def initUI(self):
self.setWindowTitle("Data Formatter")
self.menubar = fydMenuBar()
self.setMenuBar(self.menubar)
self.statusBar()
self.resultsTable = ResultsTable()
self.infoTable = InfoTable()
self.tabWidget = QtGui.QTabWidget()
self.tabWidget.addTab(self.resultsTable, "Results")
self.tabWidget.addTab(self.infoTable, "Information")
self.setCentralWidget(self.tabWidget)
self.showMaximized()
def new(self):
"""Nukes the resultsTable and starts again."""
del self.resultsTable
del self.infoTable
del self.tabWidget
self.resultsTable = ResultsTable()
self.infoTable = InfoTable()
self.tabWidget = QtGui.QTabWidget()
self.tabWidget.addTab(self.resultsTable, "Results")
self.tabWidget.addTab(self.infoTable, "Information")
self.setCentralWidget(self.tabWidget)
self.__updateView()
class DataFormatter(QtGui.QMainWindow):
def __init__(self):
super(DataFormatter, self).__init__()
self.initVars()
self.initUI()
self.initConnections()
def initVars(self):
self.path = "/home/mcv/Genotyping Project Records/Genotyping Projects/"
self.ignoreList = ["", "Population"]
def initUI(self):
self.setWindowTitle("Data Formatter")
self.menubar = fydMenuBar()
self.setMenuBar(self.menubar)
self.statusBar()
self.resultsTable = ResultsTable()
self.infoTable = InfoTable()
self.tabWidget = QtGui.QTabWidget()
self.tabWidget.addTab(self.resultsTable, "Results")
self.tabWidget.addTab(self.infoTable, "Information")
self.setCentralWidget(self.tabWidget)
self.showMaximized()
def initConnections(self):
self.menubar.clearTableAction.triggered.connect(self.new)
self.menubar.openAction.triggered.connect(self.openDialog)
self.menubar.saveAction.triggered.connect(self.saveDialog)
# self.menubar.readMarkerConfigAction.triggered.connect(self.readMarkerConfig)
self.menubar.createSamplesAction.triggered.connect(self.createSamples)
self.menubar.createPlatesAction.triggered.connect(self.createPlates)
# self.menubar.createSamplesFromExcelAction.triggered.connect(self.createSamplesFromExcel)
self.menubar.createSamplesFromExcelKeaAction.triggered.connect(self.createSamplesFromExcelKea)
self.menubar.kiwifruitWizardAction.triggered.connect(self.kiwifruitWizard)
self.menubar.brassicaRyegrassWizardAction.triggered.connect(self.brassicaRyegrassWizard)
self.menubar.keaWizardAction.triggered.connect(self.keaWizard)
self.menubar.exitAction.triggered.connect(self.close)
# self.menubar.importSamplesSpreadsheetAction.triggered.connect(self.importSamplesSpreadsheet)
self.menubar.importEBridaSamplesSpreadsheetAction.triggered.connect(self.importEBridaSamplesSpreadsheet)
self.menubar.importPlatesSpreadsheetAction.triggered.connect(self.importPlatesSpreadsheet)
self.menubar.importLightcyclerFileAction.triggered.connect(self.importLightcyclerFile)
self.menubar.importTaqmanFileAction.triggered.connect(self.importTaqmanFile)
# self.menubar.importSpecFileAction.triggered.connect(self.importSpecFile)
self.menubar.cherryPickHelpAction.triggered.connect(self.cherryPickHelp)
self.menubar.cherryPickNegativeUnknownAction.triggered.connect(self.cherryPickNegativeUnknown)
self.menubar.cherryPickFromPopulationAction.triggered.connect(self.cherryPickFromPopulation)
self.menubar.importCherryPickingAction.triggered.connect(self.importCherryPicking)
self.menubar.setCropAction.triggered.connect(self.setCrop)
self.menubar.explainCropAction.triggered.connect(self.explainCrop)
self.menubar.editPlatesAction.triggered.connect(self.editPlates)
self.menubar.viewPlateStatsAction.triggered.connect(self.viewPlateStats)
# self.menubar.viewPopulationStatsAction.triggered.connect(self.viewPopulationStats)
self.menubar.standardiseResultsAction.triggered.connect(self.standardiseResults)
self.menubar.negativiseUnknownsAction.triggered.connect(self.negativiseUnknowns)
self.menubar.addAutoResultsAction.triggered.connect(self.addAutoResults)
self.menubar.addManualResultsAction.triggered.connect(self.addManualResults)
self.menubar.setNonExistsToNoSampleAction.triggered.connect(self.setNonExistsToNoSample)
self.menubar.setNonExistsToNegativeAction.triggered.connect(self.setNonExistsToNegative)
self.menubar.includeAllAction.triggered.connect(self.includeAll)
self.menubar.excludeFailGrindsAction.triggered.connect(self.excludeFailGrinds)
self.menubar.excludeNegativeFailGrindsAction.triggered.connect(self.excludeNegativeFailGrinds)
self.menubar.excludeNonExistsAction.triggered.connect(self.excludeNonExists)
self.menubar.kiwifruitResultsAction.triggered.connect(self.kiwifruitResults)
self.menubar.brassicaRyegrassResultsAction.triggered.connect(self.brassicaRyegrassResults)
self.menubar.appleResultsAction.triggered.connect(self.appleResults)
self.menubar.outputHarvestSheetsAction.triggered.connect(self.outputHarvestSheets)
# self.menubar.outputSampleTableAction.triggered.connect(self.outputSampleTable)
self.menubar.outputForKeaAction.triggered.connect(self.outputForKea)
self.menubar.outputForEBridaAction.triggered.connect(self.outputForEBrida)
self.menubar.colouredResultsAction.triggered.connect(self.colouredResults)
self.menubar.niceKeaSpreadsheetAction.triggered.connect(self.niceKeaSpreadsheet)
########################################################################
## Private Methods
def __updateView(self):
"""Reorders the columns of self.resultsTable, and updates the
self.tableWidget dataframe to the current version of self.resultsTable"""
self.resultsTable.update()
self.infoTable.update()
def __getPlatesRecords(self):
title = "Locate plate spreadsheet..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
plateData = pd.read_excel(fileName, sheetname="Plates", header=1)
plateData = plateData[["Slipstream Identifier", "Plate Name", "Kea Name", "Non-harvested plants", "Bad Grinds"]]
plateData.columns = ["Plate ID", "Plate Name", "Plate Kea", "Non-harvested plants", "Bad Grinds"]
plateData = plateData.dropna(subset=["Plate ID"])
return plateData
def __getStatsTable(self, included, groups, by):
stats = included[[by, "Group"]].groupby([by, "Group"]).size().unstack()
plateLookup = included.drop_duplicates(by)[[by]]
columns = [by] + groups
statsTable = pd.DataFrame(columns=columns).append(plateLookup).set_index([by])
statsTable = statsTable.combine_first(stats).fillna(0).reset_index()
statsTable["Samples"] = statsTable.sum(axis=1)
statsTable = statsTable[[by, "Samples"] + groups]
return statsTable
## To make platesheets work:
def __getStatsTable(self, included, groups, by):
included = included[included.Group != "No sample"]
stats = included[["Plate ID", "Group"]]
stats = stats.groupby(["Plate ID", "Group"]).size().unstack()
plateLookup = included.drop_duplicates("Plate ID")[["Plate ID", "Plate Name"]]
columns = ["Plate ID", "Plate Name"] + groups
statsTable = pd.DataFrame(columns=columns).append(plateLookup).set_index(["Plate ID"])
statsTable = statsTable.combine_first(stats).fillna(0).reset_index()
statsTable["Samples"] = statsTable.sum(axis=1)
statsTable = statsTable[["Plate ID", "Plate Name", "Samples"] + groups]
return statsTable
def __readMarkerConfig(self, fileName):
with open(fileName, "r") as config:
for line in config.readlines():
lineList = line.split("\t")
Crop = lineList[0]
Marker = lineList[1]
Result = lineList[2]
Group = lineList[3]
Colour = lineList[4]
########################################################################
## File Menu Actions
def new(self):
"""Nukes the resultsTable and starts again."""
del self.resultsTable
del self.infoTable
del self.tabWidget
self.resultsTable = ResultsTable()
self.infoTable = InfoTable()
self.tabWidget = QtGui.QTabWidget()
self.tabWidget.addTab(self.resultsTable, "Results")
self.tabWidget.addTab(self.infoTable, "Information")
self.setCentralWidget(self.tabWidget)
self.__updateView()
def openDialog(self):
"""Opens a saved .xls file."""
title = "Open project .xls file..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
results = pd.io.excel.read_excel(fileName, sheetname="Results")
if set(results.columns) == set(self.resultsTable.table.columns):
self.resultsTable.table = results
self.infoTable.table = pd.io.excel.read_excel(fileName, sheetname="Information")
self.__updateView()
else:
dialog = QtGui.QMessageBox.information(
self,
"Open file fail...",
"The columns in this file's results\n"
+ "table are not what is expected. Please\n"
+ "make sure you have the right file, and\n"
+ "make sure the columns of the saved file\n"
+ "match those in the Results tab.",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
def saveDialog(self):
"""Saves the project as an .xls file."""
title = "Save project as..."
fileName, f = QtGui.QFileDialog.getSaveFileName(self, title, self.path)
fileName = fileName.split(".")[0]
writer = pd.ExcelWriter(fileName + ".xls")
self.resultsTable.table.to_excel(writer, "Results")
self.infoTable.table.to_excel(writer, "Information")
writer.save()
def readMarkerConfig(self):
"""Opens a specified marker config file and creates marker data."""
title = "Select marker config file..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
self.markers = self.__readMarkerConfig(fileName)
def createSamples(self):
"""Creates a given number of samples with no names or plant names."""
samples, ok = CreateSamplesDialog.create(self)
if ok:
newSamplesDF = pd.DataFrame(
samples, columns=["Plate ID", "Plate Name", "Plate Kea", "Well", "Grind", "Include"]
)
self.resultsTable.append(newSamplesDF)
self.infoTable.append(newSamplesDF[["Plate ID", "Plate Name", "Plate Kea", "Well"]])
self.__updateView()
def createPlates(self):
"""Creates a set of consecutively numbered full plates."""
samples, ok = CreatePlatesDialog.create(self)
if ok:
newSamplesDF = pd.DataFrame(
samples, columns=["Plate ID", "Plate Name", "Plate Kea", "Well", "Crop", "Grind", "Include"]
)
self.resultsTable.append(newSamplesDF)
self.infoTable.append(newSamplesDF[["Plate ID", "Plate Name", "Plate Kea", "Well"]])
self.__updateView()
def createSamplesFromExcel(self):
"""Opens an Excel spreadsheet and creates samples."""
title = "Locate sample spreadsheet..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
excelFile = pd.ExcelFile(fileName)
sheets = excelFile.sheet_names
sheet, ok = MyDialog.chooseExcelSheet(sheets)
imported = excelFile.parse(sheet)
columns = list(imported.columns)
name, well, ok = MyDialog.getIndexMatches(columns)
columnsToImport, ok = MyDialog.chooseColumns(columns)
columnsToImport = self.columns2 + columnsToImport
imported["Plate ID"] = ""
imported["Plate Name"] = imported.get(name, "")
imported["Well"] = imported.get(well, "")
imported = imported.dropna(how="all", subset=["Plate Name", "Well"])
imported = imported.set_index("Plate Name")
title = "Locate plate spreadsheet..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
plateData = pd.read_excel(fileName, sheetname="Plates", header=1)
plateData = plateData[["Slipstream Identifier", "Kea Name", "Plate Name", "Bad Grinds"]]
plateData.columns = ["Plate ID", "Kea Name", "Plate Name", "Bad Grinds"]
plateData = plateData.dropna(how="all", subset=["Kea Name"])
plateData = plateData.set_index("Kea Name")
imported.update(plateData)
imported = imported.reset_index()
badGrinds = plateData.dropna(how="all", subset=["Bad Grinds"])
badGrinds = pd.DataFrame(badGrinds["Bad Grinds"].str.split(" ").tolist(), index=badGrinds["Plate ID"]).stack()
badGrinds = badGrinds.reset_index().drop("level_1", 1)
badGrinds.columns = ["Plate ID", "Well"]
badGrinds["Grind"] = False
badGrinds = badGrinds.set_index(["Plate ID", "Well"])
self.resultsTable = self.resultsTable.append(imported[self.columns2])
self.resultsTable = self.resultsTable.set_index(["Plate ID", "Well"])
self.resultsTable.update(badGrinds)
self.resultsTable = self.resultsTable.reset_index()
self.infoTable = self.infoTable.append(imported[columnsToImport])
self.__updateView()
def createSamplesFromExcelKea(self):
"""Opens a Kea Sample Batch spreadsheet and imports the samples."""
title = "Locate Kea sample batch spreadsheet..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
excelFile = pd.ExcelFile(fileName)
imported = excelFile.parse("Data")
imported["Plate ID"] = ""
sheetColumns = ["Plate ID", "Plate No", "Position on Plate(s)", "PlantID", "Sample ID", "Plant Alt Names"]
tableColumns = ["Plate ID", "Plate Kea", "Well", "PlantID", "Sample ID", "Plant Alt Names"]
resColumns = ["Plate ID", "Plate Kea", "Well", "Population"]
imported = imported[sheetColumns]
imported.columns = tableColumns
imported = imported.dropna(how="all", subset=["Sample ID"])
self.population = ""
def addPopulations(row):
if pd.isnull(row["Plate Kea"]):
self.population = row["Sample ID"].split(" ")[0]
return self.population
imported["Population"] = imported.apply(addPopulations, 1)
imported = imported.dropna(how="all", subset=["Plate Kea", "Well"])
self.resultsTable.append(imported[resColumns])
self.infoTable.append(imported)
plateData = self.__getPlatesRecords()
self.resultsTable.importPlateData(plateData, "Plate Kea")
self.infoTable.importPlateData(plateData, "Plate Kea")
self.__updateView()
def kiwifruitWizard(self):
"""Runs a wizard to input data for a kiwifruit project."""
dialog = QtGui.QMessageBox.information(
self,
"Kiwifruit Wizard",
"You will be prompted to select files for\n"
+ "import. The files you will need are:\n"
+ " - Kea sample batch harvest sheet\n"
+ " - Plates records spreadsheet\n"
+ " - E-brida information sheet\n"
+ " - Lightcycler .txt files\n\n"
+ "After running this wizard you will have\n"
+ "all required information imported and\n"
+ "all logic on results set up.\n\n"
+ "Afterwards you will want to save the\n"
+ "project, and export the data in the\n"
+ "appropriate format.",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
self.createSamplesFromExcelKea()
self.importEBridaSamplesSpreadsheet()
self.resultsTable.setCrop("Kiwifruit")
self.importLightcyclerFile()
self.kiwifruitResults()
self.__updateView()
def brassicaRyegrassWizard(self):
"""Runs a wizard to input data for a brassica or ryegrass project."""
dialog = QtGui.QMessageBox.information(
self,
"Brassica/Ryegrass Wizard",
"You will be prompted to set up samples\n"
+ "and to select files for import. Sample\n"
+ "setup requires you to select the crop.\n"
+ "This determines which results will be\n"
+ "included in the output files.\n\n"
+ "For Brassica, select:\n"
+ "-Brassica for a normal project\n"
+ "-Brassica R-S to include Rape-Swede\n"
+ "-Brassica J/P-C to include Juncea/Pak Choy\n"
+ "-Brassica SPF for Spitfire/Other Rape\n\n"
+ "For Ryegrass, select:\n"
+ "-Ryegrass for a normal project\n"
+ "-Ryegrass501 for AR501/Other Endo\n\n"
+ "The files you will need are the plates\n"
+ "records spreadsheet and the appropriate\n"
+ "Lightcycler .txt files.\n\n"
+ "After running this wizard you will have\n"
+ "all required information imported and\n"
+ "all logic on results set up.\n\n"
+ "Afterwards you will want to save the\n"
+ "project, and export the data in the\n"
+ "appropriate format.",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
self.createPlates()
self.importPlatesSpreadsheet()
self.importLightcyclerFile()
self.resultsTable.negativiseUnknowns()
self.brassicaRyegrassResults()
self.__updateView()
def keaWizard(self):
"""Runs a wizard to input data for a kea (no ebrida) project."""
dialog = QtGui.QMessageBox.information(
self,
"Kea Wizard",
"You will be prompted to select files for\n"
+ "import. The files you will need are:\n"
+ " - Kea sample batch harvest sheet\n"
+ " - Plates records spreadsheet\n"
+ " - Lightcycler .txt files\n\n"
+ "After running this wizard you will have\n"
+ "all required information imported and\n"
+ "all logic on results set up.\n\n"
+ "Afterwards you will want to save the\n"
+ "project, and export the data in the\n"
+ "appropriate format.",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
self.createSamplesFromExcelKea()
self.setCrop()
self.importLightcyclerFile()
self.appleResults()
self.__updateView()
########################################################################
## Import Menu Actions
def importSamplesSpreadsheet(self):
"""Opens an Excel spreadsheet and adds the information to samples."""
title = "Locate samples spreadsheet..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
excelFile = pd.ExcelFile(fileName)
sheet, ok = MyDialog.chooseExcelSheet(excelFile.sheet_names)
imported = excelFile.parse(sheet)
indexBy, ok = MyDialog.chooseIndexMethod()
if indexBy == "Plate ID and Well":
plateC, wellC, ok = MyDialog.choosePlateAndWellColumns(imported.columns)
imported["Plate ID"] = imported[plateC]
imported["Well"] = imported[wellC]
imported = imported.set_index(["Plate ID", "Well"])
self.infoTable = self.infoTable.set_index(["Plate ID", "Well"])
elif indexBy == "Plate Name and Well":
plateC, wellC, ok = MyDialog.choosePlateAndWellColumns(imported.columns)
imported["Plate Name"] = imported[plateC]
imported["Well"] = imported[wellC]
imported = imported.set_index(["Plate ID", "Well"])
self.infoTable = self.infoTable.set_index(["Plate ID", "Well"])
elif indexBy == "Other column":
tabC, impC, ok = MyDialog.chooseCol(self.infoTable.columns, imported.columns)
imported = imported.set_index(impC)
self.infoTable = self.infoTable.set_index(tabC)
columnsToImport, ok = MyDialog.chooseColumns(imported.columns)
self.infoTable = self.infoTable.join(imported[columnsToImport], rsuffix="_new")
self.infoTable = self.infoTable.reset_index()
self.__updateView()
def importEBridaSamplesSpreadsheet(self):
"""Imports an EBrida Excel spreadsheet and adds the information.
Join is done on 'Plant Alt Names' table column with 'Barcode'
spreadsheet column."""
title = "Locate E-Brida spreadsheet..."
fileName, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
excelFile = pd.ExcelFile(fileName)
imported = excelFile.parse("Sheet1")
columns = {
"From Ped. Item (origin)": "From Ped. Item",
"synonym": "synonyms",
"Synonym": "synonyms",
"Synonyms": "synonyms",
"breederCrCode": "synonyms",
"BreederCrCode": "synonyms",
"breederName": "BreederName",
}
imported = imported.rename(columns=columns)
tableKey, importKey = "Plant Alt Names", "Barcode"
self.infoTable.importSampleData(imported, tableKey, importKey)
self.__updateView()
def importPlatesSpreadsheet(self):
"""Opens the Plates Records spreadsheet and adds data."""
plateData = self.__getPlatesRecords()
self.resultsTable.importPlateData(plateData, "Plate ID")
self.infoTable.importPlateData(plateData, "Plate ID")
self.__updateView()
def importLightcyclerFile(self):
"""Imports Lightcycler .txt files and adds the results, locating
samples by plate name (taken from filename) and well."""
title = "Import LC file(s)..."
filter_mask = "Lightcycler text files (*.txt)"
lightFileNames, f = QtGui.QFileDialog.getOpenFileNames(self, title, self.path, filter_mask)
fileDataLists, ok = LCDialog.importLC(lightFileNames)
if ok:
self.resultsTable.addLCFiles(fileDataLists)
self.__updateView()
def importTaqmanFile(self):
"""Imports Taqman .txt files and adds the results, locating samples
by plate name (taken from filename) and well."""
title = "Import Taqman file(s)..."
filter_mask = "Taqman text files (*.txt)"
lightFileNames, f = QtGui.QFileDialog.getOpenFileNames(self, title, self.path, filter_mask)
fileDataLists, ok = LCDialog.importLC(lightFileNames)
if ok:
self.resultsTable.addTaqFiles(fileDataLists)
self.__updateView()
def importSpecFile(self):
"""Imports csv files from the plate spec machine, creates a
standard curve for each file, converts to concentration, and adds
the data as a column"""
pass
########################################################################
## Cherry Menu Actions
def cherryPickHelp(self):
"""Displays information about how to run a round of cherrypicking."""
dialog = QtGui.QMessageBox.information(
self,
"About cherrypicking",
"Only cherrypicking for Negatives/Unknowns is fully\n"
+ "implemented currently. Multiple marker cherrypicking\n"
+ "will be available in Poo.py.\n\n"
+ "Choosing Cherry pick N/U will open a dialog where\n"
+ "can choose the location for the cherrypicking files\n"
+ "to be saved. There will be one Excel file, which gives\n"
+ "an overview, and a bunch of .csv's to run on the robot.\n\n"
+ "The Excel file is required when the results are to be\n"
+ "imported, in order for the LC results to be mapped to\n"
+ "the correct sample.\n",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
def cherryPickNegativeUnknown(self):
"""Outputs files for cherrypicking Negatives/Unknowns."""
cherryTable = self.resultsTable.getCherriesNU()
self.outputCherries(cherryTable)
def cherryPickFromPopulation(self):
"""Outputs files for cherrypicking by Population and Result."""
title = "Choose populations, results, and numbers to cherrypick..."
populations = self.resultsTable.getPopulations()
groups = self.resultsTable.getGroups()
cherryData, ok = CherryDialog.run(populations, groups)
cherryTable = self.resultsTable.getCherriesByPop(cherryData)
self.outputCherries(cherryTable)
def outputCherries(self, cherryTable):
"""Outputs cherrypicking files for the passed cherryTable."""
title = "Choose folder for output..."
directory = QtGui.QFileDialog.getExistingDirectory(self, title, self.path)
writer = pd.ExcelWriter(os.path.join(directory, "cherrypicking.xls"))
cherryTable.to_excel(writer, "All", index=False)
summarySource = cherryTable[["Run", "Source Position", "Source plate"]].drop_duplicates().reset_index(drop=True)
summaryDest = (
cherryTable[["Run", "Destination Position", "Dest plate"]].drop_duplicates().reset_index(drop=True)
)
summarySource = summarySource.pivot(index="Run", columns="Source Position", values="Source plate")
summaryDest = summaryDest.pivot(index="Run", columns="Destination Position", values="Dest plate")
summary = summarySource.join(summaryDest)
summary.to_excel(writer, "Summary")
runs = pd.unique(cherryTable.Run.ravel())
for run in runs:
runTable = cherryTable[cherryTable.Run == run]
runTable.to_excel(writer, run, index=False)
runTable.to_csv(os.path.join(directory, run + ".csv"), index=False)
writer.save()
def importCherryPicking(self):
"""Imports files for a round of Cherrypicking."""
title = "Choose cherrypicking file..."
cherryFile, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
title = "Choose lightcycler files..."
filter_mask = "Lightcycler text files (*.txt)"
lightFileNames, f = QtGui.QFileDialog.getOpenFileNames(self, title, self.path, filter_mask)
fileDataLists, ok = LCDialog.importLC(lightFileNames)
lc = pd.read_excel(cherryFile, sheetname="All")
lc = lc[["Source plate", "Dest plate", "Source Well", "Destination Well"]]
lc.columns = ["Plate ID", "CP Plate", "Well", "CP Well"]
lc["LC Well"] = ""
lc["Result"] = ""
lc["Experiment"] = ""
lc = lc.set_index(["CP Plate", "CP Well"])
for fDL in fileDataLists:
name, plate, exp, robot, pos = fDL
lcFrame = pd.read_table(name, sep="\t", header=1)
lcFrame = lcFrame.drop(["Include", "Color", "Name", "Status"], 1)
lcFrame["Experiment"] = exp
lcFrame["CP Plate"] = plate
lcFrame["CP Well"] = lcFrame["Pos"].map(lambda x: convert[robot][pos][x])
lcFrame["Group"] = lcFrame["Group"].astype(str)
lcFrame.columns = ["LC Well", "Result", "Experiment", "CP Plate", "CP Well"]
lcFrame = lcFrame.set_index(["CP Plate", "CP Well"])
lc.update(lcFrame)
lc = lc.set_index(["Plate ID", "Well"])
self.resultsTable.table = self.resultsTable.table.set_index(["Plate ID", "Well"])
self.resultsTable.table.update(lc)
self.resultsTable.table = self.resultsTable.table.reset_index()
self.__updateView()
def importCherryPickingTaq(self):
"""Taq"""
title = "Choose cherrypicking file..."
cherryFile, f = QtGui.QFileDialog.getOpenFileName(self, title, self.path)
title = "Choose lightcycler files..."
filter_mask = "Lightcycler text files (*.txt)"
lightFileNames, f = QtGui.QFileDialog.getOpenFileNames(self, title, self.path, filter_mask)
fileDataLists, ok = LCDialog.importLC(lightFileNames)
lc = pd.read_excel(cherryFile, sheetname="All")
lc = lc[["Source plate", "Dest plate", "Source Well", "Destination Well"]]
lc.columns = ["Plate ID", "CP Plate", "Well", "CP Well"]
lc["LC Well"] = ""
lc["Result"] = ""
lc["Experiment"] = ""
lc = lc.set_index(["CP Plate", "CP Well"])
for fDL in fileDataLists:
name, plate, exp, robot, pos = fDL
lcFrame = pd.read_table(name, sep="\t", header=1)
lcFrame = lcFrame.drop(["Include", "Color", "Name", "Status", "465-510", "533-580", "Score"], 1)
lcFrame["Experiment"] = exp
lcFrame["CP Plate"] = plate
lcFrame["CP Well"] = lcFrame["Pos"].map(lambda x: convert[robot][pos].get(x, ""))
lcFrame["Call"] = lcFrame["Call"].astype(str)
lcFrame.columns = ["LC Well", "Result", "Experiment", "CP Plate", "CP Well"]
lcFrame = lcFrame[lcFrame["CP Well"] != ""]
lcFrame = lcFrame.set_index(["CP Plate", "CP Well"])
lc.update(lcFrame)
lc = lc.set_index(["Plate ID", "Well"])
lc = lc[lc["Result"] != ""]
self.resultsTable.table = self.resultsTable.table.set_index(["Plate ID", "Well"])
self.resultsTable.table.update(lc)
self.resultsTable.table = self.resultsTable.table.reset_index()
self.__updateView()
########################################################################
## Data Menu Actions
def editPlates(self):
"""Opens a popup table where the data in the sample table can be
edited by plate, rather than by sample."""
plates = self.resultsTable.table[
["Plate ID", "Plate Name", "Plate Kea", "Crop", "Experiment", "Grind", "Include"]
]
plates = plates.drop_duplicates(subset=["Plate ID"])
platesData, ok = EditPlatesDialog.run(plates)
self.resultsTable.editPlates(platesData)
self.infoTable.editPlates(platesData)
self.__updateView()
def viewPlateStats(self):
"""Opens a popup with result stats organised by plate."""
included = self.resultsTable.table[self.resultsTable.table["Include"] == True]
included = included[included.Group != "No sample"]
groups = list(np.unique(included["Group"]))
statsTable = self.__getStatsTable(included, groups, "Plate ID")
ok = StatsDialog.run(statsTable)
def viewPopulationStats(self):
"""Opens a popup with result stats organised by population."""
included = self.resultsTable.table[self.resultsTable.table["Include"] == True]
groups = list(np.unique(included["Group"]))
statsTable = self.__getStatsTable(included, groups, "Population")
ok = StatsDialog.run(statsTable)
def setCrop(self):
"""Opens a popup to set crop for all samples."""
crop, ok = MyDialog.chooseCrop()
if ok:
self.resultsTable.setCrop(crop)
self.__updateView()
def explainCrop(self):
"""Opens a popup to explain which marker results are valid."""
dialog = QtGui.QMessageBox.information(
self,
"Crop explanation",
"Calls expected:\n"
+ "Brassica: Kale, Rape, Swede, Turnip\n"
+ "Brassica R-S: Kale, Rape, Swede, Turnip, Rape-Swede\n"
+ "Brassica J-P/C: Kale, Rape, Swede, Turnip, Juncea, Pak Choy\n"
+ "Brassica SPF: Spitfire, Other Rape\n"
+ "Ryegrass: AR1, AR37, Ct/wt, AR542/584, AR542, AR581\n"
+ "Ryegrass501: AR501, Other Endo\n"
+ "Kiwifruit: Male, Female, Super Male,\n"
+ " (Super) (Fem/M)ale Type (1/2/I/II)\n"
+ "Apple: 1, 2, 3, 4\n\n"
+ "Statistics provided:\n"
+ "Brassica: Kale, Rape, Swede, Turnip\n"
+ "Brassica R-S: Kale, Rape, Swede, Turnip, Rape-Swede\n"
+ "Brassica J-P/C: Kale, Rape, Swede, Turnip, Juncea, Pak Choy\n"
+ "Brassica SPF: Spitfire, Other Rape\n"
+ "Ryegrass: Group 1, Group 2, Group 3, Group 4, Group 5\n"
+ "Ryegrass501: AR501, Other Endo\n"
+ "Kiwifruit: Male, Female\n"
+ "Apple: 1, 2, 3, 4\n",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
########################################################################
## Results Menu Actions
def standardiseResults(self):
"""Corrects HRM results so you can change both 'male' and 'Male' to 'M'."""
results = np.unique(self.resultsTable.table["Result"])
standardisations, ok = MyDialog.standardiseResults(results)
if ok:
self.resultsTable.table["Result"] = self.resultsTable.table["Result"].map(lambda res: standardisations[res])
self.__updateView()
def negativiseUnknowns(self):
"""Sets all Unknown results in Results column to Negative."""
self.resultsTable.negativiseUnknowns()
self.__updateView()
def addAutoResults(self):
self.resultsTable.table["Group"] = self.resultsTable.table.apply(
lambda row: standards[row["Crop"]].get(row["Result"], np.nan), 1
)
self.__updateView()
def addManualResults(self):
"""Adds data to the Group column based on the Result column"""
results = np.unique(self.resultsTable.table["Result"])
standardisations, ok = MyDialog.standardiseResults(results)
if ok:
self.resultsTable.table["Group"] = self.resultsTable.table["Result"].map(lambda res: standardisations[res])
self.__updateView()
def setNonExistsToNoSample(self):
self.resultsTable.setNonExistsToNoSample()
def setNonExistsToNegative(self):
self.resultsTable.setNonExistsToNegative()
def includeAll(self):
self.resultsTable.includeAll()
self.__updateView()
def excludeFailGrinds(self):
self.resultsTable.excludeFailGrinds()
self.__updateView()
def excludeNegativeFailGrinds(self):
self.resultsTable.excludeNegativeFailGrinds()
self.__updateView()
def excludeNonExists(self):
self.resultsTable.excludeNonExists()
self.__updateView()
def kiwifruitResults(self):
self.addAutoResults()
self.setNonExistsToNoSample()
def brassicaRyegrassResults(self):
self.addAutoResults()
self.excludeNegativeFailGrinds()
self.excludeNonExists()
def appleResults(self):
self.addAutoResults()
self.setNonExistsToNoSample()
########################################################################
## Export Menu Actions
def __checkResults(self):
"""Makes sure there are good results in the Results and Groups
columns in preparation for export."""
if self.resultsTable.missingResults()[0]:
dialog = QtGui.QMessageBox.information(
self,
"Invalid Results",
"One or more entries in the Result column is invalid.\n"
+ "Please check all LC files imported properly.\n"
+ "There should be no nan in the Result column.",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
return False
elif self.resultsTable.missingResults()[1]:
dialog = QtGui.QMessageBox.information(
self,
"Invalid Groups",
"One or more entries in the Group column is invalid.\n"
+ "Please check for typos in the Results column,\n"
+ "and make sure the correct marker is selected.\n"
+ "Typos can be mixed with Results > Standardise\n"
+ "results. The marker can be set with Data > set\n"
+ "crop. After completing either of these steps,\n"
+ "select Results > Add groups by crop...",
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Ok,
)
return False
else:
return True
def outputHarvestSheets(self):
"""Outputs harvest spreadsheets."""
title = "Excel filename..."
exportFileName, f = QtGui.QFileDialog.getSaveFileName(self, title, self.path)
exportFileName = exportFileName.split(".")[0]
workBook = ExportWorkbook()
sampleTable = self.resultsTable.table.merge(self.infoTable.table, on=["Plate ID", "Well"], suffixes=("", "_y"))
workBook.addHarvestSheets(sampleTable)
workBook.save(exportFileName + ".xls")
def outputForKea(self):
"""Outputs an Excel file suitable for upload to Kea via the sex
testing process run."""
if self.__checkResults():
title = "Excel filename..."
exportFileName, f = QtGui.QFileDialog.getSaveFileName(self, title, self.path)
exportFileName = exportFileName.split(".")[0]
experiments = self.resultsTable.getExperiments()
experimentData, ok = ExperimentDialog.run(experiments)
if ok:
columns = ["Sample ID", "Plant Alt Names", "Plate Name", "Experiment", "Group"]
resultTable = self.resultsTable.getKeaSexTestingData()
infoTable = self.infoTable.getKeaSexTestingData()
table = resultTable.join(infoTable, rsuffix="i").reset_index()
table["Screening Date"] = table["Slipstream Expt No"].apply(lambda x: experimentData[x][0])
table["Marker Name"] = table["Slipstream Expt No"].apply(lambda x: experimentData[x][1])
table["Notes"] = ""
table["Operator"] = ""
columns = [
"Sample ID",
"Plant AltName",
"Plate",
"Screening Date",
"Slipstream Expt No",
"Marker Name",
"Sex Marker Results",
"Notes",
"Operator",
]
table = table[columns]
writer = pd.ExcelWriter(exportFileName + ".xls")
table.to_excel(writer, "Data", index=False)
writer.save()
def outputForEBrida(self):
"""Outputs results as a spreadsheet based on the recieved EBrida spreadsheet..."""
if self.__checkResults():
title = "Excel filename..."
exportFileName, f = QtGui.QFileDialog.getSaveFileName(self, title, self.path)
exportFileName = exportFileName.split(".")[0]
keys = ["Plate ID", "Well"]
resColumns = ["Group", "Plate ID", "Plate Kea", "Well"]
infoColumns = [
"Pedigree Item",
"Plot",
"Group",
"Start Date",
"From Ped. Item",
"Mother",
"Father",
"Barcode",
"synonyms",
"fundingNameCr",
"BreederName",
"Sample ID",
]
outputColumns = [
"Pedigree Item",
"Plot",
"Group",
"Start Date",
"From Ped. Item",
"Mother",
"Father",
"Barcode",
"synonyms",
"fundingNameCr",
"BreederName",
"keaID",
"Result",
"Plate ID",
"Plate Name",
"Well",
]
info = self.infoTable.table[infoColumns + keys]
results = self.resultsTable.table[resColumns]
results.columns = ["Result", "Plate ID", "Plate Kea", "Well"]
outputTable = pd.merge(info, results, on=keys, sort=False)
outputTable.rename(columns={"Sample ID": "keaID", "Plate Kea": "Plate Name"}, inplace=True)
outputTable = outputTable[outputColumns]
writer = pd.ExcelWriter(exportFileName + ".xls")
outputTable.to_excel(writer, "Sheet1", index=False)
writer.save()
def colouredResults(self):
"""Outputs an Excel file with a summary table, a sample table,
and a plate sheet for each plate."""
if self.__checkResults():
title = "Excel filename..."
exportFileName, f = QtGui.QFileDialog.getSaveFileName(self, title, self.path)
exportFileName = exportFileName.split(".")[0]
crops = list(np.unique(self.resultsTable.table["Crop"]))
groupsLists = [groups[crop] for crop in crops]
incGroups = [item for sublist in groupsLists for item in sublist]
incGroups = incGroups + ["Unknown", "Negative"]
included = self.resultsTable.table[self.resultsTable.table["Include"] == True]
exportTable = included[["Plate ID", "Plate Name", "Well", "Result", "Group"]].reset_index(drop=True)
statsTable = self.__getStatsTable(exportTable, incGroups, "Plate ID")
statsTable["Ind"] = statsTable.index.values
plates = statsTable[["Plate ID", "Plate Name"]]
ok = True
while (plates["Plate Name"].str.len() > 23).any() and ok:
plates, ok = ShortenPlateNamesDialog.run(plates)
statsTable = statsTable.set_index("Plate ID")
exportTable = exportTable.set_index("Plate ID")
plates = plates.set_index("Plate ID")
statsTable.update(plates)
exportTable.update(plates)
statsTable = statsTable.reset_index()
exportTable = exportTable.reset_index()
if ok:
workBook = ExportWorkbook()
workBook.addStatsPage(incGroups, statsTable)
workBook.addSamplePage(exportTable)
workBook.addPlateSheets(statsTable, exportTable, incGroups)
workBook.save(exportFileName + ".xls")
def niceKeaSpreadsheet(self):
"""Outputs Results and Kea data to a spreadsheet."""
if self.__checkResults():
title = "Excel filename..."
exportFileName, f = QtGui.QFileDialog.getSaveFileName(self, title, self.path)
exportFileName = exportFileName.split(".")[0]
columns = ["Plate ID", "Plate Kea", "Well", "Sample ID", "PlantID", "Group"]
table = (
self.resultsTable.table.set_index(["Plate ID", "Well"])
.join(self.infoTable.table.set_index(["Plate ID", "Well"]), rsuffix="i")
.reset_index()
)
table = table[columns]
table["Ind"] = table.index.values
workBook = ExportWorkbook()
workBook.addKeaTable(table)
workBook.save(exportFileName + ".xls")
