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 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 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 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