def loadFile(self, file: str = ""):
"""
provides a filedialog to load an additional file to the dataframe
"""
options = QFileDialog.Options()
if not file:
file, _ = QFileDialog.getOpenFileName(
self,
"QFileDialog.getOpenFileName()",
"",
"All Files (*);;mzML Files (*.mzML)",
options=options)
if file:
cdf = Tdf.getTable(self)
filelist = []
filePath = file.rsplit("/", 1)[0]
temp = file.split("/")
fileName = temp[len(temp) - 1]
if file:
# print(file)
filelist.append(fileName)
tagged_file = fh.tagfiles(self, filelist)
df = fh.createRawTable(self, tagged_file, filePath)
ndf = cdf.append(df, ignore_index=True)
Tdf.setTable(self, ndf)
self.drawTable()
else:
return False
def LabelBtn(self):
"""
Let the user choose the number of labels, it will generate
the labels for the copied rows and also links the sample to
the label. Gives an option to continue the samplecount
over fraction groups.
"""
labelnum, ok = QInputDialog.getInt(
self, "Label",
"Please specify the multiplicity " + "of the selected rows")
if ok:
rep = QMessageBox.question(
self, "Continuous Sample", "Does the samplenumber " +
"continue over multiple " + "fraction groups?",
(QMessageBox.Yes | QMessageBox.No), QMessageBox.No)
if rep == QMessageBox.Yes:
try:
Tdf.modifyLabelSample(self, labelnum, True)
except ValueError:
QMessageBox.about(self, "Warning",
"Unfortunaly, " + "your Number was <1")
else:
try:
Tdf.modifyLabelSample(self, labelnum, False)
except ValueError:
QMessageBox.about(self, "Warning",
"Unfortunaly, " + "your Number was <1")
self.drawTable()
def RemoveBtn(self):
"""
Enables the user to remove selected rows
"""
selrows = self.getSelRows()
Tdf.rmvRow(self, selrows)
self.drawTable()
def loadDir(self, filepath: str):
Files = fh.getFiles(self, filepath)
delimiters = ["_"]
preparedFiles = fh.tagfiles(self, sorted(Files), delimiters[0])
rawTable = fh.createRawTable(self, preparedFiles, filepath)
Tdf.setTable(self, rawTable)
self.drawTable()
def FractionBtn(self):
"""
Enables the user to change the Fraction of selected rows to a given
number or give a range.
"""
selrows = self.getSelRows()
# first inputdialog
fracmin, ok = QInputDialog.getInt(
self, "Fraction",
"Enter minimal Fractionnumber " + "or single Fractionnumber")
# second inputdialog if first is accepted
if ok:
fracmax, ok = QInputDialog.getInt(
self, "Fraction", "Enter maximal Fractionnumber " +
"or 0 for single Fractionnumber")
if ok:
# decision if multiple fractions are set or just one
if fracmax != 0:
if fracmax > fracmin:
# third messagedialog
rep = QMessageBox.question(
self, "Fraction Group?",
"Do you want to infer a " +
"Fraction Group from the " + "given range?",
(QMessageBox.Yes | QMessageBox.No), QMessageBox.No)
# when confirmed the fraction froup is set
# when max fraction is reached.
if rep == QMessageBox.Yes:
Tdf.modifyFraction(self, selrows, fracmin, fracmax)
fractions = fracmax - fracmin + 1
numgroups = math.ceil(len(selrows) / fractions)
splicelist = [0]
for g in range(1, numgroups + 1):
splicelist.append(g * fractions)
splicelist.append(len(selrows))
for group in range(1, numgroups + 1):
indexa = splicelist[group - 1]
indexb = splicelist[group]
subrows = selrows[indexa:indexb]
Tdf.modifyGroup(self, subrows, group)
else:
Tdf.modifyFraction(self, selrows, fracmin, fracmax)
elif fracmax == fracmin:
Tdf.modifyFraction(self, selrows, fracmin)
else:
QMessageBox.warning(
self, "Error",
"Please use " + "a higher integer " +
"number for the maximum " + "fractionnumber.")
else:
Tdf.modifyFraction(self, selrows, fracmin)
self.drawTable()
def GroupBtn(self):
"""
Enables the user to change the group of selected rows to a given
number.
"""
selrows = self.getSelRows()
groupnum, ok = QInputDialog.getInt(self, "Group Number",
"Enter Integer Groupnumber")
if ok:
Tdf.modifyGroup(self, selrows, groupnum)
self.drawTable()
def editField(self):
if len(self.table.selectedItems()) == 1:
if not self.drawtableactive:
itemchanged = self.table.currentItem()
newvalue = itemchanged.text()
row = itemchanged.row()
column = itemchanged.column()
if column != 2:
Tdf.modifyField(self, row, column, newvalue)
self.drawTable()
else:
QMessageBox.about(
self, "Warning", "Please only, " +
"modify attribute columns," + "not the filepath.\n" +
"To change the filepath," + "use remove and add file.")
self.drawTable()
def updateTableView(self, rows):
tabledf = Tdf.getTable(self)
rowcount = len(tabledf.index)
for i in range(rowcount):
self.table.setRowHidden(i, True)
for i in rows:
self.table.setRowHidden(i, False)
def exportBtn(self):
"""
Exports the table to csv or tsv;default is csv
"""
options = QFileDialog.Options()
file, _ = QFileDialog.getSaveFileName(
self,
"QFileDialog.getSaveFileName()",
"",
"All Files (*);;tsv (*.tsv);; csv (*.csv)",
options=options)
if file:
self.tablefile_loaded = True
fpath = file.split("/")[-1]
self.loaded_table = fpath
df = Tdf.getTable(self)
temp = file.split("/")
fileName = temp[len(temp) - 1]
length = len(fileName)
if length < 4:
ftype = "csv"
file = file + ".csv"
elif fileName.find('.csv', length - 4) != -1:
ftype = "csv"
elif fileName.find('.tsv', length - 4) != -1:
ftype = "tsv"
else:
ftype = "csv"
file = file + ".csv"
fh.exportTable(self, df, file, ftype)
def saveFunction(self):
"""
saves all work from the GUI in chosen folder
the prefix of the outputfiles can be choosen
"""
dlg = QFileDialog(self)
filePath = dlg.getExistingDirectory()
if filePath:
filePath = filePath + "/"
tablePath = ""
ok = False
table_empty = self.tview.table.rowCount() <= 0
if table_empty:
tablePath = ""
self.tablefile_loaded = False
self.tview.tablefile_loaded = False
if self.tablefile_loaded is False and table_empty is False \
and self.tview.tablefile_loaded is False:
prefix, ok = QInputDialog.getText(
self, "Prefix for outputfiles",
"Please specify a prefix " + "for the outputfiles")
if ok:
tablePath = filePath + prefix + "_design.tsv"
self.loaded_table = prefix + "_design.tsv"
self.tablefile_loaded = True
if self.tablefile_loaded and self.tview.tablefile_loaded is False:
tablePath = filePath + self.loaded_table
if self.tview.tablefile_loaded:
tablePath = filePath + self.tview.loaded_table
if (ok or self.tablefile_loaded or self.tview.tablefile_loaded) \
and table_empty is False:
df = Tdf.getTable(self.tview)
fh.exportTable(self.tview, df, tablePath, "tsv")
xmlPath = filePath + self.loaded_ini
try:
self.cview.tree.write(xmlPath)
except TypeError:
print("No Config loaded to be saved!")
if self.loaded_ini != "" and tablePath.split("/")[-1] != "":
QMessageBox.about(
self, "Successfully saved!", "Files have been saved as: " +
self.loaded_ini + ", " + tablePath.split("/")[-1])
elif self.loaded_ini != "":
QMessageBox.about(self, "Successfully saved!",
"ini has been saved as: " + self.loaded_ini)
elif tablePath.split("/")[-1] != "":
QMessageBox.about(
self, "Successfully saved!",
"Table has been saved as: " + tablePath.split("/")[-1])
def importBtn(self, file: str = ""):
"""
Imports table files, currently working are csv and tsv
"""
options = QFileDialog.Options()
if not file:
file, _ = QFileDialog.getOpenFileName(
self,
"QFileDialog.getOpenFileName()",
"",
"All Files (*);;tsv (*.tsv);; csv (*.csv)",
options=options)
if file:
df = fh.importTable(self, file)
Tdf.setTable(self, df)
self.drawTable()
self.tablefile_loaded = True
file = file.split("/")[-1]
self.loaded_table = file
def filterTable(self):
"""
get changes from textbox and update table when
more than 3 characters are given.
then update table with the rows that
contain the input in the give column.
"""
tb = self.textbox
givencolumn = "Spectra_Filepath"
tbinput = tb.text()
ft = Tdf.getTable(self)
validDf = not (ft.empty or ft.dropna().empty)
# print(validDf) # for debugging
# print(type(ft)) # for debugging
if len(tbinput) >= 2:
rowstoshow = ft[ft[givencolumn].str.contains(tbinput)]
self.updateTableView(rowstoshow.index)
else:
self.updateTableView(ft.index)
def drawTable(self):
"""
draws a table with the dataframe table model in tableDataFrame
"""
self.drawtableactive = True
tabledf = Tdf.getTable(self)
# print(tabledf) # For debugging
rowcount = len(tabledf.index)
colcount = len(tabledf.columns)
self.table.setRowCount(rowcount)
for r in range(rowcount):
row = tabledf.index[r]
for c in range(colcount):
col = tabledf.columns[c]
if col == 'Spectra_Filepath':
path = tabledf.at[row, col].split("/")
name = path[len(path) - 1]
self.table.setItem(r, c, QTableWidgetItem(name))
else:
item = str(tabledf.at[row, col])
self.table.setItem(r, c, QTableWidgetItem(item))
self.drawtableactive = False
def loadFunction(self, filePath: str = ""):
"""
loads all files (.tsv .ini, .fasta) from a given
directory.
If .tsv file is not present the experimental design is
filled with mzMl files
If no .ini file is present default ini file is written
and is loaded automatically
"""
if not filePath:
dlg = QFileDialog(self)
filePath = dlg.getExistingDirectory()
self.loaded_dir = filePath
self.sview.fillTable(filePath)
if filePath:
try:
self.tsvfiles = glob.glob('*.tsv')
if len(self.tsvfiles) > 1:
QMessageBox.about(
self, "Sorry!", "There are multiple '.tsv-'"
"files in the specified folder. "
"Please choose the one you intent "
"to use.")
dial = QFileDialog(self)
newFilePath = dial.getOpenFileName(self, "Choose .tsv",
filePath,
"Tables (*.tsv)")
if newFilePath[0] != '':
newFile = newFilePath[0].split("/")[-1]
self.tsvfiles = [newFile]
else:
QMessageBox.about(
self, "Sorry!", "Nothing was choosen. "
"Therefore no '.tsv'-file was "
"loaded. ")
self.tsvfiles = []
for file in self.tsvfiles:
df = fh.importTable(self.tview, file)
Tdf.setTable(self.tview, df)
self.tview.drawTable()
self.loaded_table = file
self.tablefile_loaded = True
except TypeError:
"No '.tsv' or '.csv'-file could be loaded."
if self.tablefile_loaded is False:
try:
self.tview.loadDir(filePath)
self.tablefile_loaded = True
except TypeError:
print("Could not load '.mzMl'-files.")
try:
self.iniFiles = glob.glob('*.ini')
if len(self.iniFiles) > 1:
QMessageBox.about(
self, "Sorry!", "There are multiple '.ini'-"
"files in the specified folder. "
"Please choose the one you intent "
"to use.")
dial = QFileDialog(self)
newFilePath = dial.getOpenFileName(self, "Choose .ini",
filePath,
"Config (*.ini)")
if newFilePath[0] != '':
newFile = newFilePath[0].split("/")[-1]
self.iniFiles = [newFile]
else:
QMessageBox.about(
self, "Sorry!", "Nothing was choosen. "
"Therefore no '.ini'-file was "
"loaded. ")
self.iniFiles = []
for file in self.iniFiles:
self.cview.generateTreeModel(file)
self.loaded_ini = file
self.ini_loaded = True
except TypeError:
print("Could not load .ini file.")
if self.ini_loaded is False:
try:
runcall = "ProteomicsLFQ "
writeIniFile = "-write_ini "
out = "Config.ini"
command = (runcall + writeIniFile + out)
os.chdir(filePath)
os.system(command)
iniFiles = glob.glob('*.ini')
for file in iniFiles:
self.cview.generateTreeModel(file)
self.loaded_ini = file
self.ini_loaded = True
except TypeError:
print("Could not write and load default '.ini'-file.")
try:
self.fastafiles = glob.glob('*fasta')
if len(self.fastafiles) > 1:
QMessageBox.about(
self, "Sorry!", "There are multiple '.fasta'-"
"files in the specified folder. "
"Please choose the one you intent "
"to use.")
dial = QFileDialog(self)
newFilePath = dial.getOpenFileName(
self, "Choose .fasta", filePath,
"Proteindata (*.fasta)")
if newFilePath[0] != '':
newFile = newFilePath[0].split("/")[-1]
self.fastafiles = [newFile]
else:
QMessageBox.about(
self, "Sorry!", "Nothing was choosen. "
"Therefore, no '.fasta'-file "
"was loaded. ")
self.fastafiles = []
for file in self.fastafiles:
self.fview.loadFile(file)
self.loaded_fasta = file
self.fasta_loaded = True
except TypeError:
print("Could not load '.fasta'-file.")