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 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 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 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 setCrop(self):
"""Opens a popup to set crop for all samples."""
crop, ok = MyDialog.chooseCrop()
if ok:
self.resultsTable.setCrop(crop)
self.__updateView()
