def on_output_browse(self, event):
if self.combine_ck.IsChecked():
output_file = report_chooser(self,
title='Save output file as:',
mode='w')
if output_file:
self.output_text.SetValue(output_file)
else:
folder_chooser = wx.DirDialog(self,
"Choose folder to save output:",
style=wx.DD_DEFAULT_STYLE
| wx.DD_NEW_DIR_BUTTON)
if folder_chooser.ShowModal() == wx.ID_OK:
self.output_text.SetValue(folder_chooser.GetPath())
folder_chooser.Destroy()
def on_click(self, event):
#update statusbar
self.set_status("Fragmenting...",0)
self.set_status("",1)
peptide = self.peptideString.GetValue()
peptide = re.sub(r'\[\]', '', peptide)
self.peptideString.SetValue(peptide)
ion_array = []
if self.one_plus.IsChecked():
for k,v in self.ions.items():
if v.IsChecked():
ion_array.append(v.GetName())
if self.two_plus.IsChecked():
ion_array.extend([(ion+'++') for ion in ion_array
if not ion.startswith('inty')]) # NB: generator causes infinite loop!
elif self.two_plus.IsChecked():
for k,v in self.ions.items():
if v.IsChecked() and not k.startswith('Internal'):
ion_array.append(v.GetName() + '++')
ion_array.sort()
if not peptide:
wx.MessageBox('No peptide sequence was entered.')
return
try:
frag_data = fragment_legacy(peptide, ion_array, labels = False)
except ValueError as err:
print err
wx.MessageBox('Invalid mass value.', 'Error')
# update statusbar
self.set_status("Ready", 0)
self.set_status("Done", 1)
return
except LookupError as err:
print err
wx.MessageBox('Invalid modification name or position.', 'Error')
import sys
print sys.exc_info()
# update statusbar
self.set_status("Ready", 0)
self.set_status("Done", 1)
return
pep_cleaner = re.compile(r'-?(\[.+?\]|[a-z0-9])-?')
# peptide without any modifications
sequence = pep_cleaner.sub('', peptide)
row_headers = list(sequence)
for m in re.finditer(r'(-?(\[.+?\]|[a-z])-?)', peptide):
mod = m.group(1)
if m.end() < len(peptide):
i = len(pep_cleaner.sub('', peptide[:m.end() + 1])) - 1
row_headers[i] = '%s%s' % (mod, row_headers[i])
else:
row_headers[-1] = '%s%s' % (row_headers[-1], mod)
data = [[0.0 for ion in ion_array] for aa in sequence]
# convert data to list of lists per AA
for i,ion in enumerate(ion_array):
ion_series = frag_data[i] + [None]
if ion[0] in ('x', 'y', 'z'):
ion_series.reverse()
for j,aa in enumerate(sequence):
data[j][i] = ion_series[j]
if self.writeToggleCk.GetValue():
writeFile = report_chooser(self, mode='w') or os.path.join(myData, 'pepFrag.csv')
if os.path.exists(writeFile):
os.remove(writeFile)
myreport = multiplierz.mzReport.writer(writeFile, columns=[''] + ion_array)
for i in range(len(row_headers)):
myreport.write([row_headers[i]] + data[i])
myreport.close()
else:
tableFrame = FragTable(self, -1, "Fragment Table", row_headers, ion_array, data)
tableFrame.Show()
#self.dataDisplay.displayData(row_headers, ion_array, data)
# update statusbar
self.set_status("Ready", 0)
self.set_status("Done", 1)
def addFile(self, event):
filenames = report_chooser('Select file:', mode='m')
if filenames:
self.fileList.InsertItems(filenames, 0)
def OnClickMascotFile(self, event):
file_name = report_chooser(self)
if file_name:
self.file_text.SetValue(file_name)
def OnClick(self, event):
#update statusbar
self.set_status("Digesting...", 0)
self.set_status("", 1)
fasta_split = self.proteinInput.GetValue().split('\n')
headers = []
proteins = []
for line in fasta_split:
if not line:
continue
if line[0] == '>':
headers.append(line[1:])
proteins.append('')
continue
proteins[-1] += line.upper()
enzyme = self.enzymeCB.GetValue()
missed_cleavages = int(self.missed_cleavagesCB.GetValue())
if enzyme[0] != "[":
(enzyme, spec) = enzyme.split(':')
data = []
for (i, protein) in enumerate(proteins):
try:
digests = digest(protein, enzyme, missed_cleavages)
except Exception as err:
wx.MessageBox(
'Error while parsing protein entry: %s' % protein,
"An error occurred.")
raise err
header = headers[i]
for (j, dig) in enumerate(digests):
pep = digests[j][0]
range = digests[j][1]
m_c = digests[j][2]
try:
oneMass = "%0.3f" % mz(pep, [], 1)
twoMass = "%0.3f" % mz(pep, [], 2)
threeMass = "%0.3f" % mz(pep, [], 3)
data.append(
(header, pep, range, m_c, oneMass, twoMass, threeMass))
except Exception as err:
wx.MessageBox(
'Error while parsing peptide substring: %s' % pep,
"An error occurred.")
raise err
if self.writeToggleCk.GetValue():
writeFile = report_chooser(self, mode='w') or os.path.join(
myData, 'protDigest.csv')
if os.path.exists(writeFile):
os.remove(writeFile)
cols = [
'Header', 'Sequence', 'Range', 'Missed Cleavage', '1+ Mass',
'2+ Mass', '3+ Mass'
]
report = multiplierz.mzReport.writer(writeFile, columns=cols)
for peptide in data:
pepRange = str(peptide[2][0]) + '...' + str(peptide[2][1])
report.write(peptide[:2] + (pepRange, ) + peptide[3:])
report.close()
else:
tableFrame = Table1(self, -1, "Digest Table", data)
tableFrame.Show()
#update statusbar
self.set_status("Ready", 0)
self.set_status("Done", 1)