def dnaseq_read(self,newprotein=None,fileinput=None,variable='DNAseq',var2='dnaseqfile'):
"""Read in DNA Sequences and display them above the main sequence"""
self.data['newprotein']=newprotein
# If a file is provided use that, otherwise open the dialog
if fileinput == None:
dnaseqfile = self.open_file()
else:
dnaseqfile = fileinput
self.data[var2]=dnaseqfile
# Load the DNA sequence data
# - only simple file format supported at the moment
if self.data[var2]:
S=DNA_sequence.sequence()
seqfile=self.data[var2]
DNAseq=S.read_DNA_sequence(seqfile)
# Check the DNA sequence
ok,DNAseq=mutation.check_DNA(DNAseq)
if not ok:
# Give a warning
import tkMessageBox
tkMessageBox.showwarning("DNA sequence",
'DNA sequence contains invalid characters: %s' %DNAseq
,parent=self.master)
return
self.data[variable]=DNAseq
self.update_sequence_window()
# Activate/Deactivate buttons
self.projectChanged()
return dnaseqfile
def get_characteristics(self,primer,Tm_method):
"""Get the characteristics (hairpin prop, selfcomplementarity) of a primer"""
#
# Extract the DNA sequence
#
primer_seq=primer['sequence']
import mutation
ok,primer_seq=mutation.check_DNA(primer_seq)
if ok:
#
# Hairpin propensity
#
prop,numscore=mutation.hairpin_propensity(primer_seq)
if numscore < 8:
score = 'OK'
elif numscore >= 8:
score = 'BAD'
text_hairpin='%s (%2d matches)' %(score,numscore)
#
# Self complementarity
#
complementarity_dict,maxselfscore = mutation.self_complementarity_propensity(primer_seq)
if maxselfscore < 8:
text = 'OK'
elif maxselfscore >= 8:
text = 'BAD'
text_selfcompl='%s (%2d matches)' %(text,maxselfscore)
#
# Melting temperature
#
Tm,mismatches,Tm_method_used=mutation.get_primer_Tm(DNAseq=primer['template_DNA'],primer=primer_seq,primer_start=primer['startpos'],method=Tm_method)
return text_hairpin,text_selfcompl,Tm,Tm_method_used,mismatches
return 'DNA sequenece not ok','DNA sequence not ok','DNA sequenece not ok','DNA sequence not ok'
def save_primer_from_edit(self, parent_window=None):
"""Save the primer in the DB when doing a primer Edit"""
if not parent_window:
parent_window = self.eval_win
# Check if the primer name has been changed first, and ask for confirmation of rename
if self.primername_var.get() != self.edit_primer_name or not self.edit_primer_name:
import tkMessageBox
ok = tkMessageBox.askyesno('Primer Name altered',
'Rename primer and save?\n',
parent=parent_window)
if not ok:
self.primername_var.set(self.edit_primer_name)
return
#rename primer based on value in entry widget
else:
new_name=self.primername_var.get()
if new_name:
#only rename if there isn't already a primer with the same name
if not self.data['primer_dict'].has_key(new_name):
self.data['primer_dict'][new_name]=self.data['primer_dict'][self.edit_primer_name].copy()
del self.data['primer_dict'][self.edit_primer_name]
self.edit_primer_name = new_name
self.i_parent.new_name = new_name
#otherwise don't allow rename
else:
tkMessageBox.showwarning('Primer name already present',
'Primer name already present.\nPlease choose another name',
parent=parent_window)
return
# Update the sequence and description fields for the primer
DNA=self.eval_var.get()
# Validation check if primer is changed (maybe by mistake)
if not DNA:
ok = tkMessageBox.askyesno('No sequence entered',
'No sequence entered.\nDo you wish to save anyway?',
parent=parent_window)
if not ok:
return
import mutation
ok,DNA_sequence=mutation.check_DNA(DNA)
self.data['primer_dict'][self.edit_primer_name]['sequence']=DNA_sequence
self.data['primer_dict'][self.edit_primer_name]['description']=self.descr_var.get()
#print 'Primer Info:',self.edit_primer_name,self.data['primer_dict'][self.edit_primer_name]
# Clear all graphics
if getattr(self,'pDB',None):
self.pDB.clear_pDB_objects()
# Close the window
self.eval_win.destroy()
return
def get_characteristics(self, primer, Tm_method):
"""Get the characteristics (hairpin prop, selfcomplementarity) of a primer"""
#
# Extract the DNA sequence
#
primer_seq = primer['sequence']
import mutation
ok, primer_seq = mutation.check_DNA(primer_seq)
if ok:
#
# Hairpin propensity
#
prop, numscore = mutation.hairpin_propensity(primer_seq)
if numscore < 8:
score = 'OK'
elif numscore >= 8:
score = 'BAD'
text_hairpin = '%s (%2d matches)' % (score, numscore)
#
# Self complementarity
#
complementarity_dict, maxselfscore = mutation.self_complementarity_propensity(
primer_seq)
if maxselfscore < 8:
text = 'OK'
elif maxselfscore >= 8:
text = 'BAD'
text_selfcompl = '%s (%2d matches)' % (text, maxselfscore)
#
# Melting temperature
#
Tm, mismatches, Tm_method_used = mutation.get_primer_Tm(
DNAseq=primer['template_DNA'],
primer=primer_seq,
primer_start=primer['startpos'],
method=Tm_method)
return text_hairpin, text_selfcompl, Tm, Tm_method_used, mismatches
return 'DNA sequenece not ok', 'DNA sequence not ok', 'DNA sequenece not ok', 'DNA sequence not ok'
def dnaseq_read(self,
newprotein=None,
fileinput=None,
variable='DNAseq',
var2='dnaseqfile'):
"""Read in DNA Sequences and display them above the main sequence"""
self.data['newprotein'] = newprotein
# If a file is provided use that, otherwise open the dialog
if fileinput == None:
dnaseqfile = self.open_file()
else:
dnaseqfile = fileinput
self.data[var2] = dnaseqfile
# Load the DNA sequence data
# - only simple file format supported at the moment
if self.data[var2]:
S = DNA_sequence.sequence()
seqfile = self.data[var2]
DNAseq = S.read_DNA_sequence(seqfile)
# Check the DNA sequence
ok, DNAseq = mutation.check_DNA(DNAseq)
if not ok:
# Give a warning
import tkMessageBox
tkMessageBox.showwarning(
"DNA sequence",
'DNA sequence contains invalid characters: %s' % DNAseq,
parent=self.master)
return
self.data[variable] = DNAseq
self.update_sequence_window()
# Activate/Deactivate buttons
self.projectChanged()
return dnaseqfile
def save_primer(self,parent_window=None,openpdbWin=None, this_primer=None,
calledby=None ):
"""Saves primers to database"""
# Get the parent window right
if not parent_window:
parent_window=self.eval_win
# Save the primer to the primer library
if not self.data.has_key('primer_dict'):
self.data['primer_dict']={}
# Find the next unique name
for x in range(1000):
nextname='primer_%3d' %x
if not self.data['primer_dict'].has_key(nextname):
break
# Get a name for the primer
# If calling from primer design just use little dialog, otherwise use
if calledby=='from design':
print 'Saving primer from design window'
done=None
result = self.get_text_input(parent_window,[['name',20],['description',30]])
if not result:
return None
primer_name=result[0]
description=result[1]
else:
primer_name=self.primername_var.get()
description=self.descr_var.get()
if not primer_name:
tkMessageBox.showwarning('Invalid primer name',
'I need a real primer name to store this primer',
parent=parent_window)
return
print 'Setting name to',primer_name
print 'Setting description to',description
# Store the primer
if not this_primer:
DNA=self.eval_var.get()
if not DNA:
ok = tkMessageBox.askyesno('No sequence entered',
'No sequence entered.\nDo you wish to save anyway?')
if not ok:
return
ok,sequence=mutation.check_DNA(DNA)
if ok:
self.data['primer_dict'][primer_name]={'description':description,'sequence':sequence,'startpos':None,
'hairpin_prop':self.eval_hairpin.get(),
'self-compl':self.eval_primerdimer.get(),
'introduced_sites':'Unknown'}
self.primer_save_ok(primer_name,parent_window)
#pass name of primer back to parent window for highlighting
self.i_parent.new_name = primer_name
parent_window.destroy()
print 'Primer Info:',self.data['primer_dict'][primer_name]
else:
tkMessageBox.showwarning('Invalid primer','Cannot store an invalid primer',parent=parent_window)
return
else:
# If we already have all the data then save it
this_primer['description']=description
self.data['primer_dict'][primer_name]=this_primer.copy()
self.primer_save_ok(primer_name,parent_window)
# Clear all the graphics
if getattr(self,'pDB',None):
self.pDB.clear_pDB_objects()
# If calling from mutagenic design, handle refresh of pdb here
if calledby == 'from design' and openpdbWin != None:
openpdbWin.show_pDB_contents()
openpdbWin.highlight_primer(primer_name)
openpdbWin.display_details()
return
def update_eval(self,event=None):
#
# Calculate primer-dimer and secondary structure
#
import mutation
primer_seq=self.eval_var.get()
ok,primer_seq=mutation.check_DNA(primer_seq)
#
# Score the sequence
#
if ok:
prop,numscore=mutation.hairpin_propensity(primer_seq)
if numscore < 8:
score = 'OK'
# score = numscore
elif numscore >= 8:
score = 'BAD'
#score = numscore
self.eval_hairpin.set('%s (%2d matches)' %(score,numscore))
#
# Primer-Dimer
#
complementarity_dict,maxselfscore = mutation.self_complementarity_propensity (primer_seq)
if maxselfscore < 8:
text = 'OK'
elif maxselfscore >= 8:
text = 'BAD'
self.eval_primerdimer.set('%s (%2d matches)' %(text,maxselfscore))
#
# Tm
#
# See if we can align the primer
#
Tm=None
if self.data.has_key('DNAseq'):
if self.data['DNAseq']:
import primer_alignment
A=primer_alignment.dummy_align_primer(self)
#
# Find all possible binding sites for the primer
#
sites=A.find_primer_binding_sites(primer_seq,self.data['DNAseq'])
#
# Print the number of binding sites
#
best_score=0
best_position=None
scores=[]
first_neg=1
for position,score in sites:
scores.append(score)
#
# Find the best position
#
if score>best_score:
best_score=score
best_position=position
Tm,mistmatches,Tm_method_used=mutation.get_primer_Tm(DNAseq=self.data['DNAseq'],
primer=primer_seq,
primer_start=best_position,
method=self.Tm_method.get())
#
# Draw the primer on the screen in the best position
#
this_primer={}
this_primer['sequence']=primer_seq
this_primer['startpos']=best_position
#
# Draw the new primer
#
self.pDB.display_primer(this_primer)
if not Tm:
Tm,mistmatches,Tm_method_used=mutation.get_primer_Tm(DNAseq=None,
primer=primer_seq,
primer_start=None,
method=self.Tm_method.get())
self.eval_Tm.set('%5.2f' %Tm)
self.eval_Tm_method.set(Tm_method_used)
else:
self.eval_hairpin.set('Invalid DNA sequence')
self.eval_primerdimer.set('Invalid DNA sequence')
self.eval_Tm.set('Invalid DNA sequence')
return
def save_primer(self,
parent_window=None,
openpdbWin=None,
this_primer=None,
calledby=None):
"""Saves primers to database"""
# Get the parent window right
if not parent_window:
parent_window = self.eval_win
# Save the primer to the primer library
if not self.data.has_key('primer_dict'):
self.data['primer_dict'] = {}
# Find the next unique name
for x in range(1000):
nextname = 'primer_%3d' % x
if not self.data['primer_dict'].has_key(nextname):
break
# Get a name for the primer
# If calling from primer design just use little dialog, otherwise use
if calledby == 'from design':
print 'Saving primer from design window'
done = None
result = self.get_text_input(parent_window,
[['name', 20], ['description', 30]])
if not result:
return None
primer_name = result[0]
description = result[1]
else:
primer_name = self.primername_var.get()
description = self.descr_var.get()
if not primer_name:
tkMessageBox.showwarning(
'Invalid primer name',
'I need a real primer name to store this primer',
parent=parent_window)
return
print 'Setting name to', primer_name
print 'Setting description to', description
# Store the primer
if not this_primer:
DNA = self.eval_var.get()
if not DNA:
ok = tkMessageBox.askyesno(
'No sequence entered',
'No sequence entered.\nDo you wish to save anyway?')
if not ok:
return
ok, sequence = mutation.check_DNA(DNA)
if ok:
self.data['primer_dict'][primer_name] = {
'description': description,
'sequence': sequence,
'startpos': None,
'hairpin_prop': self.eval_hairpin.get(),
'self-compl': self.eval_primerdimer.get(),
'introduced_sites': 'Unknown'
}
self.primer_save_ok(primer_name, parent_window)
#pass name of primer back to parent window for highlighting
self.i_parent.new_name = primer_name
parent_window.destroy()
print 'Primer Info:', self.data['primer_dict'][primer_name]
else:
tkMessageBox.showwarning('Invalid primer',
'Cannot store an invalid primer',
parent=parent_window)
return
else:
# If we already have all the data then save it
this_primer['description'] = description
self.data['primer_dict'][primer_name] = this_primer.copy()
self.primer_save_ok(primer_name, parent_window)
# Clear all the graphics
if getattr(self, 'pDB', None):
self.pDB.clear_pDB_objects()
# If calling from mutagenic design, handle refresh of pdb here
if calledby == 'from design' and openpdbWin != None:
openpdbWin.show_pDB_contents()
openpdbWin.highlight_primer(primer_name)
openpdbWin.display_details()
return
def save_primer_from_edit(self, parent_window=None):
"""Save the primer in the DB when doing a primer Edit"""
if not parent_window:
parent_window = self.eval_win
# Check if the primer name has been changed first, and ask for confirmation of rename
if self.primername_var.get(
) != self.edit_primer_name or not self.edit_primer_name:
import tkMessageBox
ok = tkMessageBox.askyesno('Primer Name altered',
'Rename primer and save?\n',
parent=parent_window)
if not ok:
self.primername_var.set(self.edit_primer_name)
return
#rename primer based on value in entry widget
else:
new_name = self.primername_var.get()
if new_name:
#only rename if there isn't already a primer with the same name
if not self.data['primer_dict'].has_key(new_name):
self.data['primer_dict'][new_name] = self.data[
'primer_dict'][self.edit_primer_name].copy()
del self.data['primer_dict'][self.edit_primer_name]
self.edit_primer_name = new_name
self.i_parent.new_name = new_name
#otherwise don't allow rename
else:
tkMessageBox.showwarning(
'Primer name already present',
'Primer name already present.\nPlease choose another name',
parent=parent_window)
return
# Update the sequence and description fields for the primer
DNA = self.eval_var.get()
# Validation check if primer is changed (maybe by mistake)
if not DNA:
ok = tkMessageBox.askyesno(
'No sequence entered',
'No sequence entered.\nDo you wish to save anyway?',
parent=parent_window)
if not ok:
return
import mutation
ok, DNA_sequence = mutation.check_DNA(DNA)
self.data['primer_dict'][
self.edit_primer_name]['sequence'] = DNA_sequence
self.data['primer_dict'][
self.edit_primer_name]['description'] = self.descr_var.get()
#print 'Primer Info:',self.edit_primer_name,self.data['primer_dict'][self.edit_primer_name]
# Clear all graphics
if getattr(self, 'pDB', None):
self.pDB.clear_pDB_objects()
# Close the window
self.eval_win.destroy()
return
def update_eval(self, event=None):
#
# Calculate primer-dimer and secondary structure
#
import mutation
primer_seq = self.eval_var.get()
ok, primer_seq = mutation.check_DNA(primer_seq)
#
# Score the sequence
#
if ok:
prop, numscore = mutation.hairpin_propensity(primer_seq)
if numscore < 8:
score = 'OK'
# score = numscore
elif numscore >= 8:
score = 'BAD'
#score = numscore
self.eval_hairpin.set('%s (%2d matches)' % (score, numscore))
#
# Primer-Dimer
#
complementarity_dict, maxselfscore = mutation.self_complementarity_propensity(
primer_seq)
if maxselfscore < 8:
text = 'OK'
elif maxselfscore >= 8:
text = 'BAD'
self.eval_primerdimer.set('%s (%2d matches)' %
(text, maxselfscore))
#
# Tm
#
# See if we can align the primer
#
Tm = None
if self.data.has_key('DNAseq'):
if self.data['DNAseq']:
import primer_alignment
A = primer_alignment.dummy_align_primer(self)
#
# Find all possible binding sites for the primer
#
sites = A.find_primer_binding_sites(
primer_seq, self.data['DNAseq'])
#
# Print the number of binding sites
#
best_score = 0
best_position = None
scores = []
first_neg = 1
for position, score in sites:
scores.append(score)
#
# Find the best position
#
if score > best_score:
best_score = score
best_position = position
Tm, mistmatches, Tm_method_used = mutation.get_primer_Tm(
DNAseq=self.data['DNAseq'],
primer=primer_seq,
primer_start=best_position,
method=self.Tm_method.get())
#
# Draw the primer on the screen in the best position
#
this_primer = {}
this_primer['sequence'] = primer_seq
this_primer['startpos'] = best_position
#
# Draw the new primer
#
self.pDB.display_primer(this_primer)
if not Tm:
Tm, mistmatches, Tm_method_used = mutation.get_primer_Tm(
DNAseq=None,
primer=primer_seq,
primer_start=None,
method=self.Tm_method.get())
self.eval_Tm.set('%5.2f' % Tm)
self.eval_Tm_method.set(Tm_method_used)
else:
self.eval_hairpin.set('Invalid DNA sequence')
self.eval_primerdimer.set('Invalid DNA sequence')
self.eval_Tm.set('Invalid DNA sequence')
return