def single_eng(self, path):
eng = unidec.UniDec()
eng.open_file(path)
eng.unidec_imports(everything=True, efficiency=True)
eng.pick_peaks()
# eng.dscore()
return eng
def navia_import(path):
# Create a UniDec engine to help with things
eng = unidec.UniDec()
config_obj = eng.config
try:
# Where to find NaViA session and where to save UniDEC stuff
with open(path, "r") as myfile:
data = myfile.readlines()
json_dict = json.loads(data[0])
mz_raw = np.transpose(
[json_dict['raw_data']['mz'], json_dict['raw_data']['Intensity']])
rawfile = os.path.splitext(path)[0] + ".txt"
np.savetxt(rawfile, mz_raw)
eng.open_file(rawfile)
navia2config(config_obj, json_dict)
config_obj.manuallist = navia2manualfile(json_dict,
config_obj.manualfile)
config_obj.oligomerlist = navia2ofile(json_dict, config_obj.ofile)
if len(config_obj.manuallist) > 0:
eng.config.manualfileflag = True
eng.export_config()
#eng.load_config(eng.config.confname)
return rawfile
except IOError:
print("Cannot open file '%s'." % path)
return None
def init(self, *args, **kwargs):
"""
Initialize Engine and View.
:param args:
:param kwargs:
:return:
"""
self.eng = unidec.UniDec()
self.view = UniListWindow(self, "UniDec List Viewer", self.eng.config)
# pub.subscribe(self.on_integrate, 'integrate')
# pub.subscribe(self.on_smash, 'smash')
# pub.subscribe(self.on_get_mzlimits, 'mzlimits')
# pub.subscribe(self.on_left_click, 'left_click')
if False:
p1 = "C:\\Users\\margo\\Desktop\\Marty\\wanglabsample_protease_3.txt"
p2 = "C:\\Users\\margo\\Desktop\\Marty\\wanglabsample_protease_3.txt"
p3 = "C:\\Users\\margo\\Desktop\\Marty\\wanglabsample_protease_3.txt"
paths = [[p1], [p2], [p3]]
self.populate_list(paths)
importmass = np.loadtxt(mfilename)
if importmass[0] > 0:
self.masslistbox.list.populate(importmass)
def on_import_oligos(self, e):
"""
Open a file dialog to import oligomer files.
:param e: Unused event
:return: None
"""
# TODO: This fails when the output ofile isn't square (some are unnamed and other are named)
ofilename = FileDialogs.open_file_dialog("Open Oligomer File (ofile)",
file_types="*.*")
if ofilename is not None:
importolig = np.genfromtxt(ofilename, dtype='str')
if np.shape(importolig) == (5, ) or np.shape(importolig) == (4, ):
importolig = [importolig]
self.oligomerlistbox.list.populate(importolig)
# Main App Execution
if __name__ == "__main__":
import unidec
eng = unidec.UniDec()
app = wx.App(False)
frame = MassSelection(None)
frame.init_dialog(eng.config, eng.pks, massdat=None)
frame.ShowModal()
app.MainLoop()