def save_primer_indesign(self):
"""Save the selected primer to the primer database"""
if self.primer_result.curselection():
selection = int(str(self.primer_result.curselection()[0]))
name_selected = self.primer_order[selection]
this_primer = self.foundprimers[name_selected]
if getattr(self,'pDB_open',None):
#pass a reference to the current primer db window
primerdbwin = self.pDB_open
self.save_primer(self.primer_win,primerdbwin,this_primer,'from design')
else:
#If the pDB was not found open the window and lower it
self.pDB_open = primer_database.primer_database(i_parent=self)
self.pDB_open.pDB_win.lower()
primerdbwin = self.pDB_open
self.save_primer(self.primer_win,primerdbwin,this_primer,'from design')
else:
tkMessageBox.showwarning("No Selection",'Please create or select your primer',
parent=self.primer_win)
return
def save_primer_indesign(self):
"""Save the selected primer to the primer database"""
if self.primer_result.curselection():
selection = int(str(self.primer_result.curselection()[0]))
name_selected = self.primer_order[selection]
this_primer = self.foundprimers[name_selected]
if getattr(self, 'pDB_open', None):
#pass a reference to the current primer db window
primerdbwin = self.pDB_open
self.save_primer(self.primer_win, primerdbwin, this_primer,
'from design')
else:
#If the pDB was not found open the window and lower it
self.pDB_open = primer_database.primer_database(i_parent=self)
self.pDB_open.pDB_win.lower()
primerdbwin = self.pDB_open
self.save_primer(self.primer_win, primerdbwin, this_primer,
'from design')
else:
tkMessageBox.showwarning("No Selection",
'Please create or select your primer',
parent=self.primer_win)
return
def do_evaluate_primer(self,parent=None,i_parent=None,edit_primer_seq=None,
edit_primer_descr=None, edit_primer_name=None):
# Import functions from primer_database
self.pDB=primer_database.primer_database(i_parent=self,no_window=1)
# Who is the parent?
if not parent:
parent=self.master
self.i_parent=None
else:
self.i_parent=i_parent
#
# Open a window for entering primer data
#
self.eval_win=Toplevel()
if edit_primer_seq:
self.eval_win.title('Edit primer')
else:
self.eval_win.title('Add primer')
self.eval_win.geometry('+%d+%d' %(parent.winfo_rootx()+50,
parent.winfo_rooty()+50))
# Create the string variables and attach them to entry widgets
self.primername_var=StringVar()
lab=Label(self.eval_win,text='Primer Name:')
lab.grid(row=0,column=0,sticky='news')
Ebox=Entry(self.eval_win,textvariable=self.primername_var,width=50)
Ebox.grid(row=0,column=1,columnspan=2,sticky='news')
self.eval_var=StringVar()
lab=Label(self.eval_win,text='Sequence:')
lab.grid(row=1,column=0,sticky='news')
Ebox=Entry(self.eval_win,textvariable=self.eval_var,width=50)
Ebox.grid(row=1,column=1,columnspan=2,sticky='news')
self.descr_var=StringVar()
desclab=Label(self.eval_win,text='Description:')
desclab.grid(row=2,column=0,sticky='news')
Ebox=Entry(self.eval_win,textvariable=self.descr_var,width=50)
Ebox.grid(row=2,column=1,columnspan=2,sticky='news')
#
# Do recalculate and close buttons
#
row=3
recalc=Button(self.eval_win,text='Recalculate',command=self.update_eval)
recalc.grid(row=row,column=0,sticky='news')
close=Button(self.eval_win,text='Close',command=self.close_eval)
close.grid(row=row,column=1,sticky='news')
#
# Create button for adding to the primer library and set entry values if editing
# a primer that is already present in the database
#
if edit_primer_seq:
addp=Button(self.eval_win,text='Save primer',command=self.save_primer_from_edit)
self.eval_var.set(edit_primer_seq)
self.primername_var.set(edit_primer_name)
self.descr_var.set(edit_primer_descr)
self.edit_primer_name=edit_primer_name
else:
addp=Button(self.eval_win,text='Save primer',command=self.save_primer)
addp.grid(row=row,column=2,sticky='news')
#
# Hairpin propensity
row=row+1
self.eval_hairpin=StringVar()
self.eval_hairpin.set('No primer entered')
l2=Label(self.eval_win,text='Hairpin propensity:')
l2.grid(row=row,column=0,sticky='w')
stat=Label(self.eval_win,textvariable=self.eval_hairpin)
stat.grid(row=row,column=1,sticky='news')
#
# Primer-dimer
#
row=row+1
self.eval_primerdimer=StringVar()
self.eval_primerdimer.set('No primer entered')
l2=Label(self.eval_win,text='Self complementarity:')
l2.grid(row=row,column=0,sticky='w')
stat=Label(self.eval_win,textvariable=self.eval_primerdimer)
stat.grid(row=row,column=1,sticky='news')
#
# Tm
#
row=row+1
self.eval_Tm=StringVar()
self.eval_Tm.set('No primer entered')
l2=Label(self.eval_win,text='Tm:')
l2.grid(row=row,column=0,sticky='w')
stat=Label(self.eval_win,textvariable=self.eval_Tm)
stat.grid(row=row,column=1,sticky='news')
#
# Tm calculation method
#
self.eval_Tm_method=StringVar()
self.eval_Tm_method.set(self.Tm_method)
stat=Label(self.eval_win,textvariable=self.eval_Tm_method)
stat.grid(row=row,column=2,sticky='news')
#
#
#
self.eval_win.bind('<KeyPress>',self.update_eval)
self.eval_win.grab_set()
Ebox.focus_set()
self.update_eval()
return self.eval_win
def __init__(self):
"""Dummy constructor"""
import primer_database
self.pDB=primer_database.primer_database(self,1)
return
def _design_primer(self):
# Clear text boxes
self.detailed_results.delete(1.0,END)
self.primer_result.delete(0, END)
# Get an instance of the primer DB
if not getattr(self,'pDB',None):
import primer_database
self.pDB=primer_database.primer_database(self,1)
# Clear any previous details shown in the sequence window
self.pDB.clear_pDB_objects()
#self.pDB.display_primer([],delete=1,only_delete=1)
# Get the melting temp
try:
Tm_des=self.TM_desired.get()
if Tm_des<40 or Tm_des>85:
import tkMessageBox
tkMessageBox.showwarning("Invalid Tm",'Please give a temperature in Celcius from 40 - 85',
parent=self.primer_win)
return
except:
tkMessageBox.showwarning("Invalid Tm",'Please give a temperature in Celcius from 40 - 85',
parent=self.primer_win)
return
# Get start and stop
try:
AA_number=self.resnum.get()-self.data['ORF_selected']['aastart_number']
except:
tkMessageBox.showwarning("Invalid AA number",'Please give a number from %d to %d'
%(self.data['ORF_selected']['aastart_number'],
self.data['ORF_selected']['aastart_number']+self.data['ORF_selected']['length']-1),
parent=self.primer_win)
return
# Check for out of range
if AA_number>self.data['ORF_selected']['length']-1 or AA_number<0:
import tkMessageBox
print self.data['ORF_selected']
tkMessageBox.showwarning("AA number out of range",'Please give a number from %d to %d'
%(self.data['ORF_selected']['aastart_number'],
self.data['ORF_selected']['aastart_number']+self.data['ORF_selected']['length']-1),
parent=self.primer_win)
return
# Modify AA_number to get correct number in DNA sequence
AA_number_inORF=AA_number
AA_number=AA_number+self.data['ORF_selected']['start']
new_AA=self.new_res.get()
# check that the user selected a new AA
if new_AA=='Select':
import tkMessageBox
tkMessageBox.showwarning("No new AA type selected",'You have to select a new residue type',
parent=self.primer_win)
return
# Warn if the new and old AA type are the same
old_AA=self.data['ORF_selected']['aaseq3'][AA_number_inORF]
if new_AA==old_AA:
import tkMessageBox
if not tkMessageBox.askyesno("No AA change",
"This mutation will not make a change in the amino acid sequence.\nContinue anyway?",
parent=self.primer_win):
return
# Should we look for a restriction site?
if self.silent_mut.get()==1:
find_restriction_site=1
else:
find_restriction_site=None
# Adjust the DNA sequence according to frame
offset=self.data['ORF_selected']['frame']-1
DNA_seq=self.data['DNAseq'][offset:]
# Open a progress window
self.progress_win=Toplevel()
self.progress_win.transient(self.primer_win)
self.progress_win.focus_set()
self.progress_win.title('Primer design progress')
self.progress_win.geometry('+300+150')
self.prog_x=300
self.prog_can=Canvas(self.progress_win,bg='white',width=self.prog_x,height=180)
self.prog_can.grid(row=0,column=0)
self.progress=IntVar()
self.xl=Label(self.progress_win,textvariable=self.progress)
self.xl.grid(row=1,column=0)
self.box=None
self.master.update()
# Start the generation of primers
self.cancelled=None
print 'AA_number',AA_number
import mutation
primers_results_dict, new_enzymes, enzymes_that_already_cut=mutation.exhaustive_research(DNA_seq,AA_number,
new_AA,Tm_des,self.Tm_meth,
enzyme_list=self.data['used_enzymes'],
parent=self)
if not primers_results_dict:
self.progress_win.destroy()
return
# Insert primers in the listbox
self.prog_can.create_text(5,105,text="Removing useless primers",anchor='nw')
self.master.update()
self.foundprimers = {}
count=0
for primer_seq in primers_results_dict.keys():
# Filter the primers without new restriction sites if so specified
count=count+1
name='Primer %4d' %count
if not new_enzymes.has_key(primer_seq) and find_restriction_site:
continue
elif not new_enzymes.has_key(primer_seq):
self.foundprimers[name]={}
self.foundprimers[name]['introduced_sites']=[]
else:
self.foundprimers[name]={}
self.foundprimers[name]['introduced_sites']=new_enzymes[primer_seq]
# Add the rest
self.foundprimers[name]['sequence']=primer_seq
self.foundprimers[name]['Tm']=primers_results_dict[primer_seq]['Tm']
# Copy the other properties
for property in primers_results_dict[primer_seq].keys():
self.foundprimers[name][property]=primers_results_dict[primer_seq][property]
# Delete primers that are not bringing any benefit
to_delete={}
count=0
for primer in self.foundprimers.keys():
frac_done=float(count)/float(len(self.foundprimers.keys()))
self.update_primer_progress(frac_done,4)
count=count+1
cuts=self.foundprimers[primer]['introduced_sites']
mism1=self.foundprimers[primer]['mismatches']
for primer2 in self.foundprimers.keys():
if primer==primer2:
continue
# Compare with Other primer
if cuts==self.foundprimers[primer2]['introduced_sites']:
mism2=self.foundprimers[primer2]['mismatches']
if mism2<mism1:
to_delete[primer]=1
# Delete all primer that have been tagged
for delete in to_delete.keys():
del self.foundprimers[delete]
# Fill the listbox, sort by number of mismatches
self.primer_result.delete(0, END)
self.primer_names=self.foundprimers.keys()
self.primer_names.sort()
self.primer_order=[]
for mismatch in range(20):
for primer_name in self.primer_names:
if self.foundprimers[primer_name]['mismatches']==mismatch:
self.primer_result.insert(END,primer_name+': %2d mism, Tm: %4.1f' %(mismatch,
self.foundprimers[primer_name]['Tm']))
self.primer_order.append(primer_name)
# Close the progress window
self.progress_win.destroy()
self.master.update()
# Did we find any primers?
if len(self.primer_order)==0:
import tkMessageBox
tkMessageBox.showwarning('No primers found','I could not find any primers that match your criteria.\nAlter the query and try again.')
return
# Bind button-1 presses to action
#self.primer_result.bind("<Double-Button-1>",self.display_detailed_results)
self.primer_result.bind("<ButtonRelease-1>",self.display_detailed_results)
return
def _design_primer(self):
# Clear text boxes
self.detailed_results.delete(1.0, END)
self.primer_result.delete(0, END)
# Get an instance of the primer DB
if not getattr(self, 'pDB', None):
import primer_database
self.pDB = primer_database.primer_database(self, 1)
# Clear any previous details shown in the sequence window
self.pDB.clear_pDB_objects()
#self.pDB.display_primer([],delete=1,only_delete=1)
# Get the melting temp
try:
Tm_des = self.TM_desired.get()
if Tm_des < 40 or Tm_des > 85:
import tkMessageBox
tkMessageBox.showwarning(
"Invalid Tm",
'Please give a temperature in Celcius from 40 - 85',
parent=self.primer_win)
return
except:
tkMessageBox.showwarning(
"Invalid Tm",
'Please give a temperature in Celcius from 40 - 85',
parent=self.primer_win)
return
# Get start and stop
try:
AA_number = self.resnum.get(
) - self.data['ORF_selected']['aastart_number']
except:
tkMessageBox.showwarning(
"Invalid AA number",
'Please give a number from %d to %d' %
(self.data['ORF_selected']['aastart_number'],
self.data['ORF_selected']['aastart_number'] +
self.data['ORF_selected']['length'] - 1),
parent=self.primer_win)
return
# Check for out of range
if AA_number > self.data['ORF_selected']['length'] - 1 or AA_number < 0:
import tkMessageBox
print self.data['ORF_selected']
tkMessageBox.showwarning(
"AA number out of range",
'Please give a number from %d to %d' %
(self.data['ORF_selected']['aastart_number'],
self.data['ORF_selected']['aastart_number'] +
self.data['ORF_selected']['length'] - 1),
parent=self.primer_win)
return
# Modify AA_number to get correct number in DNA sequence
AA_number_inORF = AA_number
AA_number = AA_number + self.data['ORF_selected']['start']
new_AA = self.new_res.get()
# check that the user selected a new AA
if new_AA == 'Select':
import tkMessageBox
tkMessageBox.showwarning("No new AA type selected",
'You have to select a new residue type',
parent=self.primer_win)
return
# Warn if the new and old AA type are the same
old_AA = self.data['ORF_selected']['aaseq3'][AA_number_inORF]
if new_AA == old_AA:
import tkMessageBox
if not tkMessageBox.askyesno(
"No AA change",
"This mutation will not make a change in the amino acid sequence.\nContinue anyway?",
parent=self.primer_win):
return
# Should we look for a restriction site?
if self.silent_mut.get() == 1:
find_restriction_site = 1
else:
find_restriction_site = None
# Adjust the DNA sequence according to frame
offset = self.data['ORF_selected']['frame'] - 1
DNA_seq = self.data['DNAseq'][offset:]
# Open a progress window
self.progress_win = Toplevel()
self.progress_win.transient(self.primer_win)
self.progress_win.focus_set()
self.progress_win.title('Primer design progress')
self.progress_win.geometry('+300+150')
self.prog_x = 300
self.prog_can = Canvas(self.progress_win,
bg='white',
width=self.prog_x,
height=180)
self.prog_can.grid(row=0, column=0)
self.progress = IntVar()
self.xl = Label(self.progress_win, textvariable=self.progress)
self.xl.grid(row=1, column=0)
self.box = None
self.master.update()
# Start the generation of primers
self.cancelled = None
print 'AA_number', AA_number
import mutation
primers_results_dict, new_enzymes, enzymes_that_already_cut = mutation.exhaustive_research(
DNA_seq,
AA_number,
new_AA,
Tm_des,
self.Tm_meth,
enzyme_list=self.data['used_enzymes'],
parent=self)
if not primers_results_dict:
self.progress_win.destroy()
return
# Insert primers in the listbox
self.prog_can.create_text(5,
105,
text="Removing useless primers",
anchor='nw')
self.master.update()
self.foundprimers = {}
count = 0
for primer_seq in primers_results_dict.keys():
# Filter the primers without new restriction sites if so specified
count = count + 1
name = 'Primer %4d' % count
if not new_enzymes.has_key(primer_seq) and find_restriction_site:
continue
elif not new_enzymes.has_key(primer_seq):
self.foundprimers[name] = {}
self.foundprimers[name]['introduced_sites'] = []
else:
self.foundprimers[name] = {}
self.foundprimers[name]['introduced_sites'] = new_enzymes[
primer_seq]
# Add the rest
self.foundprimers[name]['sequence'] = primer_seq
self.foundprimers[name]['Tm'] = primers_results_dict[primer_seq][
'Tm']
# Copy the other properties
for property in primers_results_dict[primer_seq].keys():
self.foundprimers[name][property] = primers_results_dict[
primer_seq][property]
# Delete primers that are not bringing any benefit
to_delete = {}
count = 0
for primer in self.foundprimers.keys():
frac_done = float(count) / float(len(self.foundprimers.keys()))
self.update_primer_progress(frac_done, 4)
count = count + 1
cuts = self.foundprimers[primer]['introduced_sites']
mism1 = self.foundprimers[primer]['mismatches']
for primer2 in self.foundprimers.keys():
if primer == primer2:
continue
# Compare with Other primer
if cuts == self.foundprimers[primer2]['introduced_sites']:
mism2 = self.foundprimers[primer2]['mismatches']
if mism2 < mism1:
to_delete[primer] = 1
# Delete all primer that have been tagged
for delete in to_delete.keys():
del self.foundprimers[delete]
# Fill the listbox, sort by number of mismatches
self.primer_result.delete(0, END)
self.primer_names = self.foundprimers.keys()
self.primer_names.sort()
self.primer_order = []
for mismatch in range(20):
for primer_name in self.primer_names:
if self.foundprimers[primer_name]['mismatches'] == mismatch:
self.primer_result.insert(
END, primer_name + ': %2d mism, Tm: %4.1f' %
(mismatch, self.foundprimers[primer_name]['Tm']))
self.primer_order.append(primer_name)
# Close the progress window
self.progress_win.destroy()
self.master.update()
# Did we find any primers?
if len(self.primer_order) == 0:
import tkMessageBox
tkMessageBox.showwarning(
'No primers found',
'I could not find any primers that match your criteria.\nAlter the query and try again.'
)
return
# Bind button-1 presses to action
#self.primer_result.bind("<Double-Button-1>",self.display_detailed_results)
self.primer_result.bind("<ButtonRelease-1>",
self.display_detailed_results)
return
def do_evaluate_primer(self,
parent=None,
i_parent=None,
edit_primer_seq=None,
edit_primer_descr=None,
edit_primer_name=None):
# Import functions from primer_database
self.pDB = primer_database.primer_database(i_parent=self, no_window=1)
# Who is the parent?
if not parent:
parent = self.master
self.i_parent = None
else:
self.i_parent = i_parent
#
# Open a window for entering primer data
#
self.eval_win = Toplevel()
if edit_primer_seq:
self.eval_win.title('Edit primer')
else:
self.eval_win.title('Add primer')
self.eval_win.geometry(
'+%d+%d' % (parent.winfo_rootx() + 50, parent.winfo_rooty() + 50))
# Create the string variables and attach them to entry widgets
self.primername_var = StringVar()
lab = Label(self.eval_win, text='Primer Name:')
lab.grid(row=0, column=0, sticky='news')
Ebox = Entry(self.eval_win, textvariable=self.primername_var, width=50)
Ebox.grid(row=0, column=1, columnspan=2, sticky='news')
self.eval_var = StringVar()
lab = Label(self.eval_win, text='Sequence:')
lab.grid(row=1, column=0, sticky='news')
Ebox = Entry(self.eval_win, textvariable=self.eval_var, width=50)
Ebox.grid(row=1, column=1, columnspan=2, sticky='news')
self.descr_var = StringVar()
desclab = Label(self.eval_win, text='Description:')
desclab.grid(row=2, column=0, sticky='news')
Ebox = Entry(self.eval_win, textvariable=self.descr_var, width=50)
Ebox.grid(row=2, column=1, columnspan=2, sticky='news')
#
# Do recalculate and close buttons
#
row = 3
recalc = Button(self.eval_win,
text='Recalculate',
command=self.update_eval)
recalc.grid(row=row, column=0, sticky='news')
close = Button(self.eval_win, text='Close', command=self.close_eval)
close.grid(row=row, column=1, sticky='news')
#
# Create button for adding to the primer library and set entry values if editing
# a primer that is already present in the database
#
if edit_primer_seq:
addp = Button(self.eval_win,
text='Save primer',
command=self.save_primer_from_edit)
self.eval_var.set(edit_primer_seq)
self.primername_var.set(edit_primer_name)
self.descr_var.set(edit_primer_descr)
self.edit_primer_name = edit_primer_name
else:
addp = Button(self.eval_win,
text='Save primer',
command=self.save_primer)
addp.grid(row=row, column=2, sticky='news')
#
# Hairpin propensity
row = row + 1
self.eval_hairpin = StringVar()
self.eval_hairpin.set('No primer entered')
l2 = Label(self.eval_win, text='Hairpin propensity:')
l2.grid(row=row, column=0, sticky='w')
stat = Label(self.eval_win, textvariable=self.eval_hairpin)
stat.grid(row=row, column=1, sticky='news')
#
# Primer-dimer
#
row = row + 1
self.eval_primerdimer = StringVar()
self.eval_primerdimer.set('No primer entered')
l2 = Label(self.eval_win, text='Self complementarity:')
l2.grid(row=row, column=0, sticky='w')
stat = Label(self.eval_win, textvariable=self.eval_primerdimer)
stat.grid(row=row, column=1, sticky='news')
#
# Tm
#
row = row + 1
self.eval_Tm = StringVar()
self.eval_Tm.set('No primer entered')
l2 = Label(self.eval_win, text='Tm:')
l2.grid(row=row, column=0, sticky='w')
stat = Label(self.eval_win, textvariable=self.eval_Tm)
stat.grid(row=row, column=1, sticky='news')
#
# Tm calculation method
#
self.eval_Tm_method = StringVar()
self.eval_Tm_method.set(self.Tm_method)
stat = Label(self.eval_win, textvariable=self.eval_Tm_method)
stat.grid(row=row, column=2, sticky='news')
#
#
#
self.eval_win.bind('<KeyPress>', self.update_eval)
self.eval_win.grab_set()
Ebox.focus_set()
self.update_eval()
return self.eval_win
def __init__(self):
"""Dummy constructor"""
import primer_database
self.pDB = primer_database.primer_database(self, 1)
return