCore.QAbstractTableModel.__init__(self, parent, *args)
self.arraydata = data
self.headerdata = headers
def rowCount(self, parent):
return len(self.arraydata)
def columnCount(self, parent):
if len(self.arraydata) > 0:
return len(self.arraydata[0])
else:
return -1
def data(self, index, role):
if index.isValid() and role == QtCore.Qt.DisplayRole:
return QtCore.QVariant(self.arraydata[index.row()][index.column()])
return QtCore.QVariant()
def headerData(self, col, orientation, role):
if orientation == QtCore.Qt.Horizontal and role == QtCore.Qt.DisplayRole:
return QtCore.QVariant(self.headerdata[col])
return QtCore.QVariant()
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = SortTableNumericStrCol(self.arraydata, Ncol)
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
def save(self, filename):
fout = open(filename, 'w')
for header in self.headerdata:
fout.write(str(header) + '\t')
fout.write('\n')
for row in self.arraydata:
for item in row:
fout.write(str(item) + '\t')
fout.write('\n')
fout.close()
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = SortTableNumericStrCol(self.arraydata, Ncol)
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = SortTableNumericStrCol(self.arraydata, Ncol)
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
# Prepare table
# ['Benjamini-Hochberg FDR', 'Bonferroni', 'No correction', 'Sidak', 'Storey FDR']
print 'Sidak table:',
groupMultCompMethodIndex = 3 # 'No correction'
groupMultCompMethod = groupMultCompMethodOptions[groupMultCompMethodIndex]
# run significance test
groupStatsTest.run(test, groupSignTestType, groupConfIntervMethod, float(groupNominalCoverage), groupProfile)
# apply multiple test correction
groupStatsTest.results.performMultCompCorrection(multCompDict[groupMultCompMethod])
groupStatsTest.results.setSelectedFeatures(selectedFeatures)
groupStatsTest.results.filterFeatures(groupSignLevelFilter, groupSeqFilter, group1Filter, group2Filter, groupParentSeqFilter, groupParentGroup1Filter, groupParentGroup2Filter, groupEffectSizeMeasure1, groupMinEffectSize1, effectSizeOperator, groupMinEffectSize2, groupMinEffectSize2)
tableData, tableHeadings = groupStatsTest.results.tableData(False)
tableData = SortTableStrCol(tableData, 0)
filename = os.path.join(saveFolder, saveTableTemplate.format(g1=groupName1, g2=groupName2))
print '"{0}"'.format(filename),
fout = open(filename, 'w')
for heading in tableHeadings:
fout.write(heading + '\t')
fout.write('\n')
for row in tableData:
for entry in row:
fout.write(str(entry) + '\t')
fout.write('\n')
fout.close()
print 'DONE.'
else:
print 'No Active Data, SKIP.'
