class PooTabs(QtGui.QTabWidget):
def __init__(self):
super(PooTabs, self).__init__()
self.setTabsClosable(True)
self.clearAll()
########################################################################
## Deleting, opening, and saving
def clearAll(self):
'''Deletes all stored data and creates a blank Sample table.'''
self.clear()
self.sampleTable = False
self.keaTable = False
self.ebridaTable = False
self.addSampleTable()
def openSaved(self,excelFile):
'''Adds data from a saved file.'''
for sheetName in excelFile.sheet_names:
if sheetName == 'Project':
pass
elif sheetName == 'Samples':
samples = excelFile.parse('Samples').astype(str)
self.addSampleTable()
self.sampleTable.appendSamples(samples)
elif sheetName == 'Kea':
samples = excelFile.parse('Kea').astype(str)
self.addKeaTable()
self.keaTable.appendSamples(samples)
elif sheetName == 'EBrida':
samples = excelFile.parse('EBrida').astype(str)
self.addEbridaTable()
self.ebridaTable.appendSamples(samples)
else:
samples = excelFile.parse(sheetName).astype(str)
screenTable = ScreenTable(sheetName)
screenTable.appendSamples(samples)
self.addTab(screenTable,sheetName)
def makeProjectName(self):
'''Creates a project name string in the format
year-firstplate-lastplate.'''
return self.sampleTable.makeProjectName()
def toWriter(self,writer):
'''Adds all tabs to the passed Excel writer object and returns it.'''
for i in range(self.count()):
self.widget(i).table.to_excel(writer,self.tabText(i),index=False)
return writer
########################################################################
## Utilities
def getSamplesCommonData(self):
'''Returns the Plate ID, Plate Name, Plate Kea, and Well columns
of the Sample Table.'''
return self.sampleTable.getSamplesCommonData()
def getColumnEntryList(self,column):
'''Returns a list of all entries for the given column, for the
current screening table.'''
return self.currentWidget().getColumnEntryList(column)
def update(self,key,dataframe):
'''Uses the data in dataframe to update table by key.'''
self.currentWidget().update(key,dataframe)
def setColumn(self,column,value):
'''Sets all rows in a column to value.'''
self.currentWidget().setColumn(column,value)
def replace(self,column,dictionary):
'''Uses the passed dictionary to replace selected entries of column
in the currenctly active table.'''
self.currentWidget().replace(column,dictionary)
def getColumnsWithSelect(self,columns=[],selected=False):
'''Returns the passed columns of the table, for the samples with
True in the selected column. The table is indexed by Plate ID and Well.'''
return self.currentWidget().getColumnsWithSelect(columns,selected)
def renameScreen(self,screen):
'''Renames the currently active round of screening.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
self.setTabText(self.currentIndex(),screen)
return self.currentWidget().renameScreen(screen)
def setCurrentMarker(self,marker):
'''Returns the marker name for the currently active screening tab.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
return self.currentWidget().setMarker(marker)
def getCurrentMarker(self):
'''Returns the marker name for the currently active screening tab.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
return ' '
else:
return self.currentWidget().getMarker()
def setPopulation(self,by):
'''Sets the Population column of the Sample table to the passed
option.'''
if by == 'All':
self.sampleTable.table['Population'] = 'All'
elif by == 'Plate ID':
self.sampleTable.table['Population'] = self.sampleTable.table['Plate ID']
elif by == 'Kea':
keaPops = keaTable.getColumnsWithSelect('Population')
self.sampleTable.update(keaPops)
def setByPopulation(self,column,data):
'''Sets the given column of the currently active widget to the
value given in the data table.'''
populations = self.sampleTable.getColumnsWithSelect(['Population'])
populations[column] = np.nan
populations = populations.reset_index()
populations = populations.set_index('Population')
populations.update(data)
populations = populations.reset_index()[['Plate ID','Well',column]]
populations = populations.set_index(['Plate ID','Well'],drop=False)
self.update(['Plate ID','Well'],populations)
def setIncludeByPopulationAndGroup(self,included):
'''Sets the Include column of the currently active widget to the
value given in the included table.'''
populations = self.sampleTable.getColumnsWithSelect(['Population'])
samples = self.currentWidget().getColumnsWithSelect(['Group'])
samples = pd.merge(samples,populations,how='inner',left_index=True,right_index=True)
samples['Include'] = False
def makeIncludes(x):
mySamples = samples.loc[(samples.Population==x.Population) & (samples.Group.isin(x.Groups))]
mySamples = mySamples.head(x.Samples)
mySamples['Include']=True
mySamples = mySamples[['Include']]
samples.update(mySamples)
included.apply(makeIncludes,1)
self.update(['Plate ID','Well'],samples)
def setIncludeByPopulationAndGroup2(self,included):
'''Sets the Include column of the currently active widget to the
value given in the included table.'''
populations = self.sampleTable.getColumnsWithSelect(['Population'])
samples = self.currentWidget().getColumnsWithSelect(['Group'])
samples = pd.merge(samples,populations,how='inner',left_index=True,right_index=True)
samples['Include'] = False
def makeIncludes(x):
mySamples = samples.loc[(samples.Population==x.Population) & (samples.Group==x.Group)]
mySamples = mySamples.head(x.Samples)
mySamples['Include']=True
mySamples = mySamples[['Include']]
samples.update(mySamples)
included.apply(makeIncludes,1)
self.update(['Plate ID','Well'],samples)
def getPlateStats(self):
'''Gets a Plate based Group stats table.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() not in sourceTables:
data = self.currentWidget().getColumnsWithSelect(['Group'],'Include')
data = data.reset_index()[['Plate ID','Group']]
data = data.groupby(['Plate ID','Group']).size().unstack().fillna(0)
data['Samples'] = data.sum(axis=1)
return data
else:
return False
def getPopulationStats(self):
'''Gets a Population based Group stats table.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() not in sourceTables:
data = self.currentWidget().getColumnsWithSelect(['Group'],'Include')
popdata = self.sampleTable.getColumnsWithSelect(['Population'])
data = pd.merge(data,popdata,how='left',left_index=True,right_index=True)
data = data.reset_index()[['Population','Group']]
data = data.groupby(['Population','Group']).size().unstack().fillna(0)
data['Samples'] = data.sum(axis=1)
return data
else:
return False
def getCurrentStatsTable(self,by,results):
'''Calls the other two functions. Added to preserve the coloured
Kea output table format. Results button does nothing - it used to
select the column. I'm doing backwards compatibility!'''
if by == 'Plate':
return self.getPlateStats()
elif by == 'Population':
return self.getPopulationStats()
########################################################################
## Adding and filling
def addSampleTable(self):
'''Adds a Sample table, if one does not already exist.'''
if not self.sampleTable:
self.sampleTable = SampleTable()
self.insertTab(0,self.sampleTable,'Samples')
self.tabBar().setTabButton(0,QtGui.QTabBar.RightSide,None)
def addKeaTable(self):
'''Adds a Kea Table, if no Kea Table exists.'''
if not self.keaTable:
self.keaTable = KeaTable()
self.insertTab(1,self.keaTable,'Kea')
self.tabBar().setTabButton(1,QtGui.QTabBar.RightSide,None)
def addEbridaTable(self):
'''Adds an Ebrida table, if no Ebrida table exists.'''
if not self.ebridaTable:
self.ebridaTable = EbridaTable()
self.insertTab(2,self.ebridaTable,'EBrida')
self.tabBar().setTabButton(2,QtGui.QTabBar.RightSide,None)
def addAndFillKeaTable(self):
'''Adds a Kea table and copies data from the Sample table, if a
Kea table does not already exist.'''
if not self.keaTable:
self.addKeaTable()
samples = self.getSamplesCommonData()
self.keaTable.appendSamples(samples)
def addAndFillEbridaTable(self):
'''Adds an Ebrida table and copies data from the Kea table, if an
Ebrida table does not already exist.'''
if not self.ebridaTable:
self.addEbridaTable()
samples = self.keaTable.getEbridaIndexData()
self.ebridaTable.appendSamples(samples)
def addAndFillEbridaTableNoKea(self):
'''Adds an Ebrida table if an Ebrida table does not already exist.'''
if not self.ebridaTable:
self.addEbridaTable()
samples = self.getSamplesCommonData()
self.ebridaTable.appendSamples(samples)
def appendSamples(self,samples):
'''Appends the samples in the passed dataframe to all three of
the Sample, Kea, and Ebrida tables, if they exist.'''
if self.sampleTable: self.sampleTable.appendSamples(samples)
if self.keaTable: self.keaTable.appendSamples(samples)
if self.ebridaTable: self.ebridaTable.appendSamples(samples)
def updateSourceTables(self,index,newData):
'''Updates the Sample, Kea, and Ebrida tables with data from the
passed dataframe, if those tables exist.'''
if self.sampleTable: self.sampleTable.update(index,newData)
if self.keaTable: self.keaTable.update(index,newData)
if self.ebridaTable: self.ebridaTable.update(index,newData)
def updateKeaData(self,keaData):
'''Updates the Kea table with data from the passed dataframe.
If no Kea table exists, one is created and populated with data
from the Samples table.'''
self.addAndFillKeaTable()
self.ebridaTable.addIndexedInfo(keaData,['Plate Kea','Well'])
def updateEbridaData(self,ebridaData):
'''Updates the Ebrida table with data from the passed dataframe.
If no Ebrida table exists, one is created and populated with data
from the Kea table.'''
self.addAndFillEbridaTable()
self.ebridaTable.addIndexedInfo(ebridaData.table,'Barcode')
def updateEbridaDataNoKea(self,ebridaData):
'''Updates the Ebrida table with data from the passed dataframe.
If no Ebrida table exists, one is created and populated with data
from the Kea table.'''
self.addAndFillEbridaTableNoKea()
self.ebridaTable.update(['Plate Name','Well'],ebridaData.table.set_index(['Plate Name','Well']))
########################################################################
## Screening and cherrypicking
def addScreen(self,plateNames,includeAll,oldPlates,newMarker,controls):
'''Adds a new screen table based on the passed data.'''
fromSource,samples = self.getInclude(includeAll)
screenTable = ScreenTable(plateNames)
screenTable.addSamples(fromSource,includeAll,oldPlates,newMarker,samples,controls)
self.addTab(screenTable,plateNames)
def getInclude(self,includeAll):
'''Gets the samples to include in the next round of screening.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
return True, self.sampleTable.getInclude(includeAll)
return False, self.currentWidget().getInclude(includeAll)
def getNegativeUnknowns(self,controls):
'''Returns a table of Negatives and Unknowns, with new wells and
plates added.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
return self.currentWidget().getNegativeUnknowns(controls)
def getPotentialContaminants(self):
'''Returns a table of possible contaminants.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
return self.currentWidget().getPotentialContaminants()
def getNegativeUnknownContaminants(self,controls,contaminants):
'''Returns a table of Negatives, Unknowns, and Contaminants, with
new wells and plates added.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
return self.currentWidget().getNegativeUnknownContaminants(controls,contaminants)
def getSamplesForLoading(self):
'''Gets from/to data for samples to load active Screening tab.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
return self.currentWidget().getSamplesForLoading()
def importLC(self,lc):
'''Imports data from the give fileDataLists and updates the active
screening tab.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass # Add "Add screening"?
else:
self.currentWidget().importLC(lc)
def addResultGroup(self,markerTable):
'''Adds Results and Groups to currently active tab using markerTable.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
self.currentWidget().addResultGroup(markerTable)
########################################################################
## Including and outputting
def getNonExists(self):
'''Returns a table of Falses for non-existing samples.'''
return self.sampleTable.getNonExists()
def getNegativeFailGrinds(self):
'''Returns a table of Falses for Negative, Failgrind samples.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
pass
else:
failGrinds = self.sampleTable.getFailGrinds()
negatives = self.currentWidget().getNegatives()
negativeFailGrinds = failGrinds.join(negatives,how='inner')
negativeFailGrinds['Output'] = False
return negativeFailGrinds[['Output']]
########################################################################
## Output stuff
def getEbridaHarvestData(self):
'''Returns the data required for outputting harvest platesheets.'''
return self.keaTable.getEbridaIndexData()
def getSampleTable(self):
'''Gets the sample, kea, and ebrida data, and puts it into one
big table ready to have results added to it.'''
sampleTableColumns = ['Plate Name']
samples = self.sampleTable.getColumnsWithSelect(sampleTableColumns,'Output')
if self.keaTable:
keaTableColumns = ['Plate Kea','Sample ID','PlantID','Plant Alt Names',
'Population','Sample Batch']
keaData = self.keaTable.getColumnsWithSelect(keaTableColumns)
samples = pd.merge(samples,keaData,how='left',left_index=True,right_index=True)
if self.ebridaTable:
ebridaTableColumns = ['Pedigree Item','Plot','Group','Start Date',
'From Ped. Item','Mother','Father','Barcode',
'fundingNameCr','BreederName','synonyms']
ebridaData = self.ebridaTable.getColumnsWithSelect(ebridaTableColumns)
samples = pd.merge(samples,ebridaData,how='left',left_index=True,right_index=True)
return samples
def getScreenResultsTable(self):
'''Gets a results table for current round of screening.'''
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
if self.currentWidget() in sourceTables:
return False
samples = self.getSampleTable()
columns = ['Experiment','Experiment Date','Marker','Result','Group']
results = self.currentWidget().getColumnsWithSelect(columns,'Output')
samples = pd.merge(samples,results,how='right',left_index=True,right_index=True)
samples = samples.reset_index()
return samples
# def getAllResultsTableOld(self):
# '''Gets a results table for all rounds of screening.'''
# samples = self.getSampleTable()
# sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
# markers = []
# for i in range(self.count()):
# if self.widget(i) in sourceTables:
# pass
# else:
# markers.append(self.widget(i).getMarker())
# screen = self.widget(i).getColumnsWithSelect(['Marker','Result','Group'],'Output')
# screen = screen.reset_index().set_index(['Plate ID','Well','Marker'])
# screen = screen.unstack().reset_index().set_index(['Plate ID','Well'])
# samples = pd.merge(samples,screen,how='inner',left_index=True,right_index=True)
# samples = samples.reset_index()
# return markers,samples
def getAllResultsTable(self):
'''Gets results table for all rounds of screening.'''
results = pd.DataFrame(columns=[])
samples = self.getSampleTable()
sourceTables = (self.sampleTable, self.keaTable, self.ebridaTable)
for i in range(self.count()):
if self.widget(i) in sourceTables:
pass
else:
screen = self.widget(i).getColumnsWithSelect(['Marker','Result','Group'],'Output')
screen = screen.reset_index().set_index(['Plate ID','Well'])
screen = pd.merge(samples,screen,how='inner',left_index=True,right_index=True).fillna('Not tested')
results = results.append(screen)
return results.reset_index()
def addEbridaTable(self): '''Adds an Ebrida table, if no Ebrida table exists.''' if not self.ebridaTable: self.ebridaTable = EbridaTable() self.insertTab(2,self.ebridaTable,'EBrida') self.tabBar().setTabButton(2,QtGui.QTabBar.RightSide,None)