def open_file(self, evt):
'''Function for opening file'''
self.dir_to_open = default_filepath
self.dir_to_open = os.path.dirname(
os.path.abspath(inspect.getfile(
inspect.currentframe()))) #current script directory
dlg = wx.FileDialog(self,
style=wx.OPEN | wx.FILE_MUST_EXIST,
defaultDir=self.dir_to_open,
wildcard='GenBank files (*.gb)|*|Any file (*)|*')
if dlg.ShowModal() == wx.ID_CANCEL:
return # the user does not want to open that file!
genbank.gb.fileName = dlg.GetFilename()
all_path = dlg.GetPath()
dire = dlg.GetDirectory()
dlg.Destroy()
if (genbank.gb.fileName == None or genbank.gb.fileName == ""):
return 1
name, extension = genbank.gb.fileName.split('.')
if extension.lower() == 'gb':
genbank.gb = genbank.gbobject(
all_path) #make a genbank object and read file
self.SetTitle(genbank.gb.fileName + ' - DNApy')
if genbank.gb.clutter == True: #if tags from ApE or Vector NTI is found in file
dlg = wx.MessageDialog(
self,
style=wx.YES_NO | wx.CANCEL,
message=
'This file contains tags from the Vector NTI or ApE programs. Keeping these tags may break compatibility with other software. Removing them will clean up the file, but may result in the loss of some personalized styling options when this file is viewed in Vector NTI or ApE. Do you wish to REMOVE these tags?'
)
result = dlg.ShowModal()
dlg.Destroy()
if result == wx.ID_YES: #if yes, remove clutter
genbank.gb.clean_clutter()
#enable the tools
self.frame_1_toolbar.EnableTool(502, True)
self.frame_1_toolbar.EnableTool(503, True)
self.frame_1_toolbar.EnableTool(504, True)
self.frame_1_toolbar.EnableTool(505, True)
self.frame_1_toolbar.EnableTool(506, True)
self.frame_1_toolbar.EnableTool(511, True)
self.frame_1_toolbar.EnableTool(512, True)
self.fileopen = True
#self.DNApy.update_ownUI()
else:
print("error, not a gb file")
self.Bind(wx.EVT_UPDATE_UI, self.update_statusbar)
# update gui to find eestriction sites etc
self.update_globalUI()
def NCBIfetchGB(id):
'''
Same as NCBIfetch, but instead of returning a text string it returns a genbank object.
'''
file = NCBIfetch(id).split('\n') #get file and split it
file = [x+'\n' for x in file] #add back the linebreaks
x = genbank.gbobject()
x.readgb(file)
return x
def open_file(self, evt):
'''Function for opening file'''
self.dir_to_open = default_filepath
self.dir_to_open = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) #current script directory
dlg = wx.FileDialog( self, style=wx.OPEN|wx.FILE_MUST_EXIST, defaultDir=self.dir_to_open ,wildcard='GenBank files (*.gb)|*|Any file (*)|*')
if dlg.ShowModal() == wx.ID_CANCEL:
return # the user does not want to open that file!
genbank.gb.fileName = dlg.GetFilename()
all_path=dlg.GetPath()
dire=dlg.GetDirectory()
dlg.Destroy()
if(genbank.gb.fileName == None or genbank.gb.fileName == "" ):
return 1
name, extension = genbank.gb.fileName.split('.')
if extension.lower() == 'gb':
genbank.gb = genbank.gbobject(all_path) #make a genbank object and read file
self.SetTitle(genbank.gb.fileName+' - DNApy')
if genbank.gb.clutter == True: #if tags from ApE or Vector NTI is found in file
dlg = wx.MessageDialog(self, style=wx.YES_NO|wx.CANCEL, message='This file contains tags from the Vector NTI or ApE programs. Keeping these tags may break compatibility with other software. Removing them will clean up the file, but may result in the loss of some personalized styling options when this file is viewed in Vector NTI or ApE. Do you wish to REMOVE these tags?')
result = dlg.ShowModal()
dlg.Destroy()
if result == wx.ID_YES: #if yes, remove clutter
genbank.gb.clean_clutter()
#enable the tools
self.frame_1_toolbar.EnableTool(502, True)
self.frame_1_toolbar.EnableTool(503, True)
self.frame_1_toolbar.EnableTool(504, True)
self.frame_1_toolbar.EnableTool(505, True)
self.frame_1_toolbar.EnableTool(506, True)
self.frame_1_toolbar.EnableTool(511, True)
self.frame_1_toolbar.EnableTool(512, True)
self.fileopen = True
#self.DNApy.update_ownUI()
else:
print("error, not a gb file")
self.Bind(wx.EVT_UPDATE_UI, self.update_statusbar)
# update gui to find eestriction sites etc
self.update_globalUI()
def new_file(self, evt):
'''Create new gb file'''
if self.fileopen == False: #if no file is open, make blank gb file
genbank.gb = genbank.gbobject() #make new gb in panel
self.SetTitle('NewFile - DNApy')
# self.page_change("")
self.frame_1_toolbar.EnableTool(502, 1)
self.frame_1_toolbar.EnableTool(503, 1)
self.frame_1_toolbar.EnableTool(504, 1)
self.frame_1_toolbar.EnableTool(505, 1)
self.frame_1_toolbar.EnableTool(506, 1)
self.frame_1_toolbar.EnableTool(511, 1)
self.frame_1_toolbar.EnableTool(512, 1)
self.Bind(wx.EVT_UPDATE_UI, self.update_statusbar)
self.fileopen = True
elif self.fileopen == True: #if a file IS open, make a new window
subprocess.Popen("python ~/Python_files/DNApy/main.py 1", shell=True) #this needs a fix for windows
def new_file(self, evt):
'''Create new gb file'''
if self.fileopen == False: #if no file is open, make blank gb file
genbank.gb = genbank.gbobject() #make new gb in panel
self.SetTitle('NewFile - DNApy')
# self.page_change("")
self.frame_1_toolbar.EnableTool(502, 1)
self.frame_1_toolbar.EnableTool(503, 1)
self.frame_1_toolbar.EnableTool(504, 1)
self.frame_1_toolbar.EnableTool(505, 1)
self.frame_1_toolbar.EnableTool(506, 1)
self.frame_1_toolbar.EnableTool(511, 1)
self.frame_1_toolbar.EnableTool(512, 1)
self.Bind(wx.EVT_UPDATE_UI, self.update_statusbar)
self.fileopen = True
# TODO fix the weird paths
elif self.fileopen == True: #if a file IS open, make a new window
subprocess.Popen("python ~/Python_files/DNApy/main.py 1",
shell=True) #this needs a fix for windows
frame = wx.Frame(None, -1, title="Feature Edit", size=(700,300))
panel = FeatureEdit(frame, -1)
frame.Centre()
frame.Show(True)
self.SetTopWindow(frame)
return True
if __name__ == '__main__': #if script is run by itself and not loaded
files={} #list with all configuration files
files['default_dir'] = os.path.abspath(os.path.dirname(sys.argv[0]))+"/"
files['default_dir']=string.replace(files['default_dir'], "\\", "/")
files['default_dir']=string.replace(files['default_dir'], "library.zip", "")
settings=files['default_dir']+"settings" ##path to the file of the global settings
execfile(settings) #gets all the pre-assigned settings
genbank.dna_selection = (0, 0) #variable for storing current DNA selection
genbank.feature_selection = False #variable for storing current feature selection
import sys
assert len(sys.argv) == 3, 'Error, this script requires a path to a genbank file and a feature index (integer) as an argument.'
print('Opening %s' % str(sys.argv[1]))
genbank.gb = genbank.gbobject(str(sys.argv[1])) #make a genbank object and read file
genbank.feature_selection = sys.argv[2]
app = MyApp(0)
app.MainLoop()
panel = DNAedit(frame, -1)
frame.Centre()
frame.Show(True)
self.SetTopWindow(frame)
return True
if __name__ == '__main__': #if script is run by itself and not loaded
files={} #list with all configuration files
files['default_dir'] = os.path.abspath(os.path.dirname(sys.argv[0]))+"/"
files['default_dir']=string.replace(files['default_dir'], "\\", "/")
files['default_dir']=string.replace(files['default_dir'], "library.zip", "")
settings=files['default_dir']+"settings" ##path to the file of the global settings
exec(compile(open(settings).read(), settings, 'exec')) #gets all the pre-assigned settings
genbank.dna_selection = (0, 0, -1) #variable for storing current DNA selection
genbank.feature_selection = False #variable for storing current feature selection
genbank.search_hits = []
import sys
assert len(sys.argv) == 2, 'Error, this script requires a path to a genbank file as an argument.'
print(('Opening %s' % str(sys.argv[1])))
genbank.gb = genbank.gbobject(str(sys.argv[1])) #make a genbank object and read file
app = MyApp(0)
app.MainLoop()
