def loadFileMzML(self, file_path):
self.isAnnoOn = False
self.msexperimentWidget = QSplitter(Qt.Vertical)
# data processing
scans = self.readMS(file_path)
# set Widgets
self.spectrum_widget = SpectrumWidget()
self.scan_widget = ScanTableWidget(scans)
self.seqIons_widget = SequenceIonsWidget()
self.error_widget = ErrorWidget()
self.tic_widget = TICWidget()
self.drawTic(scans)
# connected signals
self.scan_widget.sigScanClicked.connect(self.updateWidgetDataFromRow)
self.tic_widget.sigRTClicked.connect(self.ticToTable)
self.msexperimentWidget.addWidget(self.tic_widget)
self.msexperimentWidget.addWidget(self.seqIons_widget)
self.msexperimentWidget.addWidget(self.spectrum_widget)
self.msexperimentWidget.addWidget(self.error_widget)
self.msexperimentWidget.addWidget(self.scan_widget)
self.mainlayout.addWidget(self.msexperimentWidget)
# set widget sizes, where error plot is set smaller
widget_height = self.msexperimentWidget.sizeHint().height()
size_list = [
widget_height, widget_height, widget_height, widget_height * 0.5,
widget_height
]
self.msexperimentWidget.setSizes(size_list)
# default : first row selected.
self.scan_widget.table_view.selectRow(0)
class ControllerWidget(QWidget):
"""
Used to merge spectrum, table, TIC, error plot and sequenceIons widgets together.
"""
def __init__(self, *args, **kwargs):
QWidget.__init__(self, *args, **kwargs)
self.mainlayout = QHBoxLayout(self)
self.isAnnoOn = True
self.clickedRT = None
self.seleTableRT = None
self.mzs = np.array([])
self.ppm = np.array([])
self.colors = np.array([])
self.scanIDDict = {}
self.curr_table_index = None
self.filteredIonFragments = []
self.peakAnnoData = None
def clearLayout(self, layout):
for i in reversed(range(layout.count())):
layout.itemAt(i).widget().setParent(None)
def loadFileMzML(self, file_path):
self.isAnnoOn = False
self.msexperimentWidget = QSplitter(Qt.Vertical)
# data processing
scans = self.readMS(file_path)
# set Widgets
self.spectrum_widget = SpectrumWidget()
self.scan_widget = ScanTableWidget(scans)
self.seqIons_widget = SequenceIonsWidget()
self.error_widget = ErrorWidget()
self.tic_widget = TICWidget()
self.drawTic(scans)
# connected signals
self.scan_widget.sigScanClicked.connect(self.updateWidgetDataFromRow)
self.tic_widget.sigRTClicked.connect(self.ticToTable)
self.msexperimentWidget.addWidget(self.tic_widget)
self.msexperimentWidget.addWidget(self.seqIons_widget)
self.msexperimentWidget.addWidget(self.spectrum_widget)
self.msexperimentWidget.addWidget(self.error_widget)
self.msexperimentWidget.addWidget(self.scan_widget)
self.mainlayout.addWidget(self.msexperimentWidget)
# set widget sizes, where error plot is set smaller
widget_height = self.msexperimentWidget.sizeHint().height()
size_list = [
widget_height, widget_height, widget_height, widget_height * 0.5,
widget_height
]
self.msexperimentWidget.setSizes(size_list)
# default : first row selected.
self.scan_widget.table_view.selectRow(0)
def loadFileIdXML(self, file_path):
prot_ids = []
pep_ids = []
pyopenms.IdXMLFile().load(file_path, prot_ids, pep_ids)
Ions = {}
# extract ID data from file
for peptide_id in pep_ids:
pep_mz = peptide_id.getMZ()
pep_rt = peptide_id.getRT()
for hit in peptide_id.getHits():
pep_seq = str(hit.getSequence().toString())
if "." in pep_seq:
pep_seq = pep_seq[3:-1]
else:
pep_seq = pep_seq[2:-1]
for anno in hit.getPeakAnnotations():
ion_charge = anno.charge
ion_mz = anno.mz
ion_label = anno.annotation
Ions[ion_label] = [ion_mz, ion_charge]
self.scanIDDict[round(pep_rt, 3)] = {
'm/z': pep_mz,
'PepSeq': pep_seq,
'PepIons': Ions
}
Ions = {}
self.saveIdData()
def saveIdData(
self): # save ID data in table (correct rows) for later usage
rows = self.scan_widget.table_model.rowCount(self.scan_widget)
for row in range(0, rows - 1):
tableRT = round(
self.scan_widget.table_model.index(row, 2).data(), 3)
if tableRT in self.scanIDDict:
index_seq = self.scan_widget.table_model.index(row, 6)
self.scan_widget.table_model.setData(
index_seq, self.scanIDDict[tableRT]['PepSeq'],
Qt.DisplayRole)
index_ions = self.scan_widget.table_model.index(row, 7)
# data needs to be a string, but reversible -> using json.dumps()
self.scan_widget.table_model.setData(
index_ions,
json.dumps(self.scanIDDict[tableRT]['PepIons']),
Qt.DisplayRole)
def readMS(self, file_path):
# read MzML files
exp = pyopenms.MSExperiment()
pyopenms.MzMLFile().load(file_path, exp)
return exp
def drawTic(self, scans):
self.tic_widget.setTIC(scans.getTIC())
def ticToTable(self,
rt): # connect Tic info to table, and select specific row
self.clickedRT = round(rt * 60, 3)
if self.clickedRT != self.seleTableRT:
self.scan_widget.table_view.selectRow(self.findClickedRT())
def findClickedRT(self): # find clicked RT in the scan table
rows = self.scan_widget.table_model.rowCount(self.scan_widget)
for row in range(0, rows - 1):
if self.clickedRT == round(
self.scan_widget.table_model.index(row, 2).data(), 3):
index = self.scan_widget.table_model.index(row, 2)
try:
self.curr_table_index = self.scan_widget.proxy.mapFromSource(
index) # use proxy to get from filtered model index
return self.curr_table_index.row()
except ValueError:
print('could not found ModelIndex of row')
# for the future calculate ppm and add it to the table
def errorData(self, ions_data):
if ions_data not in "-":
ions_data_dict = json.loads(ions_data)
if ions_data_dict != {}:
self.colors, self.mzs = self.filterColorsMZIons(ions_data_dict)
mzs_size = len(self.mzs)
self.ppm = np.random.randint(0, 3, size=mzs_size)
self.error_widget.setMassErrors(
self.mzs, self.ppm,
self.colors) # works for a static np.array
else:
self.error_widget.clear()
else:
self.error_widget.clear()
def filterColorsMZIons(
self, ions_data_dict
): # create color/mz array by distinguishing between prefix & suffix ions
self.peakAnnoData = {
} # key is ion annotation (e.g. b2): [mz, color distinguishing prefix, suffix]
colors = []
mzs = []
col_red = (255, 0, 0) # suffix
col_blue = (0, 0, 255) # prefix
for fragData in self.filteredIonFragments:
anno = fragData[0]
if anno[0] in "abc":
colors.append(col_blue)
mzs.append(ions_data_dict[anno][0])
self.peakAnnoData[fragData[1]] = [
ions_data_dict[anno][0], col_blue
]
elif anno[0] in "xyz":
colors.append(col_red)
mzs.append(ions_data_dict[anno][0])
self.peakAnnoData[fragData[1]] = [
ions_data_dict[anno][0], col_red
]
return np.array(colors), np.array(mzs)
def updateWidgetDataFromRow(
self, index
): # after clicking on a new row, update spectrum, error plot, peptideSeq
# current row RT value
self.seleTableRT = round(index.siblingAtColumn(2).data(), 3)
# set new spectrum with setting that all peaks should be displayed
self.spectrum_widget.setSpectrum(self.scan_widget.curr_spec,
zoomToFullRange=True)
# only draw sequence with given ions for MS2 and error plot
if index.siblingAtColumn(0).data() == 'MS2':
self.drawSeqIons(
index.siblingAtColumn(6).data(),
index.siblingAtColumn(7).data())
self.errorData(index.siblingAtColumn(7).data())
if self.peakAnnoData is not None: # peakAnnoData created with existing ions in errorData (bc of coloring)
self.spectrum_widget.setPeakAnnotations(
self.createPeakAnnotation())
self.spectrum_widget.redrawPlot()
else:
self.spectrum_widget._clear_peak_annotations()
self.spectrum_widget.redrawPlot()
# otherwise delete old data
elif index.siblingAtColumn(0).data() == 'MS1':
self.seqIons_widget.clear()
self.error_widget.clear()
self.peakAnnoData = None
self.spectrum_widget._clear_peak_annotations()
self.spectrum_widget.redrawPlot()
def createPeakAnnotation(self):
pStructList = []
# for the future -> check clashes like in the TIC widget and then add labels (should be done in SpectrumWidget)
for anno, data in self.peakAnnoData.items():
mz, anno_color = data[0], data[1]
index = self.find_nearest_Index(self.spectrum_widget._mzs, mz)
pStructList.append(
PeakAnnoStruct(mz=self.spectrum_widget._mzs[index],
intensity=self.spectrum_widget._ints[index],
text_label=anno,
symbol=None,
symbol_color=anno_color))
return pStructList
def find_nearest_Index(self, array, value):
array = np.asarray(array)
idx = (np.abs(array - value)).argmin()
return idx
def drawSeqIons(self, seq, ions): # generate provided peptide sequence
seq = re.sub(r'\([^)]*\)', '',
seq) # remove content in brackets -> easier usage
# only draw sequence for M2 with peptide and ion data
if seq not in "-" and ions not in "-":
self.seqIons_widget.setPeptide(seq)
ions_dict = json.loads(
ions) # transform string data back to a dict
if ions_dict != {}:
self.suffix, self.prefix = self.filterIonsPrefixSuffixData(
ions_dict)
self.seqIons_widget.setPrefix(self.prefix)
self.seqIons_widget.setSuffix(self.suffix)
else: # no ions data
self.prefix, self.suffix = {}, {}
self.seqIons_widget.setPrefix(self.prefix)
self.seqIons_widget.setSuffix(self.suffix)
self.peakAnnoData = None
else:
self.seqIons_widget.clear()
self.peakAnnoData = None
def filterIonsPrefixSuffixData(
self,
ions): # filter raw ion data and return suffix and prefix dicts
suffix = {}
prefix = {}
ions_anno = list(ions.keys())
self.filteredIonFragments = [
] # annotation(s) of raw ion data (used as key(s))
for anno in ions_anno:
if anno[1].isdigit() and anno[0] in "abcyxz":
index, anno_short = self.filterAnnotationIon(anno)
if (index in suffix) and (anno[0] in "yxz") and (
anno_short
not in suffix[index]): # avoid double annos e.g. y14
suffix[index].append(anno_short)
elif (index in prefix) and (anno[0] in "abc") and (
anno_short not in prefix[index]):
prefix[index].append(anno_short)
elif anno[0] in "yxz": # non existing keys
suffix[index] = [anno_short]
elif anno[0] in "abc": # non existing keys
prefix[index] = [anno_short]
return suffix, prefix
def filterAnnotationIon(self, fragment_anno):
# filter from raw ion data annotation index and filtered annotation name (e.g. y2)
index = [s for s in re.findall(r'-?\d+\.?\d*', fragment_anno)][0]
ion_anno = fragment_anno.split(index)[0] + index
self.filteredIonFragments.append((fragment_anno, ion_anno))
return int(index), ion_anno
import sys
from PyQt5.QtWidgets import QApplication
import pyopenms
from GUI_EXAMPLE_BASE import GUI_EXAMPLE_BASE
sys.path.insert(0, '../view')
from SequenceIonsWidget import SequenceIonsWidget
if __name__ == '__main__':
app = QApplication(sys.argv)
ex = GUI_EXAMPLE_BASE() # plain QMainWindow with basic layout and menu bar
example_widget = SequenceIonsWidget(ex)
example_widget.setPeptide("HLDKIDMLKSLD")
example_widget.setPrefix({
1: ["a1", "b1", "c1"],
3: ["a3", "b3", "c3"],
5: ["a3", "b3", "c3"]
})
example_widget.setSuffix({
1: ["x1", "x3"],
2: ["x2", "y2"],
4: ["x4", "y4", "z4"]
})
ex.setExampleWidget(example_widget)
ex.show()
sys.exit(app.exec_())